Patent Publication Number: US-10329575-B2

Title: Regulatory sequence for plants

Description:
This application is a Divisional of U.S. application Ser. No. 11/004,678 filed Dec. 3, 2004, which is a Continuation of application Ser. No. 10/886,468, filed Jul. 6, 2004 (now U.S. Pat. No. 8,877,916), which is a Continuation of application Ser. No. 10/653,278, filed on Sep. 3, 2003, which is a continuation-in-part of the following applications, the entire contents of which are hereby incorporated by reference: 
                                                 Application               Filed   Number   Status                      Feb. 1, 2001   09/775,870   Abandoned           Feb. 25, 2003   10/372,233   Abandoned           Aug. 9, 2001   09/924,702   Abandoned                    
Moreover,
 
     Application Ser. No. 10/372,233 listed above is a Continuation of application Ser. No. 10/158,820, filed on Jun. 3, 2002, the entire contents of which is also hereby incorporated by reference. Application Ser. No. 10/158,820 is a Continuation of application Ser. No. 09/938,697, filed on Aug. 24, 2001, the entire contents of which is hereby incorporated by reference. 
     Application Ser. No. 09/938,697 is a continuation-in-part of the following non-provisional and provisional applications, to which the present application claims priority under 35 USC § 119(e) and § 120, the entire contents of which are hereby incorporated by reference: 
     
       
         
           
               
               
               
             
               
                   
               
               
                   
                   
                 Application 
               
               
                   
                 Filed 
                 Number 
               
               
                   
               
             
            
               
                   
                 Jan. 5, 2001 
                 09/754,185 
               
               
                   
                 Jan. 31, 2001 
                 09/774,340 
               
               
                   
                 Feb. 1, 2001 
                 09/776,014 
               
               
                   
                 Feb. 1, 2001 
                 09/775,870 
               
               
                   
                 Apr. 26, 2001 
                 09/842,246 
               
               
                   
                 Apr. 26, 2000 
                 60/200,034 
               
               
                   
                 May 1, 2001 
                 09/845,209 
               
               
                   
                 May 17, 2000 
                 60/205,233 
               
               
                   
                 May 1, 2000 
                 60/201,017 
               
               
                   
                 Aug. 9, 2001 
                 09/924,702 
               
               
                   
                 Aug. 9, 2000 
                 60/224,390 
               
               
                   
                 Aug. 25, 2000 
                 60/228,208 
               
               
                   
                 Aug. 25, 2000 
                 60/228,052 
               
               
                   
                 Aug. 25, 2000 
                 60/228,049 
               
               
                   
                 Aug. 25, 2000 
                 60/228,132 
               
               
                   
                 Aug. 25, 2000 
                 60/228,152 
               
               
                   
                 Aug. 25, 2000 
                 60/228,135 
               
               
                   
                 Aug. 25, 2000 
                 60/228,322 
               
               
                   
                 Aug. 25, 2000 
                 60/228,156 
               
               
                   
                 Aug. 25, 2000 
                 60/228,323 
               
               
                   
                 Aug. 25, 2000 
                 60/228,133 
               
               
                   
                 Aug. 25, 2000 
                 60/228,320 
               
               
                   
                 Aug. 25, 2000 
                 60/228,159 
               
               
                   
                 Aug. 25, 2000 
                 60/228,047 
               
               
                   
                 Aug. 25, 2000 
                 60/228,202 
               
               
                   
                 Aug. 25, 2000 
                 60/228,163 
               
               
                   
                 Aug. 25, 2000 
                 60/228,153 
               
               
                   
                 Aug. 25, 2000 
                 60/228,179 
               
               
                   
                 Aug. 25, 2000 
                 60/228,180 
               
               
                   
                 Aug. 25, 2000 
                 60/228,209 
               
               
                   
                 Aug. 25, 2000 
                 60/228,177 
               
               
                   
                 Aug. 25, 2000 
                 60/227,791 
               
               
                   
                 Aug. 25, 2000 
                 60/228,207 
               
               
                   
                 Aug. 25, 2000 
                 60/228,151 
               
               
                   
                 Aug. 25, 2000 
                 60/227,770 
               
               
                   
                 Aug. 25, 2000 
                 60/228,025 
               
               
                   
                 Aug. 25, 2000 
                 60/227,781 
               
               
                   
                 Aug. 25, 2000 
                 60/227,783 
               
               
                   
                 Aug. 25, 2000 
                 60/227,731 
               
               
                   
                 Aug. 25, 2000 
                 60/227,732 
               
               
                   
                 Aug. 25, 2000 
                 60/227,729 
               
               
                   
                 Aug. 25, 2000 
                 60/228,167 
               
               
                   
                 Aug. 25, 2000 
                 60/227,734 
               
               
                   
                 Aug. 25, 2000 
                 60/227,792 
               
               
                   
                 Aug. 25, 2000 
                 60/228,098 
               
               
                   
                 Aug. 25, 2000 
                 60/227,730 
               
               
                   
                 Aug. 25, 2000 
                 60/228,048 
               
               
                   
                 Aug. 25, 2000 
                 60/227,728 
               
               
                   
                 Aug. 25, 2000 
                 60/227,773 
               
               
                   
                 Aug. 25, 2000 
                 60/228,033 
               
               
                   
                 Aug. 25, 2000 
                 60/228,024 
               
               
                   
                 Aug. 25, 2000 
                 60/227,769 
               
               
                   
                 Aug. 25, 2000 
                 60/227,780 
               
               
                   
                 Aug. 25, 2000 
                 60/227,725 
               
               
                   
                 Aug. 25, 2000 
                 60/227,774 
               
               
                   
                 Aug. 25, 2000 
                 60/227,976 
               
               
                   
                 Aug. 25, 2000 
                 60/228,046 
               
               
                   
                 Aug. 25, 2000 
                 60/227,733 
               
               
                   
                 Aug. 25, 2000 
                 60/227,929 
               
               
                   
                 Aug. 25, 2000 
                 60/228,096 
               
               
                   
                 Aug. 25, 2000 
                 60/227,931 
               
               
                   
                 Aug. 25, 2000 
                 60/228,178 
               
               
                   
                 Aug. 25, 2000 
                 60/228,061 
               
               
                   
                 Aug. 25, 2000 
                 60/228,150 
               
               
                   
                 Aug. 25, 2000 
                 60/228,041 
               
               
                   
                 Aug. 25, 2000 
                 60/227,793 
               
               
                   
                 Aug. 25, 2000 
                 60/228,031 
               
               
                   
                 Aug. 25, 2000 
                 60/228,217 
               
               
                   
                 Aug. 25, 2000 
                 60/228,027 
               
               
                   
                 Aug. 25, 2000 
                 60/228,043 
               
               
                   
                 Aug. 25, 2000 
                 60/228,026 
               
               
                   
                 Aug. 25, 2000 
                 60/228,038 
               
               
                   
                 Aug. 25, 2000 
                 60/228,036 
               
               
                   
                 Aug. 25, 2000 
                 60/227,790 
               
               
                   
                 Aug. 25, 2000 
                 60/228,039 
               
               
                   
                 Aug. 25, 2000 
                 60/228,030 
               
               
                   
                 Aug. 25, 2000 
                 60/228,032 
               
               
                   
                 Aug. 25, 2000 
                 60/228,149 
               
               
                   
                 Aug. 25, 2000 
                 60/228,040 
               
               
                   
                 Aug. 25, 2000 
                 60/227,777 
               
               
                   
                 Aug. 25, 2000 
                 60/228,037 
               
               
                   
                 Aug. 25, 2000 
                 60/228,028 
               
               
                   
                 Aug. 25, 2000 
                 60/228,055 
               
               
                   
                 Aug. 25, 2000 
                 60/227,932 
               
               
                   
                 Aug. 25, 2000 
                 60/227,936 
               
               
                   
                 Aug. 25, 2000 
                 60/228,044 
               
               
                   
                 Aug. 25, 2000 
                 60/228,216 
               
               
                   
                 Aug. 25, 2000 
                 60/228,065 
               
               
                   
                 Aug. 25, 2000 
                 60/227,975 
               
               
                   
                 Aug. 25, 2000 
                 60/228,181 
               
               
                   
                 Aug. 25, 2000 
                 60/228,187 
               
               
                   
                 Aug. 25, 2000 
                 60/228,064 
               
               
                   
                 Aug. 25, 2000 
                 60/227,954 
               
               
                   
                 Aug. 25, 2000 
                 60/228,074 
               
               
                   
                 Aug. 25, 2000 
                 60/227,939 
               
               
                   
                 Aug. 25, 2000 
                 60/228,165 
               
               
                   
                 Aug. 25, 2000 
                 60/228,221 
               
               
                   
                 Aug. 25, 2000 
                 60/228,063 
               
               
                   
                 Aug. 25, 2000 
                 60/228,240 
               
               
                   
                 Aug. 25, 2000 
                 60/227,955 
               
               
                   
                 Aug. 25, 2000 
                 60/228,161 
               
               
                   
                 Aug. 25, 2000 
                 60/228,164 
               
               
                   
                 Aug. 25, 2000 
                 60/228,054 
               
               
                   
                 Aug. 25, 2000 
                 60/228,189 
               
               
                   
                 Aug. 25, 2000 
                 60/227,982 
               
               
                   
                 Aug. 25, 2000 
                 60/227,978 
               
               
                   
                 Aug. 25, 2000 
                 60/228,053 
               
               
                   
                 Aug. 25, 2000 
                 60/227,979 
               
               
                   
               
            
           
         
       
     
     Application Ser. No. 09/924,702 listed above claims priority under 35 USC § 119(e) of the following application. The entire contents of which are hereby incorporated by reference. 
     
       
         
           
               
               
               
               
             
               
                   
               
               
                   
                 Filed 
                 Application No. 
                 Status 
               
               
                   
               
             
            
               
                   
                 Aug. 9, 2000 
                 60/224,390 
                 Expired 
               
               
                   
               
            
           
         
       
     
     The entire contents of the applications listed in the tables above are expressly incorporated herein by reference. 
     In addition, this application claims priority to application Ser. No. 10/645,822, filed Aug. 22, 2003, which is a Continuation-In-Part of the following applications. The entire contents of which are hereby incorporated by reference: 
     
       
         
           
               
               
               
             
               
                   
               
               
                   
                   
                 Application 
               
               
                 Number 
                 Filed 
                 Number 
               
               
                   
               
             
            
               
                   
               
            
           
           
               
               
               
            
               
                 1 
                 5 Jan., 2001 
                 09/754,184 
               
               
                 2 
                 9 Apr., 2003 
                 10/409,117 
               
               
                 3 
                 4 Apr., 2001 
                 09/824,790 
               
               
                 4 
                 17 Jun., 2003 
                 10/462,849 
               
               
                 5 
                 29 Dec., 2000 
                 09/750,044 
               
               
                 6 
                 21 Nov., 2002 
                 10/300,941 
               
               
                 7 
                 6 Jan., 2003 
                 10/336,798 
               
               
                 8 
                 7 Nov., 2002 
                 10/289,416 
               
               
                 9 
                 9 Dec., 2002 
                 10/314,246 
               
               
                 10 
                 4 Aug., 2003 
                 10/633,229 
               
               
                 11 
                 6 Jan., 2003 
                 10/336,816 
               
               
                 12 
                 13 Jan., 2003 
                 10/340,649 
               
               
                 13 
                 13 Jan., 2003 
                 10/340,584 
               
               
                 14 
                 29 Jul., 2003 
                 10/628,535 
               
               
                 15 
                 15 Jul., 2003 
                 10/618,812 
               
               
                 16 
                 5 May, 2003 
                 10/428,842 
               
               
                 17 
                 15 Jul., 2003 
                 10/618,811 
               
               
                 18 
                 21 Jul., 2000 
                 09/620,394 
               
               
                 19 
                 9 Nov., 2000 
                 09/708,427 
               
               
                 20 
                 15 Aug., 2003 
                 10/642,811 
               
               
                 21 
                 2 Jan., 2001 
                 09/750,910 
               
               
                 22 
                 18 Dec., 2002 
                 60/433,952 
               
               
                 23 
                 08 May, 2003 
                 10/431,436 
               
               
                 24 
                 10 Feb., 2003 
                 10/360,648 
               
               
                 25 
                 12 Aug., 2002 
                 10/216,621 
               
               
                 26 
                 16 Jun., 2003 
                 10/461,476 
               
               
                 27 
                 29 Oct., 2002 
                 10/282,058 
               
               
                 28 
                 3 Mar., 2003 
                 10/376,785 
               
               
                 29 
                 3 Mar., 2003 
                 10/376,797 
               
               
                 30 
                 25 Feb., 2000 
                 09/513,996 
               
               
                 31 
                 24 Aug., 2001 
                 09/935,625 
               
               
                 32 
                 28 Feb., 2003 
                 10/375,265 
               
               
                 33 
                 3 Mar., 2003 
                 10/376,766 
               
               
                 34 
                 12 Oct., 2000 
                 09/686,093 
               
               
                 35 
                 6 Oct., 2000 
                 09/680,498 
               
               
                 36 
                 28 Sep., 2000 
                 09/671,635 
               
               
                 37 
                 22 Sep., 2000 
                 09/667,517 
               
               
                 38 
                 20 Sep., 2000 
                 09/665,714 
               
               
                 39 
                 20 Jul., 2000 
                 09/621,323 
               
               
                 40 
                 4 Aug., 2000 
                 09/633,191 
               
               
                 41 
                 30 Aug., 2000 
                 09/651,370 
               
               
                 42 
                 1 May, 2003 
                 10/426,837 
               
               
                 43 
                 1 Nov., 2000 
                 09/702,841 
               
               
                 44 
                 25 Oct., 2000 
                 09/696,751 
               
               
                 45 
                 2 Feb., 2003 
                 10/356,562 
               
               
                 46 
                 6 Jan., 2003 
                 10/336,799 
               
               
                 47 
                 21 Jan., 2003 
                 10/347,322 
               
               
                 48 
                 4 Apr., 2003 
                 10/406,556 
               
               
                 49 
                 13 Jan., 2003 
                 10/340,820 
               
               
                 50 
                 18 Jul., 2003 
                 10/621,442 
               
               
                   
               
            
           
         
       
     
     Through the 50 applications listed above, the present application also claims priority to and incorporates by reference the following applications: 
     Number 2 
     Application Ser. No. 10/409,117 is a continuation of application Ser. No. 10/084,376 filed Feb. 28, 2002, to which the present application also claims priority to and incorporates by reference. Furthermore, application Ser. No. 10/084,376 is a continuation of application Ser. No. 09/924,701 filed Aug. 9, 2001, to which the present application also claims priority to and incorporates by reference. Moreover, application Ser. No. 09/924,701 claims priority to under 35 USC 119(e) of provisional Application No. 60/224,391 filed Aug. 9, 2000, to which the present application also claims priority to and incorporates by reference. 
     Number 3 
     Application Ser. No. 09/824,790 listed above is a continuation-in-part of the following applications to which the present application also claims priority and incorporates by reference: 
     
       
         
           
               
               
               
             
               
                   
               
               
                   
                 Appln. No. 
                 Filed 
               
               
                   
               
             
            
               
                   
                 60/199,123 
                 Apr. 24, 2000 
               
               
                   
                 60/194,698 
                 Apr. 5, 2000 
               
               
                   
                 60/196,168 
                 Apr. 11, 2000 
               
               
                   
                 60/197,397 
                 Apr. 14, 2000 
               
               
                   
                 60/195,258 
                 Apr. 7, 2000 
               
               
                   
                 60/194,884 
                 Apr. 6, 2000 
               
               
                   
                 60/196,483 
                 Apr. 12, 2000 
               
               
                   
                 60/194,682 
                 Apr. 5, 2000 
               
               
                   
                 60/194.385 
                 Apr. 4, 2000 
               
               
                   
                 60/198,400 
                 Apr. 19, 2000 
               
               
                   
                 60/198.765 
                 Apr. 21, 2000 
               
               
                   
                 60/198,629 
                 Apr. 20, 2000 
               
               
                   
                 60/198.268 
                 Apr. 17, 2000 
               
               
                   
               
            
           
         
       
     
     Application Ser. No. 10/462,849 listed above claims priority under 35 USC § 119(e) of provisional Application No. 60/389,140 filed Jun. 17, 2002 the entire contents of which are also hereby incorporated by reference. 
     Number 6 
     Application Ser. No. 10/300,941 listed above is a continuation-in-part of application Ser. No. 09/617,682 filed on Jul. 19, 2000, application Ser. No. 09/617,681 filed on Jul. 19, 2000, and application Ser. No. 09/688,051 filed on Oct. 13, 2000, the entire contents of all three (3) of these applications are hereby incorporated by reference. 
     Through the three applications mentioned above, application Ser. No. 10/300,941 also claims priority under 35 USC § 119(e) of the following provisional applications, the entire contents of which are hereby incorporated by reference: 
                                         Filing Date   Appln. No.                      Jul. 19, 1999   60/144,331           Jul. 19, 1999   60/144,333           Oct. 13, 1999   60/159,294                    
Number 7
 
     Application Ser. No. 10/336,798 listed above is a continuation of application Ser. No. 10/136,365, filed on May 2, 2002, the entire contents of which are also hereby incorporated by reference. Through application Ser. No. 10/136,365, this application also claims priority under 35 USC § 119(e) and § 120 of the following applications, the entire contents of which are hereby incorporated by reference: 
     
       
         
           
               
               
               
               
             
               
                   
               
               
                 Country 
                 Filing Date 
                 Client No. 
                 Application No. 
               
               
                   
               
             
            
               
                 United States 
                 Dec. 8, 2000 
                 80180.003 
                 09/731,809 
               
            
           
           
               
            
               
                 which is a conversion of and claims priority to the following 
               
               
                 provisional applications: 
               
            
           
           
               
               
               
               
            
               
                 United States 
                 Dec. 8, 1999 
                 80180.001 
                 60/169,692 
               
               
                 United States 
                 Dec. 8, 1999 
                 80180.002 
                 60/169,691 
               
               
                   
               
            
           
         
       
     
     Application Ser. No. 10/289,416 listed above is a continuation of application Ser. No. 10/103,783 filed on Mar. 25, 2002, the entire contents of which are hereby incorporated by reference. Through application Ser. No. 10/103,783, this application also claims priority claims priority under 35 USC § 119(e) and § 120 of the following applications, the entire contents of which are hereby incorporated by reference: 
                                         Filing       Application           Date   Client No.   No.   Status                  Jan. 19, 2001   80182.003   09/764,425   Abandoned                 Which claims priority of the provisional applications listed below:                             Jan. 19, 2000   80182.002   60/176,866   Expired       Jan. 19, 2000   80183.002   60/176,867   Expired       Jan. 20, 2000   80184.002   60/176,910   Expired       Jan. 26, 2000   00152.001   60/178,166   Expired       Jan. 27, 2000   80182.001   60/178,544   Expired       Jan. 27, 2000   80183.001   60/178,546   Expired       Jan. 27, 2000   80184.001   60/178,545   Expired                    
Number 9
 
     Application Ser. No. 10/314,246 listed above is a continuation of application Ser. No. 09/570,582 filed on May 12, 2000, the entire contents of which are hereby incorporated by reference. Through application Ser. No. 09/570,582, this application claims priority under 35 USC § 119(e) of the following application, the entire contents of which are hereby incorporated by reference: 
                                                 Filing Date   Application No.   Status                          May 14, 1999   60/134,221   Expired                        
Number 10
 
     Application Ser. No. 10/633,229 listed above is a continuation of application Ser. No. 09/649,866, filed on Aug. 23, 2000, the entire contents of which are hereby incorporated by reference. Through application Ser. No. 09/649,866, this application also claims priority under 35 USC § 119(e) of the following provisional application, the entire contents of which are hereby incorporated by reference: 
                                                 Filing Date   Application No.   Status                          Aug. 23, 1999   60/149,930   Expired                        
Number 11
 
     Application Ser. No. 10/336,816 listed above is a continuation of application Ser. No. 10/119,718 filed on Apr. 11, 2002, the entire contents of which are hereby incorporated by reference. Through application Ser. No. 10/119,718, this application also claims priority under 35 U.S.C. § 120 of the following application, the entire contents of which are hereby incorporated by reference: 
                                                 Filing Date   Application No.   Status                          Aug. 10, 2001   09/925,897   Abandoned                        
Number 12
 
     Application Ser. No. 10/340,649 listed above is a continuation of application Ser. No. 10/112,879 filed on Apr. 2, 2002, the entire contents of which are hereby incorporated by reference. Through application Ser. No. 10/112,879 this application also claims priority under 35 USC § 119(e) and § 120 of the following applications, the entire contents of which are hereby incorporated by reference: 
                                         Country   Filing Date   Application No.   Status                  United   Jun. 16, 2000   09/594,599   Abandoned       States                             which claims priority to the following provisional application:                             United   Jun. 16, 1999   60/139,453   Expired       States                    
Number 13
 
     Application Ser. No. 10/340,584 listed above is a continuation of application Ser. No. 10/128,238 filed on Apr. 24, 2002, the entire contents of which are also hereby incorporated by reference. Through application Ser. No. 10/128,238, the present application also claims priority under 35 USC § 120 of the following application, the entire contents of which are hereby incorporated by reference: 
                                                 Application No.   Filing Date   Status                          09/925,483   Aug. 10, 2001   Abandoned                        
Number 14
 
     Application Ser. No. 10/628,535 listed above is a continuation-in-part of application Ser. No. 09/637,780, filed on Aug. 11, 2000, the entire contents of which are hereby incorporated by reference. Through application Ser. No. 09/637,780, this application also claims priority under 35 USC § 119(e) of the following provisional application, the entire contents of which are hereby incorporated by reference: 
                                                 Filing Date   Application No.   Status                          Aug. 13, 1999   60/148,684   Expired                        
Number 15
 
     Application Ser. No. 10/618,812 listed above is a continuation of application Ser. No. 09/689,980, filed on Oct. 13, 2000, the entire contents of which are hereby incorporated by reference. Through application Ser. No. 09/689,980, this application also claims priority under 35 USC § 119(e) of the following application, the entire contents of which are hereby incorporated by reference: 
                                                 Filing Date   Application No.   Status                          Oct. 14, 1999   60/159,331   Expired                        
Number 16
 
     Application Ser. No. 10/428,842 listed above is a continuation of application Ser. No. 09/620,111 filed Jul. 21, 2000, the entire contents of which are hereby incorporated by reference. Application Ser. No. 09/620,111 claims priority under 35 USC 119(e) of provisional Application No. 60/145,089, filed Jul. 22, 1999, the entire contents of which are also hereby incorporated by reference. 
     Number 17 
     Application Ser. No. 10/618,811 listed above claims priority under 35 USC § 119(e) of provisional Application No. 60/395,650 filed Jul. 15, 2002 the entire contents of which are hereby incorporated by reference. 
     Number 18 
     Application Ser. No. 09/620,394 listed above claims priority under 35 USC § 119(e), of the following applications, the entire contents of which are hereby incorporated by reference: 
                                                 Filing Date   Application No.   Status                          Jul. 21, 1999   60/145,088   Expired                        
Number 19
 
     Application Ser. No. 09/708,427 listed above is a continuation-in-part and claims priority under 35 USC § 120 of the following applications, the entire contents of which are hereby incorporated by reference: 
     
       
         
           
               
               
               
               
             
               
                   
               
               
                   
                 Filing Date 
                 Appln No. 
                 Client No. 
               
               
                   
               
             
            
               
                   
                 Jan. 7, 2000 
                 09/479,221 
                 80070.002 
               
               
                   
                 Apr. 28, 2000 
                 09/559,232 
                 80123.002 
               
               
                   
                 Jun. 16, 2000 
                 09/595,331 
                 80132.024 
               
               
                   
                 Jul. 14, 2000 
                 09/614,388 
                 80134.017 
               
               
                   
                 Jul. 19, 2000 
                 09/617,683 
                 80134.020 
               
               
                   
                 Jul. 20, 2000 
                 09/620,998 
                 80134.026 
               
               
                   
                 Jul. 21, 2000 
                 09/620,313 
                 80134.023 
               
               
                   
                 Jul. 21, 2000 
                 09/620,390 
                 80134.021 
               
               
                   
                 Jul. 21, 2000 
                 09/620,314 
                 80134.025 
               
               
                   
                 Aug. 2, 2000 
                 09/630,442 
                 80137.004 
               
               
                   
                 Aug. 4, 2000 
                 09/635,643 
                 80138.004 
               
               
                   
                 Aug. 4, 2000 
                 09/635,640 
                 80138.003 
               
               
                   
                 Aug. 9, 2000 
                 09/635,642 
                 80139.004 
               
               
                   
                 Aug. 10, 2000 
                 09/635,641 
                 80139.003 
               
               
                   
                 Aug. 16, 2000 
                 09/643,672 
                 80142.003 
               
               
                   
                 Aug. 18, 2000 
                 09/643,671 
                 80143.004 
               
               
                   
                 Aug. 25, 2000 
                 09/649,868 
                 80144.003 
               
               
                   
                 Aug. 25, 2000 
                 09/649,867 
                 80144.004 
               
               
                   
                 Oct. 13, 2000 
                 09/689,981 
                 80148.003 
               
               
                   
                 Oct. 13, 2000 
                 09/688,050 
                 80145.004 
               
               
                   
                 Oct. 13, 2000 
                 09/688,052 
                 80146.004 
               
               
                   
                 Oct. 13, 2000 
                 09/689,982 
                 80147.003 
               
               
                   
                 Oct. 13, 2000 
                 09/689,983 
                 80147.004 
               
               
                   
               
            
           
         
       
     
     Application Ser. No. 09/708,427 also claims priority under 35 USC § 119(e) of the following provisional applications, the entire contents of which are hereby incorporated by reference: 
                                             Filing Date   Application No.   Status                      Nov. 10, 1999   60/164,319   Expired           Nov. 9, 1999   60/164,260   Expired           Nov. 10, 1999   60/164,317   Expired           Nov. 9, 1999   60/164,259   Expired           Nov. 10, 1999   60/164,321   Expired           Nov. 10, 1999   60/164,318   Expired           Nov. 24, 1999   60/167,382   Expired           Nov. 23, 1999   60/167,362   Expired                    
Number 20
 
     Application Ser. No. 10/642,811 listed above is a continuation of application Ser. No. 09/689,984, filed on Oct. 13, 2000, the entire contents of which are hereby incorporated by reference. Through application Ser. No. 09/689,984, this application also claims priority under 35 USC § 119(e) of the following provisional application, the entire contents of which are hereby incorporated by reference: 
                                                 Filing Date   Application No.   Status                          Oct. 14, 1999   60/159,330   Expired                        
Number 23
 
     Application Ser. No. 10/431,436 listed above is a continuation of application Ser. No. 10/227,279, filed on Aug. 26, 2002, the entire contents of which are hereby incorporated by reference. 
     Application Ser. No. 10/227,279 is a continuation of application Ser. No. 09/940,245, filed on Aug. 24, 2001, the entire contents of which are also hereby incorporated by reference. 
     Application Ser. No. 09/940,245, is a Continuation-In-Part of the following applications to which the present application also claims priority under 35 USC § 119(e) and § 120, the entire contents of which are hereby incorporated by reference: 
                                         Filing Date   Appln. No                                                    Apr. 6, 2000   09/543,680   which claims                   priority to           Apr. 6, 1999   60/128,234   and           Apr. 8, 1999   60/128,714               May 4, 2000   09/566,262   which claims                   priority to           May 4, 1999   60/132,484               May 5, 2000   09/565,309   which claims                   priority to           May 5, 1999   60/132,485               May 5, 2000   09/565,308   which claims                   priority to           May 6, 1999   60/132,487               May 5, 2000   09/565,307   which claims                   priority to           May 6, 1999   60/132,486               May 5, 2000   09/565,310   which claims                   priority to           May 7, 1999   60/132,863               May 11, 2000   09/572,408   which claims                   priority to           May 11, 1999   60/134,256               May 12, 2000   09/570,768   and           May 12, 2000   09/570,738   which both                   claim priority           May 14, 1999   60/134,219   and           May 14, 1999   60/134,218               May 18, 2000   09/573,655   which claims                   priority to           May 18, 1999   60/134,768   and           May 19, 1999   60/134,941   and           May 20, 1999   60/135,124   and           May 21, 1999   60/135,353   and           May 24, 1999   60/135,629   and           May 25, 1999   60/136,021   and           May 27, 1999   60/136,392   and           May 28, 1999   60/136,782   and           Jun. 1, 1999   60/137,222   and           Jun. 3, 1999   60/137,528   and           Jun. 4, 1999   60/137,502   and           Jun. 7, 1999   60/137,724   and           Jun. 8, 1999   60/138,094               Jun. 16, 2000   09/595,330   which claims                   priority to           Jun. 18, 1999   60/139,458               Jun. 16, 2000   09/595,333   which claims                   priority to           Jun. 18, 1999   60/139,454               Jun. 16, 2000   09/595,328   which claims                   priority to           Jun. 18, 1999   60/139,459               Jun. 16, 2000   09/595,335   which claims                   priority to           Jun. 18, 1999   60/139,461               Jun. 16, 2000   09/595,329   which claims                   priority to           Jun. 18, 1999   60/139,462               Jun. 16, 2000   09/595,332   which claims                   priority to           Jun. 18, 1999   60/139,457               Jun. 16, 2000   09/594,598   which claims                   priority to           Jun. 18, 1999   60/139,460               Jun. 16, 2000   09/594,595   which claims                   priority to           Jun. 18, 1999   60/139,456               Jun. 9, 2000   09/592,459   which claims                   priority to           Jun. 10, 1999   60/138,540   and           Jun. 10, 1999   60/138,847               Jun. 16, 2000   09/594,597   which claims                   priority to           Jun. 18, 1999   60/139,463               Jun. 16, 2000   09/595,298   which claims                   priority to           Jun. 18, 1999   60/139,455               Jun. 14, 2000   09/593,710   which claims                   priority to           Jun. 14, 1999   60/139,119               Jun. 23, 2000   09/602,016   which claims                   priority to           Jun. 24, 1999   60/140,695               Jun. 29, 2000   09/606,181   which claims                   priority to           Jun. 29, 1999   60/140,991               Jun. 30, 2000   09/607,081   which claims                   priority to           Jul. 1, 1999   60/141,842               Jun. 30, 2000   09/610,157   which claims                   priority to           Jul. 1, 1999   60/142,154               Jun. 30, 2000   09/609,198   which claims                   priority to           Jul. 2, 1999   60/142,055               Jul. 6, 2000   09/611,409   which claims                   priority to           Jul. 6, 1999   60/142,390               Jul. 7, 2000   09/612,645   which claims                   priority to           Jul. 8, 1999   60/142,803               Jul. 7, 2000   09/613,547   which claims                   priority to           Jul. 9, 1999   60/142,920               Jul. 21, 2000   09/620,393   which claims                   priority to           Jul. 21, 1999   60/145,086               Jul. 14, 2000   09/614,450   which claims                   priority to           Jul. 16, 1999   60/144,085   and           Jul. 19, 1999   60/144,334               Jul. 21, 2000   09/621,900   which claims                   priority to           Jul. 23, 1999   60/145,224               Jul. 20, 2000   09/620,978   which claims                   priority to           Jul. 20, 1999   60/144,884               Jul. 27, 2000   09/628,984   which claims                   priority to           Jul. 27, 1999   60/145,918   and           Aug. 5, 1999   60/147,192               Jul. 27, 2000   09/628,987   which claims                   priority to           Jul. 27, 1999   60/145,919               Aug. 2, 2000   09/628,985   which claims                   priority to           Aug. 2, 1999   60/146,388                    
Number 24
 
     Application Ser. No. 10/360,648 listed above is a continuation of application Ser. No. 10/156,076, filed on May 29, 2002, which in turn is a continuation of application Ser. No. 09/940,256 filed on Aug. 24, 2001, the entire contents of these applications are hereby incorporated by reference. 
     Through application Ser. No. 09/940,256, the present application claims priority under 35 USC § 119(e), § 119(a-d) and § 120 of the following applications, the entire contents of which are also hereby incorporated by reference: 
                                                 Filing Date   Application No.                       1.   Apr. 6, 2000   09/543,680            2.   Apr. 6, 1999   60/128,234            3.   Apr. 8, 1999   60/128,714            4.   May 4, 2000   09/566,262            5.   May 4, 1999   60/132,484            6.   May 5, 2000   09/565,309            7.   May 5, 1999   60/132,485            8.   May 5, 2000   09/565,308            9.   May 6, 1999   60/132,487           10.   May 5, 2000   09/565,307           11.   May 6, 1999   60/132,486           12.   May 5, 2000   09/565,310           13.   May 7, 1999   60/132,863           14.   May 11, 2000   09/572,408           15.   May 11, 1999   60/134,256           16.   May 12, 2000   09/570,768           17.   May 12, 2000   09/570,738           18.   May 14, 1999   60/134,219           19.   May 14, 1999   60/134,218           20.   May 18, 2000   09/573,655           21.   May 18, 1999   60/134,768           22.   May 19, 1999   60/134,941           23.   May 20, 1999   60/135,124           24.   May 21, 1999   60/135,353           25.   May 24, 1999   60/135,629           26.   May 25, 1999   60/136,021           27.   May 27, 1999   60/136,392           28.   May 28, 1999   60/136,782           29.   Jun. 1, 1999   60/137,222           30.   Jun. 3, 1999   60/137,528           31.   Jun. 4, 1999   60/137,502           32.   Jun. 7, 1999   60/137,724           33.   Jun. 8, 1999   60/138,094           34.   Jun. 16, 2000   09/595,330           35.   Jun. 18, 1999   60/139,458           36.   Jun. 16, 2000   09/595,333           37.   Jun. 18, 1999   60/139,454           38.   Jun. 16, 2000   09/595,328           39.   Jun. 18, 1999   60/139,459           40.   Jun. 16, 2000   09/595,335           41.   Jun. 18, 1999   60/139,461           42.   Jun. 16, 2000   09/595,329           43.   Jun. 18, 1999   60/139,462           44.   Jun. 16, 2000   09/595,332           45.   Jun. 18, 1999   60/139,457           46.   Jun. 16, 2000   09/594,598           47.   Jun. 18, 1999   60/139,460           48.   Jun. 16, 2000   09/594,595           49.   Jun. 18, 1999   60/139,456           50.   Jun. 9, 2000   09/592,459           51.   Jun. 10, 1999   60/138,540           52.   Jun. 10, 1999   60/138,847           53.   Jun. 16, 2000   09/594,597           54.   Jun. 18, 1999   60/139,463           55.   Jun. 16, 2000   09/595,298           56.   Jun. 18, 1999   60/139,455           57.   Jun. 14, 2000   09/593,710           58.   Jun. 14, 1999   60/139,119           59.   Jun. 23, 2000   09/602,016           60.   Jun. 24, 1999   60/140,695           61.   Jun. 29, 2000   09/606,181           62.   Jun. 29, 1999   60/140,991           63.   Jun. 30, 2000   09/607,081           64.   Jul. 1, 1999   60/141,842           65.   Jun. 30, 2000   09/610,157           66.   Jul. 1, 1999   60/142,154           67.   Jun. 30, 2000   09/609,198           68.   Jul. 2, 1999   60/142,055           69.   Jul. 6, 2000   09/611,409           70.   Jul. 6, 1999   60/142,390           71.   Jul. 7, 2000   09/612,645           72.   Jul. 8, 1999   60/142,803           73.   Jul. 7, 2000   09/613,547           74.   Jul. 9, 1999   60/142,920           75.   Jul. 21, 2000   09/620,393           76.   Jul. 21, 1999   60/145,086           77.   Jul. 14, 2000   09/614,450           78.   Jul. 16, 1999   60/144,085           79.   Jul. 19, 1999   60/144,334           80.   Jul. 21, 2000   09/621,900           81.   Jul. 23, 1999   60/145,224           82.   Jul. 20, 2000   09/620,978           83.   Jul. 20, 1999   60/144,884           84.   Jul. 27, 2000   09/628,984           85.   Jul. 27, 1999   60/145,918           86.   Aug. 5, 1999   60/147,192           87.   Jul. 27, 2000   09/628,987           88.   Jul. 27, 1999   60/145,919           89.   Aug. 2, 2000   09/628,985           90.   Aug. 2, 1999   60/146,388                    
Number 25
 
     Application Ser. No. 10/216,621 listed above is a continuation of U.S. application Ser. No. 09/940,257 filed Aug. 24, 2001, the entire contents of which are hereby incorporated by reference. Application Ser. No. 09/940,257 is a continuation-in-part and claims priority under 35 USC § 119(e), § 119(a-d) and § 120 of the following 821 applications, the entire contents of which are also hereby incorporated by reference: 
                                                 Filing Date   Application No.                                                          1.   3 Sep. 1999   09/391,631   which claims                       priority to             2.   4 Sep. 1998   60/099,671   and             3.   4 Sep. 1998   60/099,672   and             4.   11 Sep. 1998   60/099,933   and             5.   17 Sep. 1998   60/100,864   and             6.   18 Sep. 1998   60/101,042   and             7.   24 Sep. 1998   60/101,682   and             8.   30 Sep. 1998   60/102,533   and             9.   30 Sep. 1998   60/102,460   and            10.   5 Oct. 1998   60/103,116   and            11.   5 Oct. 1998   60/103,141   and            12.   9 Oct. 1998   60/103,574   and            13.   13 Oct. 1998   60/103,907   and            14.   29 Oct. 1998   60/106,105   and            15.   30 Oct. 1998   60/106,218   and            16.   6 Nov. 1998   60/107,282   and            17.   10 Nov. 1998   60/107,836   and            18.   16 Nov. 1998   60/108,526   and            19.   17 Nov. 1998   60/108,901   and            20.   20 Nov. 1998   60/109,267   and            21.   23 Nov. 1998   60/109,594   and            22.   30 Nov. 1998   60/110,263   and            23.   1 Dec. 1998   60/110,495   and            24.   2 Dec. 1998   60/110,626   and            25.   3 Dec. 1998   60/110,701   and            26.   7 Dec. 1998   60/111,339   and            27.   9 Dec. 1998   60/111,589   and            28.   14 Dec. 1998   60/112,096   and            29.   15 Dec. 1998   60/112,224   and            30.   16 Dec. 1998   60/112,624   and            31.   17 Dec. 1998   60/112,862   and            32.   7 Jan. 1999   60/115,152   and            33.   7 Jan. 1999   60/115,156   and            34.   8 Jan. 1999   60/115,365   and            35.   11 Jan. 1999   60/115,339   and            36.   13 Jan. 1999   60/115,847   and            37.   21 Jan. 1999   60/116,674   and            38.   22 Jan. 1999   60/116,962   and            39.   18 Feb. 1999   60/120,583   and            40.   22 Feb. 1999   60/121,072   and            41.   2 Mar. 1999   60/122,568   and            42.   12 Mar. 1999   60/123,941                43.   5 Oct. 1999   09/413,198   which claims                       priority to            44.   5 Oct. 1998   60/103,116   and            45.   5 Oct. 1998   60/103,141   and            46.   6 Oct. 1998   60/103,215   and            47.   8 Oct. 1998   60/103,554   and            48.   9 Oct. 1998   60/103,574   and            49.   13 Oct. 1998   60/103,907   and            50.   14 Oct. 1998   60/104,268   and            51.   16 Oct. 1998   60/104,680   and            52.   19 Oct. 1998   60/104,828   and            53.   20 Oct. 1998   60/105,008   and            54.   21 Oct. 1998   60/105,142   and            55.   22 Oct. 1998   60/105,533   and            56.   26 Oct. 1998   60/105,571   and            57.   27 Oct. 1998   60/105,815   and            58.   29 Oct. 1998   60/106,105   and            59.   30 Oct. 1998   60/106,218                60.   5 Oct. 1999   09/412,922   which claims                       priority to            61.   5 Oct. 1998   60/103,116   and            62.   5 Oct. 1998   60/103,141   and            63.   6 Oct. 1998   60/103,215   and            64.   8 Oct. 1998   60/103,554   and            65.   9 Oct. 1998   60/103,574   and            66.   13 Oct. 1998   60/103,907   and            67.   14 Oct. 1998   60/104,268   and            68.   16 Oct. 1998   60/104,680   and            69.   19 Oct. 1998   60/104,828   and            70.   20 Oct. 1998   60/105,008   and            71.   21 Oct. 1998   60/105,142   and            72.   22 Oct. 1998   60/105,533   and            73.   26 Oct. 1998   60/105,571   and            74.   27 Oct. 1998   60/105,815   and            75.   29 Oct. 1998   60/106,105   and            76.   30 Oct. 1998   60/106,218   and            77.   2 Nov. 1998   60/106,685   and            78.   6 Nov. 1998   60/107,282   and            79.   9 Nov. 1998   60/107,720   and            80.   9 Nov. 1998   60/107,719   and            81.   10 Nov. 1998   60/107,836   and            82.   12 Nov. 1998   60/108,190   and            83.   16 Nov. 1998   60/108,526   and            84.   17 Nov. 1998   60/108,901   and            85.   19 Nov. 1998   60/109,124   and            86.   19 Nov. 1998   60/109,127   and            87.   20 Nov. 1998   60/109,267   and            88.   23 Nov. 1998   60/109,594   and            89.   25 Nov. 1998   60/110,053   and            90.   25 Nov. 1998   60/110,050   and            91.   27 Nov. 1998   60/110,158   and            92.   30 Nov. 1998   60/110,263   and            93.   1 Dec. 1998   60/110,495   and            94.   2 Dec. 1998   60/110,626   and            95.   3 Dec. 1998   60/110,701   and            96.   7 Dec. 1998   60/111,339   and            97.   9 Dec. 1998   60/111,589   and            98.   10 Dec. 1998   60/111,782   and            99.   11 Dec. 1998   60/111,812   and           100.   14 Dec. 1998   60/112,096   and           101.   15 Dec. 1998   60/112,224   and           102.   16 Dec. 1998   60/112,624   and           103.   17 Dec. 1998   60/112,862   and           104.   18 Dec. 1998   60/112,912   and           105.   21 Dec. 1998   60/113,248   and           106.   22 Dec. 1998   60/113,522   and           107.   23 Dec. 1998   60/113,826   and           108.   28 Dec. 1998   60/113,998   and           109.   29 Dec. 1998   60/114,384   and           110.   30 Dec. 1998   60/114,455   and           111.   4 Jan. 1999   60/114,740   and           112.   6 Jan. 1999   60/114,866   and           113.   7 Jan. 1999   60/115,153   and           114.   7 Jan. 1999   60/115,152   and           115.   7 Jan. 1999   60/115,151   and           116.   7 Jan. 1999   60/115,155   and           117.   7 Jan. 1999   60/115,156   and           118.   7 Jan. 1999   60/115,154   and           119.   8 Jan. 1999   60/115,364   and           120.   8 Jan. 1999   60/115,365   and           121.   11 Jan. 1999   60/115,339   and           122.   12 Jan. 1999   60/115,518   and           123.   13 Jan. 1999   60/115,847   and           124.   14 Jan. 1999   60/115,905   and           125.   15 Jan. 1999   60/116,383   and           126.   15 Jan. 1999   60/116,384   and           127.   19 Jan. 1999   60/116,329   and           128.   19 Jan. 1999   60/116,340   and           129.   21 Jan. 1999   60/116,674   and           130.   21 Jan. 1999   60/116,672   and           131.   22 Jan. 1999   60/116,960   and           132.   22 Jan. 1999   60/116,962   and           133.   28 Jan. 1999   60/117,756   and           134.   3 Feb. 1999   60/118,672   and           135.   4 Feb. 1999   60/118,808   and           136.   5 Feb. 1999   60/118,778   and           137.   8 Feb. 1999   60/119,029   and           138.   9 Feb. 1999   60/119,332   and           139.   10 Feb. 1999   60/119,462   and           140.   12 Feb. 1999   60/119,922   and           141.   16 Feb. 1999   60/120,196   and           142.   16 Feb. 1999   60/120,198   and           143.   18 Feb. 1999   60/120,583   and           144.   22 Feb. 1999   60/121,072   and           145.   23 Feb. 1999   60/121,334   and           146.   24 Feb. 1999   60/121,470   and           147.   25 Feb. 1999   60/121,704   and           148.   26 Feb. 1999   60/122,107   and           149.   1 Mar. 1999   60/122,266   and           150.   2 Mar. 1999   60/122,568   and           151.   3 Mar. 1999   60/122,611   and           152.   4 Mar. 1999   60/121,775   and           153.   5 Mar. 1999   60/123,534   and           154.   9 Mar. 1999   60/123,680   and           155.   10 Mar. 1999   60/123,715   and           156.   10 Mar. 1999   60/123,726   and           157.   11 Mar. 1999   60/124,263   and           158.   12 Mar. 1999   60/123,941               159.   28 Oct. 1999   09/428,944   which claims                       priority to           160.   2 Nov. 1998   60/106,685   and           161.   6 Nov. 1998   60/107,282   and           162.   9 Nov. 1998   60/107,720   and           163.   9 Nov. 1998   60/107,719   and           164.   10 Nov. 1998   60/107,836   and           165.   12 Nov. 1998   60/108,190   and           166.   16 Nov. 1998   60/108,526   and           167.   17 Nov. 1998   60/108,901   and           168.   19 Nov. 1998   60/109,124   and           169.   19 Nov. 1998   60/109,127   and           170.   20 Nov. 1998   60/109,267   and           171.   23 Nov. 1998   60/109,594   and           172.   25 Nov. 1998   60/110,053   and           173.   25 Nov. 1998   60/110,050   and           174.   27 Nov. 1998   60/110,158   and           175.   30 Nov. 1998   60/110,263               176.   1 Dec. 1999   09/451,320   which claims                       priority to           177.   1 Dec. 1998   60/110,495   and           178.   2 Dec. 1998   60/110,626   and           179.   3 Dec. 1998   60/110,701   and           180.   7 Dec. 1998   60/111,339   and           181.   9 Dec. 1998   60/111,589   and           182.   10 Dec. 1998   60/111,782   and           183.   11 Dec. 1998   60/111,812   and           184.   14 Dec. 1998   60/112,096   and           185.   15 Dec. 1998   60/112,224   and           186.   16 Dec. 1998   60/112,624   and           187.   17 Dec. 1998   60/112,862   and           188.   18 Dec. 1998   60/112,912   and           189.   21 Dec. 1998   60/113,248   and           190.   22 Dec. 1998   60/113,522   and           191.   23 Dec. 1998   60/113,826   and           192.   28 Dec. 1998   60/113,998   and           193.   29 Dec. 1998   60/114,384   and           194.   30 Dec. 1998   60/114,455   and           195.   7 Jan. 1999   60/115,153   and           196.   7 Jan. 1999   60/115,152   and           197.   7 Jan. 1999   60/115,151   and           198.   7 Jan. 1999   60/115,155   and           199.   7 Jan. 1999   60/115,156   and           200.   8 Jan. 1999   60/115,364   and           201.   22 Jan. 1999   60/116,960               202.   3 Feb. 2000   09/497,191   which claims                       priority to           203.   3 Feb. 1999   60/118,672   and           204.   4 Feb. 1999   60/118,808   and           205.   5 Feb. 1999   60/118,778   and           206.   8 Feb. 1999   60/119,029   and           207.   9 Feb. 1999   60/119,332   and           208.   10 Feb. 1999   60/119,462   and           209.   12 Feb. 1999   60/119,922   and           210.   16 Feb. 1999   60/120,196   and           211.   16 Feb. 1999   60/120,198   and           212.   18 Feb. 1999   60/120,583   and           213.   22 Feb. 1999   60/121,072   and           214.   23 Feb. 1999   60/121,334   and           215.   24 Feb. 1999   60/121,470   and           216.   25 Feb. 1999   60/121,704   and           217.   26 Feb. 1999   60/122,107               218.   1 Mar. 2000   09/517,537   which claims                       priority to           219.   1 Mar. 1999   60/122,266   and           220.   2 Mar. 1999   60/122,568   and           221.   3 Mar. 1999   60/122,611   and           222.   4 Mar. 1999   60/121,775   and           223.   5 Mar. 1999   60/123,534   and           224.   9 Mar. 1999   60/123,680   and           225.   10 Mar. 1999   60/123,715   and           226.   10 Mar. 1999   60/123,726   and           227.   11 Mar. 1999   60/124,263   and           228.   12 Mar. 1999   60/123,941               229.   11 Aug. 2000   09/637,565   which claims                       priority to           230.   12 Aug. 1999   60/148,342               231.   11 Aug. 2000   09/637,564   which claims                       priority to           232.   12 Aug. 1999   60/148,340               233.   11 Aug. 2000   09/637,792   which claims                       priority to           234.   12 Aug. 1999   60/148,337               235.   23 Feb. 2001   09/790,663   which claims                       priority to           236.   25 Feb. 2000   60/185,140   and           237.   28 Feb. 2000   60/185,398   and           238.   29 Feb. 2000   60/185,750               239.   1 Mar. 2001   09/795,359   which claims                       priority to           240.   1 Mar. 2000   60/186,277   and           241.   3 Mar. 2000   60/186,670   and           242.   7 Mar. 2000   60/187,379   and           243.   9 Mar. 2000   60/187,985   and           244.   10 Mar. 2000   60/188,174   and           245.   13 Mar. 2000   60/188,687   and           246.   15 Mar. 2000   60/189,460   and           247.   16 Mar. 2000   60/189,958   and           248.   17 Mar. 2000   60/189,965   and           249.   20 Mar. 2000   60/190,090   and           250.   23 Mar. 2000   60/191,549   and           251.   24 Mar. 2000   60/191,826   and           252.   27 Mar. 2000   60/192,420   and           253.   29 Mar. 2000   60/192,855   and           254.   30 Mar. 2000   60/193,243   and           255.   31 Mar. 2000   60/193,469               256.   16 Mar. 2001   09/804,470   which claims                       priority to           257.   16 Mar. 2000   60/190,120   and           258.   16 Mar. 2000   60/189,947   and           259.   16 Mar. 2000   60/189,948   and           260.   16 Mar. 2000   60/190,121               261.   4 Apr. 2001   09/824,790   which claims                       priority to           262.   6 Apr. 2000   60/194,884   and           263.   4 Apr. 2000   60/194,385   and           264.   5 Apr. 2000   60/194,682   and           265.   5 Apr. 2000   60/194,698   and           266.   7 Apr. 2000   60/195,258   and           267.   11 Apr. 2000   60/196,168   and           268.   12 Apr. 2000   60/196,483   and           269.   14 Apr. 2000   60/197,397   and           270.   17 Apr. 2000   60/198,268   and           271.   19 Apr. 2000   60/198,400   and           272.   20 Apr. 2000   60/198,629   and           273.   21 Apr. 2000   60/198,765   and           274.   24 Apr. 2000   60/199,123               275.   11 Apr. 2001   09/832,192   which claims                       priority to           276.   12 Apr. 2000   60/196,212   and           277.   11 Apr. 2000   60/196,211   and           278.   14 Apr. 2000   60/197,869   and           279.   13 Apr. 2000   60/196,213   and           280.   17 Apr. 2000   60/197,870   and           281.   17 Apr. 2000   60/197,871   and           282.   28 Apr. 2000   60/200,373   and           283.   28 Apr. 2000   60/200,773               284.   26 Apr. 2001   09/842,246   which claims                       priority to           285.   26 Apr. 2000   60/200,034               286.   1 May 2001   09/845,208   which claims                       priority to           287.   1 May 2000   60/200,763   and           288.   1 May 2000   60/201,016   and           289.   1 May 2000   60/200,762   and           290.   1 May 2000   60/200,761   and           291.   11 May 2000   60/203,671   and           292.   11 May 2000   60/203,672   and           293.   11 May 2000   60/203,669   and           294.   11 May 2000   60/203,622               295.   1 May 2001   09/845,318   which claims                       priority to           296.   1 May 2000   60/201,018   and           297.   17 May 2000   60/205,325               298.   1 May 2001   09/845,209   which claims                       priority to           299.   1 May 2000   60/201,017   and           300.   17 May 2000   60/205,233               301.   1 Jun. 2001   09/870,646   which claims                       priority to           302.   1 Jun. 2000   60/208,648               303.   1 Jun. 2001   09/870,476   which claims                       priority to           304.   1 Jun. 2000   60/208,324   and           305.   5 Jun. 2000   60/208,919   and           306.   5 Jun. 2000   60/208,917   and           307.   8 Jun. 2000   60/210,008               308.   1 Jun. 2001   09/870,664   which claims                       priority to           309.   1 Jun. 2000   60/208,312   and           310.   5 Jun. 2000   60/208,918   and           311.   5 Jun. 2000   60/208,920   and           312.   8 Jun. 2000   60/210,006   and           313.   9 Jun. 2000   60/210,564   and           314.   13 Jun. 2000   60/211,214   and           315.   22 Jun. 2000   60/213,249   and           316.   27 Jun. 2000   60/214,535   and           317.   28 Jun. 2000   60/214,799   and           318.   30 Jun. 2000   60/215,127               319.   13 Jun. 2001   09/878,974   which claims                       priority to           320.   13 Jun. 2000   60/211,210   and           321.   15 Jun. 2000   60/211,539   and           322.   19 Jun. 2000   60/212,414   and           323.   20 Jun. 2000   60/212,677   and           324.   20 Jun. 2000   60/212,713   and           325.   22 Jun. 2000   60/213,195   and           326.   22 Jun. 2000   60/213,221   and           327.   27 Jun. 2000   60/214,760               328.   12 Jul. 2001   09/902,613   which claims                       priority to           329.   1 Aug. 2000   60/223,114               330.   13 Jul. 2001   09/903,497   which claims                       priority to           331.   13 Jul. 2000   60/217,846   and           332.   3 Aug. 2000   60/223,099               333.   1 Aug. 2001   09/918,556   which claims                       priority to           334.   1 Aug. 2000   60/223,115               335.   3 Aug. 2001   09/920,626   which claims                       priority to           336.   3 Aug. 2000   60/223,100   and           337.   18 Aug. 2000   60/226,325   and           338.   31 Aug. 2000   60/237,361               339.   7 Aug. 2001   09/922,661   which claims                       priority to           340.   7 Aug. 2000   60/223,329   and           341.   31 Aug. 2000   60/229,521   and           342.   18 Aug. 2000   60/226,381               343.   9 Aug. 2001   09/924,702   which claims                       priority to           344.   9 Aug. 2000   60/224,390               345.   16 Aug. 2001   09/930,244   which claims                       priority to           346.   31 Aug. 2000   60/237,362   and           347.   16 Aug. 2000   60/225,848               348.   16 Aug. 2001   09/930,231   which claims                       priority to           349.   16 Aug. 2000   60/225,849               350.   16 Aug. 2001   09/930,223   which claims                       priority to           351.   16 Aug. 2000   60/225,847               352.   20 Aug. 2001   09/931,911   which claims                       priority to           353.   31 Aug. 2000   60/229,520               354.   26 Feb. 2002   10/082,096   which is a                       1.53(b)                       continuation of           355.   1 Mar. 2001   09/795,347   which claims                       priority to           356.   2 Mar. 2000   60/186,390   and           357.   1 Mar. 2000   60/186,283   and           358.   1 Mar. 2000   60/186,296   and           359.   2 Mar. 2000   60/187,178   and           360.   2 Mar. 2000   60/186,386   and           361.   2 Mar. 2000   60/186,387   and           362.   3 Mar. 2000   60/186,748   and           363.   3 Mar. 2000   60/186,669   and           364.   7 Mar. 2000   60/187,378   and           365.   8 Mar. 2000   60/187,896   and           366.   8 Mar. 2000   60/187,888   and           367.   10 Mar. 2000   60/188,187   and           368.   10 Mar. 2000   60/188,186   and           369.   10 Mar. 2000   60/188,185   and           370.   10 Mar. 2000   60/188,175   and           371.   14 Mar. 2000   60/189,080   and           372.   14 Mar. 2000   60/189,052   and           373.   15 Mar. 2000   60/189,461   and           374.   15 Mar. 2000   60/189,462   and           375.   16 Mar. 2000   60/189,953   and           376.   16 Mar. 2000   60/189,959   and           377.   20 Mar. 2000   60/190,069   and           378.   20 Mar. 2000   60/190,070   and           379.   20 Mar. 2000   60/190,545   and           380.   20 Mar. 2000   60/190,089   and           381.   22 Mar. 2000   60/191,084   and           382.   22 Mar. 2000   60/191,097   and           383.   23 Mar. 2000   60/191,543   and           384.   23 Mar. 2000   60/191,545   and           385.   24 Mar. 2000   60/191,823   and           386.   24 Mar. 2000   60/191,825   and           387.   27 Mar. 2000   60/192,421   and           388.   27 Mar. 2000   60/192,308   and           389.   29 Mar. 2000   60/192,940   and           390.   29 Mar. 2000   60/192,941   and           391.   30 Mar. 2000   60/193,244   and           392.   30 Mar. 2000   60/193,245   and           393.   31 Mar. 2000   60/193,453   and           394.   31 Mar. 2000   60/193,455               395.   28 Feb. 2002   10/084,376   which is a                       1.53(b)                       continuation of           396.   9 Aug. 2001   09/924,701   which claims                       priority to           397.   9 Aug. 2000   60/224,391               398.   4 Mar. 2002   10/086,239   which is a                       1.53(b)                       continuation of           399.   1 May 2001   09/845,206   which claims                       priority to           400.   2 May 2000   60/201,275   and           401.   1 May 2000   60/200,879   and           402.   2 May 2000   60/201,305   and           403.   4 May 2000   60/201,740   and           404.   4 May 2000   60/201,750   and           405.   5 May 2000   60/202,112   and           406.   5 May 2000   60/202,180   and           407.   9 May 2000   60/202,914   and           408.   9 May 2000   60/202,636   and           409.   9 May 2000   60/202,919   and           410.   9 May 2000   60/202,634   and           411.   10 May 2000   60/202,968   and           412.   10 May 2000   60/202,963   and           413.   11 May 2000   60/203,457   and           414.   11 May 2000   60/203,279   and           415.   12 May 2000   60/203,916   and           416.   12 May 2000   60/203,915   and           417.   15 May 2000   60/204,388   and           418.   15 May 2000   60/204,122   and           419.   16 May 2000   60/204,568   and           420.   16 May 2000   60/204,569   and           421.   17 May 2000   60/204,830   and           422.   17 May 2000   60/204,829   and           423.   18 May 2000   60/205,201   and           424.   18 May 2000   60/205,058   and           425.   19 May 2000   60/205,242   and           426.   19 May 2000   60/205,243   and           427.   22 May 2000   60/205,572   and           428.   22 May 2000   60/205,576   and           429.   23 May 2000   60/206,316   and           430.   23 May 2000   60/206,319   and           431.   24 May 2000   60/206,553   and           432.   24 May 2000   60/206,545   and           433.   26 May 2000   60/207,367   and           434.   26 May 2000   60/207,243   and           435.   26 May 2000   60/207,239   and           436.   26 May 2000   60/207,354   and           437.   30 May 2000   60/207,452   and           438.   30 May 2000   60/207,329               439.   7 Mar. 2002   10/091,527   which is a                       1.53(b)                       continuation of           440.   26 Apr. 2001   09/842,088   which claims                       priority to           441.   26 Apr. 2000   60/200,031               442.   13 Mar. 2002   10/095,465   which is a                       1.53(b)                       continuation of           443.   4 Apr. 2001   09/824,882   which claims                       priority to           444.   4 Apr. 2000   60/194,404   and           445.   4 Apr. 2000   60/194,398   and           446.   5 Apr. 2000   60/194,683   and           447.   5 Apr. 2000   60/194,697   and           448.   6 Apr. 2000   60/194,874   and           449.   6 Apr. 2000   60/194,872   and           450.   6 Apr. 2000   60/194,885   and           451.   6 Apr. 2000   60/195,045   and           452.   7 Apr. 2000   60/195,283   and           453.   7 Apr. 2000   60/195,257   and           454.   11 Apr. 2000   60/196,169   and           455.   11 Apr. 2000   60/196,089   and           456.   12 Apr. 2000   60/196,487   and           457.   12 Apr. 2000   60/196,289   and           458.   12 Apr. 2000   60/196,485   and           459.   12 Apr. 2000   60/196,486   and           460.   17 Apr. 2000   60/197,687   and           461.   17 Apr. 2000   60/197,678   and           462.   17 Apr. 2000   60/198,133   and           463.   17 Apr. 2000   60/197,671   and           464.   19 Apr. 2000   60/198,386   and           465.   19 Apr. 2000   60/198,373   and           466.   20 Apr. 2000   60/198,619   and           467.   20 Apr. 2000   60/198,623   and           468.   21 Apr. 2000   60/198,767   and           469.   21 Apr. 2000   60/198,763   and           470.   24 Apr. 2000   60/199,124   and           471.   24 Apr. 2000   60/199,122   and           472.   26 Apr. 2000   60/199,828   and           473.   26 Apr. 2000   60/199,818   and           474.   27 Apr. 2000   60/200,103   and           475.   27 Apr. 2000   60/200,102   and           476.   15 Mar. 2002   10/097,600   which is a                       1.53(b)                       continuation of           477.   12 Apr. 2001   09/832,934   which is a                       1.53(b)                       continuation of           478.   11 Aug. 2000   09/637,820   which claims                       priority to           479.   12 Aug. 1999   60/148,347               480.   15 Mar. 2002   10/097,295   which is a                       1.53(b)                       continuation of           481.   15 Jun. 2001   09/881,096   which claims                       priority to           482.   15 Jun. 2000   60/211,538   and           483.   19 Jun. 2000   60/212,623   and           484.   20 Jun. 2000   60/212,727   and           485.   22 Jun. 2000   60/213,270   and           486.   27 Jun. 2000   60/214,524               487.   18 Mar. 2002   10/198,315   which is a                       1.53(b)                       continuation of           488.   1 Jun. 2001   09/870,699   which claims                       priority to           489.   1 Jun. 2000   60/208,421               490.   18 Mar. 2002   10/098,506   which is a                       1.53(b)                       continuation of           491.   1 Jun. 2001   09/870,713   which claims                       priority to           492.   2 Jun. 2000   60/209,338               493.   25 Mar. 2002   10/103,845   which is a                       1.53(b)                       continuation of           494.   5 Jul. 2001   09/898,063   which claims                       priority to           495.   5 Jul. 2000   60/216,362   and           496.   11 Jul. 2000   60/217,384   and           497.   18 Jul. 2000   60/219,033   and           498.   25 Jul. 2000   60/220,811   and           499.   25 Jul. 2000   60/220,652               500.   27 Mar. 2002   10/106,718   which is a                       1.53(b)                       continuation of           501.   5 Jul. 2001   09/898,064   which claims                       priority to           502.   5 Jul. 2000   60/216,361   and           503.   11 Jul. 2000   60/217,476   and           504.   18 Jul. 2000   60/219,004   and           505.   25 Jul. 2000   60/220,647   and           506.   25 Jul. 2000   60/220,484               507.   1 Apr. 2002   10/109,638   which is a                       1.53(b)                       continuation of           508.   12 Jul. 2001   09/902,614   which claims                       priority to           509.   12 Jul. 2000   60/218,548   and           510.   3 Aug. 2000   60/223,116               511.   10 Apr. 2002   10/119,275   which is a                       1.53(b)                       continuation of           512.   16 Aug. 2001   09/930,214   which claims                       priority to           513.   31 Aug. 2000   60/229,520   and           514.   16 Aug. 2000   60/225,850               515.   17 Apr. 2002   10/123,117   which is a                       1.53(b)                       continuation of           516.   3 Aug. 2001   09/921,135   which claims                       priority to           517.   3 Aug. 2000   60/223,101   and           518.   31 Aug. 2000   60/229,519   and           519.   18 Aug. 2000   60/226,323               520.   17 Apr. 2002   10/123,222   which is a                       1.53(b)                       continuation of           521.   11 Jul. 2001   09/902,093   which claims                       priority to           522.   11 Jul. 2000   60/217,385   and           523.   18 Jul. 2000   60/219,021   and           524.   25 Jul. 2000   60/220,814   and           525.   14 Aug. 2000   60/224,516   and           526.   15 Aug. 2000   60/225,302   and           527.   21 Aug. 2000   60/226,725   and           528.   23 Aug. 2000   60/227,026   and           529.   30 Aug. 2000   60/228,897               530.   17 Apr. 2002   10/123,159   which is a                       1.53(b)                       continuation of           531.   13 Jul. 2001   09/903,988   which claims                       priority to           532.   14 Jul. 2000   60/218,566   and           533.   3 Aug. 2000   60/223,098               534.   17 Apr. 2002   10/123,111   which is a                       1.53(b)                       continuation of           535.   14 Aug. 2001   09/928,372   which claims                       priority to           536.   14 Aug. 2000   60/224,517   and           537.   15 Aug. 2000   60/225,303   and           538.   21 Aug. 2000   60/226,452   and           539.   23 Aug. 2000   60/227,024   and           540.   30 Aug. 2000   60/228,898               541.   18 Apr. 2002   10/124,666   which is a                       1.53(b)                       continuation of           542.   17 Aug. 2001   09/931,043   which claims                       priority to           543.   18 Aug. 2000   60/226,324               544.   29 Apr. 2002   10/133,891   which is a                       1.53(b)                       continuation of           545.   31 Jan. 2001   09/774,340               546.   29 Apr. 2002   10/133,893   which is a                       1.53(b)                       continuation of           547.   19 Oct. 2000   09/691,039               548.   29 Apr. 2002   10/134,014   which is a                       1.53(b)                       continuation of           549.   21 Dec. 2000   09/741,043               550.   29 Apr. 2002   10/133,373   which is a                       1.53(b)                       continuation of           551.   19 Oct. 2000   09/691,045               552.   29 Apr. 2002   10/133,905   which is a                       1.53(b)                       continuation of           553.   19 Oct. 2000   09/691,019               554.   29 Apr. 2002   10/133,376   which is a                       1.53(b)                       continuation of           555.   1 Jun. 2001   09/870,675   which claims                       priority to           556.   2 Jun. 2000   60/208,649               557.   6 May 2002   10/138,320   which is a                       1.53(b)                       continuation of           558.   4 Jan. 2000   09/478,081   which claims                       priority to           559.   4 Jan. 1999   60/114,740   and           560.   6 Jan. 1999   60/114,866   and           561.   7 Jan. 1999   60/115,154   and           562.   8 Jan. 1999   60/115,365   and           563.   11 Jan. 1999   60/115,339   and           564.   12 Jan. 1999   60/115,518   and           565.   13 Jan. 1999   60/115,847   and           566.   14 Jan. 1999   60/115,905   and           567.   15 Jan. 1999   60/116,383   and           568.   15 Jan. 1999   60/116,384   and           569.   19 Jan. 1999   60/116,329   and           570.   19 Jan. 1999   60/116,340   and           571.   21 Jan. 1999   60/116,674   and           572.   21 Jan. 1999   60/116,672   and           573.   22 Jan. 1999   60/116,962   and           574.   28 Jan. 1999   60/117,756               575.   25 Aug. 2000   60/228,025               576.   25 Aug. 2000   60/227,781               577.   25 Aug. 2000   60/227,783               578.   25 Aug. 2000   60/227,731               579.   25 Aug. 2000   60/227,732               580.   25 Aug. 2000   60/227,729               581.   25 Aug. 2000   60/228,167               582.   25 Aug. 2000   60/227,734               583.   25 Aug. 2000   60/227,792               584.   25 Aug. 2000   60/227,733               585.   25 Aug. 2000   60/227,730               586.   25 Aug. 2000   60/227,770               587.   25 Aug. 2000   60/227,728               588.   25 Aug. 2000   60/227,773               589.   25 Aug. 2000   60/228,033               590.   25 Aug. 2000   60/228,024               591.   25 Aug. 2000   60/227,769               592.   25 Aug. 2000   60/227,780               593.   25 Aug. 2000   60/227,725               594.   25 Aug. 2000   60/227,774               595.   25 Aug. 2000   60/228,163               596.   25 Aug. 2000   60/228,046               597.   25 Aug. 2000   60/228,098               598.   25 Aug. 2000   60/228,047               599.   25 Aug. 2000   60/228,052               600.   25 Aug. 2000   60/228,049               601.   25 Aug. 2000   60/228,132               602.   25 Aug. 2000   60/228,152               603.   25 Aug. 2000   60/228,135               604.   25 Aug. 2000   60/228,322               605.   25 Aug. 2000   60/228,156               606.   25 Aug. 2000   60/228,323               607.   25 Aug. 2000   60/228,133               608.   25 Aug. 2000   60/228,320               609.   25 Aug. 2000   60/228,159               610.   25 Aug. 2000   60/228,151               611.   25 Aug. 2000   60/228,202               612.   25 Aug. 2000   60/228,208               613.   25 Aug. 2000   60/228,153               614.   25 Aug. 2000   60/228,179               615.   25 Aug. 2000   60/228,180               616.   25 Aug. 2000   60/228,209               617.   25 Aug. 2000   60/228,178               618.   25 Aug. 2000   60/228,177               619.   25 Aug. 2000   60/227,976               620.   25 Aug. 2000   60/228,207               621.   25 Aug. 2000   60/228,048               622.   25 Aug. 2000   60/228,096               623.   25 Aug. 2000   60/227,932               624.   25 Aug. 2000   60/227,936               625.   25 Aug. 2000   60/228,044               626.   25 Aug. 2000   60/228,216               627.   25 Aug. 2000   60/228,065               628.   25 Aug. 2000   60/227,975               629.   25 Aug. 2000   60/228,181               630.   25 Aug. 2000   60/228,063               631.   25 Aug. 2000   60/228,064               632.   25 Aug. 2000   60/228,055               633.   25 Aug. 2000   60/228,074               634.   25 Aug. 2000   60/227,939               635.   25 Aug. 2000   60/227,955               636.   25 Aug. 2000   60/228,053               637.   25 Aug. 2000   60/227,978               638.   25 Aug. 2000   60/227,982               639.   25 Aug. 2000   60/228,189               640.   25 Aug. 2000   60/228,054               641.   25 Aug. 2000   60/228,164               642.   25 Aug. 2000   60/228,161               643.   25 Aug. 2000   60/228,165               644.   25 Aug. 2000   60/228,221               645.   25 Aug. 2000   60/228,240               646.   25 Aug. 2000   60/227,979               647.   25 Aug. 2000   60/227,954               648.   25 Aug. 2000   60/228,217               649.   25 Aug. 2000   60/227,929               650.   25 Aug. 2000   60/228,043               651.   25 Aug. 2000   60/227,931               652.   25 Aug. 2000   60/228,187               653.   25 Aug. 2000   60/228,061               654.   25 Aug. 2000   60/228,150               655.                       656.   25 Aug. 2000   60/227,793               657.   25 Aug. 2000   60/228,031               658.   25 Aug. 2000   60/228,028               659.   25 Aug. 2000   60/228,027               660.   25 Aug. 2000   60/228,026               661.   25 Aug. 2000   60/228,038               662.   25 Aug. 2000   60/228,036               663.   25 Aug. 2000   60/227,790               664.   25 Aug. 2000   60/228,039               665.   25 Aug. 2000   60/228,030               666.   25 Aug. 2000   60/228,032               667.   25 Aug. 2000   60/228,149               668.   25 Aug. 2000   60/228,040               669.   25 Aug. 2000   60/227,777               670.   25 Aug. 2000   60/228,037               671.   25 Aug. 2000   60/227,791               672.   25 Aug. 2000   60/228,041               673.   6 Sep. 2000   60/231,840               674.   6 Sep. 2000   60/231,837               675.   6 Sep. 2000   60/231,833               676.   6 Sep. 2000   60/231,835               677.   6 Sep. 2000   60/231,834               678.   6 Sep. 2000   60/230,430               679.   6 Sep. 2000   60/230,434               680.   13 Sep. 2000   60/232,044               681.   13 Sep. 2000   60/232,043               682.   15 Sep. 2000   60/232,858               683.   15 Sep. 2000   60/232,865               684.   18 Sep. 2000   60/233,621               685.   18 Sep. 2000   60/233,634               686.   20 Sep. 2000   60/234,179               687.   20 Sep. 2000   60/234,178               688.   21 Sep. 2000   60/234,233               689.   21 Sep. 2000   60/234,217               690.   21 Sep. 2000   60/234,220               691.   25 Sep. 2000   60/234,968               692.   25 Sep. 2000   60/234,979               693.   25 Sep. 2000   60/234,974               694.   25 Sep. 2000   60/235,118               695.   26 Sep. 2000   60/234,949               696.   27 Sep. 2000   60/235,577               697.   28 Sep. 2000   60/235,934               698.   29 Sep. 2000   60/236,380               699.   2 Oct. 2000   60/236,732               700.   2 Oct. 2000   60/237,035               701.   4 Oct. 2000   60/237,379               702.   4 Oct. 2000   60/237,505               703.   5 Oct. 2000   60/237,686               704.   10 Oct. 2000   60/238,473               705.   10 Oct. 2000   60/238,472               706.   10 Oct. 2000   60/238,456               707.   10 Oct. 2000   60/238,421               708.   11 Oct. 2000   60/239,091               709.   11 Oct. 2000   60/239,245               710.   17 Oct. 2000   60/240,862               711.   17 Oct. 2000   60/240,863               712.   19 Oct. 2000   60/241,368               713.   19 Oct. 2000   60/241,367               714.   19 Oct. 2000   09/691,020               715.   19 Oct. 2000   09/691,044               716.   19 Oct. 2000   09/691,028               717.   19 Oct. 2000   09/691,056               718.   19 Oct. 2000   09/691,038               719.   19 Oct. 2000   09/691,031               720.   19 Oct. 2000   09/691,018               721.   20 Oct. 2000   60/241,751               722.   20 Oct. 2000   60/241,750               723.   23 Oct. 2000   60/242,065               724.   23 Oct. 2000   60/242,072               725.   24 Oct. 2000   60/242,686               726.   25 Oct. 2000   60/242,705               727.   25 Oct. 2000   60/242,706               728.   26 Oct. 2000   60/243,289               729.   26 Oct. 2000   60/243,288               730.   27 Oct. 2000   60/243,398               731.   27 Oct. 2000   60/243,478               732.   30 Oct. 2000   60/243,723               733.   30 Oct. 2000   60/243,735               734.   1 Nov. 2000   60/244,691               735.   1 Nov. 2000   60/244,747               736.   2 Nov. 2000   60/244,923               737.   2 Nov. 2000   60/244,920               738.   3 Nov. 2000   60/245,164               739.   3 Nov. 2000   60/245,165               740.   6 Nov. 2000   60/245,676               741.   6 Nov. 2000   60/245,576               742.   9 Nov. 2000   60/246,732               743.   13 Nov. 2000   60/247,010               744.   13 Nov. 2000   60/247,051               745.   13 Nov. 2000   60/247,050               746.   13 Nov. 2000   60/247,049               747.   15 Nov. 2000   60/248,198               748.   15 Nov. 2000   60/248,197               749.   16 Nov. 2000   60/248,555               750.   17 Nov. 2000   60/249,256               751.   17 Nov. 2000   60/249,257               752.   20 Nov. 2000   60/249,454               753.   20 Nov. 2000   60/249,453               754.   21 Nov. 2000   60/252,080               755.   22 Nov. 2000   60/252,464               756.   22 Nov. 2000   60/252,465               757.   24 Nov. 2000   60/252,598               758.   24 Nov. 2000   60/252,590               759.   28 Nov. 2000   60/253,140               760.   29 Nov. 2000   60/253,722               761.   29 Nov. 2000   60/253,748               762.   1 Dec. 2000   60/250,356               763.   4 Dec. 2000   60/250,464               764.   6 Dec. 2000   60/251,387               765.   7 Dec. 2000   60/251,504               766.   7 Dec. 2000   60/251,508               767.   8 Dec. 2000   60/251,853               768.   8 Dec. 2000   60/251,854               769.   11 Dec. 2000   60/254,174               770.   11 Dec. 2000   60/254,196               771.   13 Dec. 2000   60/254,891               772.   15 Dec. 2000   60/256,503               773.   15 Dec. 2000   60/255,415               774.   18 Dec. 2000   60/255,891               775.   18 Dec. 2000   60/255,892               776.   19 Dec. 2000   60/256,306               777.   21 Dec. 2000   60/256,929               778.   27 Dec. 2000   60/257,978               779.   29 Dec. 2000   09/750,044               780.   2 Jan. 2001   60/258,880               781.   2 Jan. 2001   09/750,910               782.   3 Jan. 2001   09/752,823               783.   5 Jan. 2001   09/754,184               784.   5 Jan. 2001   09/754,185               785.   19 Jan. 2001   60/262,389               786.   19 Jan. 2001   60/262,359               787.   26 Jan. 2001   60/264,026               788.   26 Jan. 2001   60/264,027               789.   29 Jan. 2001   60/264,282               790.   29 Jan. 2001   60/264,257               791.   31 Jan. 2001   09/774,106               792.   31 Jan. 2001   09/774,089               793.   31 Jan. 2001   09/774,090               794.   1 Feb. 2001   09/775,870               795.   1 Feb. 2001   09/776,014               796.   6 Feb. 2001   60/266,468               797.   6 Feb. 2001   60/266,469               798.   7 Feb. 2001   60/266,863               799.   8 Feb. 2001   09/778,734               800.   9 Feb. 2001   60/267,425               801.   9 Feb. 2001   60/267,430               802.   9 Feb. 2001   60/267,426               803.   12 Feb. 2001   60/267,707               804.   12 Feb. 2001   60/267,706               805.   14 Feb. 2001   60/268,366               806.   16 Feb. 2001   60/268,921               807.   21 Feb. 2001   60/269,890               808.   21 Feb. 2001   60/269,891               809.   21 Feb. 2001   60/269,892               810.   21 Feb. 2001   60/269,893               811.   22 Feb. 2001   60/270,122               812.   26 Feb. 2001   60/270,913               813.   26 Feb. 2001   60/270,912               814.   28 Feb. 2001   60/271,724               815.   28 Feb. 2001   60/271,725               816.   2 Mar. 2001   60/272,467               817.   5 Mar. 2001   60/272,783               818.   7 Mar. 2001   60/273,554               819.   7 Mar. 2001   60/273,553               820.   7 Mar. 2001   60/273,552               821.   2 Apr. 2001   09/823,082                    
Number 26
 
     Application Ser. No. 10/461,476 listed above is a continuation of application Ser. No. 10/191,406, filed on Jul. 10, 2002, the entire contents of which are hereby incorporated by reference. Application Ser. No. 10/191,406 is a continuation of application Ser. No. 09/940,255 filed Aug. 24, 2001 the entire contents of which are also hereby incorporated by reference. Moreover, application Ser. No. 09/940,255 is a continuation-in-part of all the following nonprovisional applications to which the present application also incorporates by reference and claims priority under 35 USC § 120: 
     
       
         
           
               
               
               
               
             
               
                   
               
               
                   
                   
                 Appln No. 
                 Filing Date 
               
               
                   
               
             
            
               
                   
                  1. 
                 09/391,631 
                 Sep. 3, 1999 
               
               
                   
                  2. 
                 09/413,198 
                 Oct. 5, 1999 
               
               
                   
                  3. 
                 09/412,922 
                 Oct. 5, 1999 
               
               
                   
                  4. 
                 09/428,944 
                 Oct. 28, 1999 
               
               
                   
                  5. 
                 09/451,320 
                 Dec. 1, 1999 
               
               
                   
                  6. 
                 09/478,081 
                 Oct. 4, 2000 
               
               
                   
                  7. 
                 09/497,191 
                 Feb. 3, 2000 
               
               
                   
                  8. 
                 09/517,537 
                 Mar. 1, 2000 
               
               
                   
                  9. 
                 09/637,820 
                 Aug. 11, 2000 
               
               
                   
                 10. 
                 09/637,565 
                 Aug. 11, 2000 
               
               
                   
                 11. 
                 09/637,564 
                 Aug. 11, 2000 
               
               
                   
                 12. 
                 09/637,792 
                 Aug. 11, 2000 
               
               
                   
                 13. 
                 09/691,039 
                 Oct. 19, 2000 
               
               
                   
                 14. 
                 09/691,020 
                 Oct. 19, 2000 
               
               
                   
                 15. 
                 09/691,044 
                 Oct. 19, 2000 
               
               
                   
                 16. 
                 09/691,028 
                 Oct. 19, 2000 
               
               
                   
                 17. 
                 09/691,045 
                 Oct. 19, 2000 
               
               
                   
                 18. 
                 09/691,056 
                 Oct. 19, 2000 
               
               
                   
                 19. 
                 09/691,038 
                 Oct. 19, 2000 
               
               
                   
                 20. 
                 09/691,031 
                 Oct. 19, 2000 
               
               
                   
                 21. 
                 09/691,019 
                 Oct. 19, 2000 
               
               
                   
                 22. 
                 09/691,018 
                 Oct. 19, 2000 
               
               
                   
                 23. 
                 09/741,043 
                 Dec. 21, 2000 
               
               
                   
                 24. 
                 09/750,044 
                 Dec. 29, 2000 
               
               
                   
                 25. 
                 09/750,910 
                 Jan. 2, 2001 
               
               
                   
                 26. 
                 09/752,823 
                 Jan. 3, 2001 
               
               
                   
                 27. 
                 09/754,184 
                 Jan. 5, 2001 
               
               
                   
                 28. 
                 09/754,185 
                 Jan. 5, 2001 
               
               
                   
                 29. 
                 09/774,106 
                 Jan. 31, 2001 
               
               
                   
                 30. 
                 09/774,089 
                 Jan. 31, 2001 
               
               
                   
                 31. 
                 09/774,090 
                 Jan. 31, 2001 
               
               
                   
                 32. 
                 09/774,340 
                 Jan. 31, 2001 
               
               
                   
                 33. 
                 09/775,870 
                 Feb. 1, 2001 
               
               
                   
                 34. 
                 09/776,014 
                 Feb. 1, 2001 
               
               
                   
                 35. 
                 09/778,734 
                 Feb. 8, 2001 
               
               
                   
                 36. 
                 09/790,663 
                 Feb. 23, 2001 
               
               
                   
                 37. 
                 09/795,347 
                 Mar. 1, 2001 
               
               
                   
                 38. 
                 09/795,359 
                 Mar. 1, 2001 
               
               
                   
                 39. 
                 09/804,470 
                 Mar. 16, 2001 
               
               
                   
                 40. 
                 09/823,082 
                 Apr. 2, 2001 
               
               
                   
                 41. 
                 09/824,790 
                 Apr. 4, 2001 
               
               
                   
                 42. 
                 09/824,882 
                 Apr. 4, 2001 
               
               
                   
                 43. 
                 09/832,192 
                 Apr. 11, 2001 
               
               
                   
                 44. 
                 09/832,934 
                 Apr. 12, 2001 
               
               
                   
                 45. 
                 09/842,088 
                 Apr. 26, 2001 
               
               
                   
                 46. 
                 09/842,246 
                 Apr. 26, 2001 
               
               
                   
                 47. 
                 09/845,208 
                 May 1, 2001 
               
               
                   
                 48. 
                 09/845,206 
                 May 1, 2001 
               
               
                   
                 49. 
                 09/845,318 
                 May 1, 2001 
               
               
                   
                 50. 
                 09/845,209 
                 May 1, 2001 
               
               
                   
                 51. 
                 09/870,713 
                 Jun. 1, 2001 
               
               
                   
                 52. 
                 09/870,699 
                 Jun. 1, 2001 
               
               
                   
                 53. 
                 09/870,675 
                 Jun. 1, 2001 
               
               
                   
                 54. 
                 09/870,646 
                 Jun. 1, 2001 
               
               
                   
                 55. 
                 09/870,476 
                 Jun. 1, 2001 
               
               
                   
                 56. 
                 09/870,664 
                 Jun. 1, 2001 
               
               
                   
                 57. 
                 09/878,974 
                 Jun. 13, 2001 
               
               
                   
                 58. 
                 09/881,096 
                 Jun. 15, 2001 
               
               
                   
                 59. 
                 09/898,063 
                 Jul. 5, 2001 
               
               
                   
                 60. 
                 09/898,064 
                 Jul. 5, 2001 
               
               
                   
                 61. 
                 09/902,093 
                 Jul. 11, 2001 
               
               
                   
                 62. 
                 09/902,613 
                 Jul. 12, 2001 
               
               
                   
                 63. 
                 09/902,614 
                 Jul. 12, 2001 
               
               
                   
                 64. 
                 09/903,497 
                 Jul. 13, 2001 
               
               
                   
                 65. 
                 09/903,988 
                 Jul. 13, 2001 
               
               
                   
                 66. 
                 09/918,556 
                 Aug. 1, 2001 
               
               
                   
                 67. 
                 09/920,626 
                 Aug. 3, 2001 
               
               
                   
                 68. 
                 09/921,135 
                 Aug. 3, 2001 
               
               
                   
                 69. 
                 09/922,661 
                 Aug. 7, 2001 
               
               
                   
                 70. 
                 09/924,702 
                 Aug. 9, 2001 
               
               
                   
                 71. 
                 09/924,701 
                 Aug. 9, 2001 
               
               
                   
                 72. 
                 09/928,372 
                 Aug. 14, 2001 
               
               
                   
                 73. 
                 09/930,244 
                 Aug. 16, 2001 
               
               
                   
                 74. 
                 09/930,231 
                 Aug. 16, 2001 
               
               
                   
                 75. 
                 09/930,214 
                 Aug. 16, 2001 
               
               
                   
                 76. 
                 09/930,223 
                 Aug. 16, 2001 
               
               
                   
                 77. 
                 09/931,043 
                 Aug. 17, 2001 
               
               
                   
                 78. 
                 09/931,911 
                 Aug. 20, 2001 
               
               
                   
               
            
           
         
       
     
     Furthermore, the some of the above-listed 78 nonprovisional applications themselves claim priority under 35 USC § 119(e) of the following applications to which the present application also claims priority and incorporates by reference: 
                                             Appln No   Filing Date                                                    1.   09/391,631   Sep. 3, 1999   which claims                   priority to           60/099,671   Sep. 4, 1998               60/099,672   Sep. 4, 1998               60/099,933   Sep. 11, 1998               60/100,864   Sep. 17, 1998               60/101,042   Sep. 18, 1998               60/101,682   Sep. 24, 1998               60/102,533   Sep. 30, 1998               60/102,460   Sep. 30, 1998               60/103,116   Oct. 5, 1998               60/103,141   Oct. 5, 1998               60/103,574   Oct. 9, 1998               60/103,907   Oct. 13, 1998               60/106,105   Oct. 29, 1998               60/106,218   Oct. 30, 1998               60/107,282   Nov. 6, 1998               60/107,836   Nov. 10, 1998               60/108,526   Nov. 16, 1998               60/108,901   Nov. 17, 1998               60/109,267   Nov. 20, 1998               60/109,594   Nov. 23, 1998               60/110,263   Nov. 30, 1998               60/110,495   Dec. 1, 1998               60/110,626   Dec. 2, 1998               60/110,701   Dec. 3, 1998               60/111,339   Dec. 7, 1998               60/111,589   Dec. 9, 1998               60/112,096   Dec. 14, 1998               60/112,224   Dec. 15, 1998               60/112,624   Dec. 16, 1998               60/112,862   Dec. 17, 1998               60/115,152   Jan. 7, 1999               60/115,156   Jan. 7, 1999               60/115,365   Jan. 8, 1999               60/115,339   Jan. 11, 1999               60/115,847   Jan. 13, 1999               60/116,674   Jan. 21, 1999               60/116,962   Jan. 22, 1999               60/120,583   Feb. 18, 1999               60/121,072   Feb. 22, 1999               60/122,568   Mar. 2, 1999               60/123,941   Mar. 12, 1999           2.   09/413,198   Oct. 5, 1999   which claims                   priority to           60/103,116   Oct. 5, 1998               60/103,141   Oct. 5, 1998               60/103,215   Oct. 6, 1998               60/103,554   Oct. 8, 1998               60/103,574   Oct. 9, 1998               60/103,907   Oct. 13, 1998               60/104,268   Oct. 14, 1998               60/104,680   Oct. 16, 1998               60/104,828   Oct. 19, 1998               60/105,008   Oct. 20, 1998               60/105,142   Oct. 21, 1998               60/105,533   Oct. 22, 1998               60/105,571   Oct. 26, 1998               60/105,815   Oct. 27, 1998               60/106,105   Oct. 29, 1998               60/106,218   Oct. 30, 1998           3.   09/412,922   Oct. 5, 1999   which claims                   priority to           60/103,116   Oct. 5, 1998               60/103,141   Oct. 5, 1998               60/103,215   Oct. 6, 1998               60/103,554   Oct. 8, 1998               60/103,574   Oct. 9, 1998               60/103,907   Oct. 13, 1998               60/104,268   Oct. 14, 1998               60/104,680   Oct. 16, 1998               60/104,828   Oct. 19, 1998               60/105,008   Oct. 20, 1998               60/105,142   Oct. 21, 1998               60/105,533   Oct. 22, 1998               60/105,571   Oct. 26, 1998               60/105,815   Oct. 27, 1998               60/106,105   Oct. 29, 1998               60/106,218   Oct. 30, 1998               60/106,685   Nov. 2, 1998               60/107,282   Nov. 6, 1998               60/107,720   Nov. 9, 1998               60/107,719   Nov. 9, 1998               60/107,836   Nov. 10, 1998               60/108,190   Nov. 12, 1998               60/108,526   Nov. 16, 1998               60/108,901   Nov. 17, 1998               60/109,124   Nov. 19, 1998               60/109,127   Nov. 19, 1998               60/109,267   Nov. 20, 1998               60/109,594   Nov. 23, 1998               60/110,053   Nov. 25, 1998               60/110,050   Nov. 25, 1998               60/110,158   Nov. 27, 1998               60/110,263   Nov. 30, 1998               60/110,495   Dec. 1, 1998               60/110,626   Dec. 2, 1998               60/110,701   Dec. 3, 1998               60/111,339   Dec. 7, 1998               60/111,589   Dec. 9, 1998               60/111,782   Dec. 10, 1998               60/111,812   Dec. 11, 1998               60/112,096   Dec. 14, 1998               60/112,224   Dec. 15, 1998               60/112,624   Dec. 16, 1998               60/112,862   Dec. 17, 1998               60/112,912   Dec. 18, 1998               60/113,248   Dec. 21, 1998               60/113,522   Dec. 22, 1998               60/113,826   Dec. 23, 1998               60/113,998   Dec. 28, 1998               60/114,384   Dec. 29, 1998               60/114,455   Dec. 30, 1998               60/114,740   Jan. 4, 1999               60/114,866   Jan. 6, 1999               60/115,153   Jan. 7, 1999               60/115,152   Jan. 7, 1999               60/115,151   Jan. 7, 1999               60/115,155   Jan. 7, 1999               60/115,156   Jan. 7, 1999               60/115,154   Jan. 7, 1999               60/115,364   Jan. 8, 1999               60/115,365   Jan. 8, 1999               60/115,339   Jan. 11, 1999               60/115,518   Jan. 12, 1999               60/115,847   Jan. 13, 1999               60/115,905   Jan. 14, 1999               60/116,383   Jan. 15, 1999               60/116,384   Jan. 15, 1999               60/116,329   Jan. 19, 1999               60/116,340   Jan. 19, 1999               60/116,674   Jan. 21, 1999               60/116,672   Jan. 21, 1999               60/116,960   Jan. 22, 1999               60/116,962   Jan. 22, 1999               60/117,756   Jan. 28, 1999               60/118,672   Feb. 3, 1999               60/118,808   Feb. 4, 1999               60/118,778   Feb. 5, 1999               60/119,029   Feb. 8, 1999               60/119,332   Feb. 9, 1999               60/119,462   Feb. 10, 1999               60/119,922   Feb. 12, 1999               60/120,196   Feb. 16, 1999               60/120,198   Feb. 16, 1999               60/120,583   Feb. 18, 1999               60/121,072   Feb. 22, 1999               60/121,334   Feb. 23, 1999               60/121,470   Feb. 24, 1999               60/121,704   Feb. 25, 1999               60/122,107   Feb. 26, 1999               60/122,266   Mar. 1, 1999               60/122,568   Mar. 2, 1999               60/122,611   Mar. 3, 1999               60/121,775   Mar. 4, 1999               60/123,534   Mar. 5, 1999               60/123,680   Mar. 9, 1999               60/123,715   Mar. 10, 1999               60/123,726   Mar. 10, 1999               60/124,263   Mar. 11, 1999               60/123,941   Mar. 12, 1999           4.   09/428,944   Oct. 28, 1999   which claims                   priority to           60/106,685   Nov. 2, 1998               60/107,282   Nov. 6, 1998               60/107,720   Nov. 9, 1998               60/107,719   Nov. 9, 1998               60/107,836   Nov. 10, 1998               60/108,190   Nov. 12, 1998               60/108,526   Nov. 16, 1998               60/108,901   Nov. 17, 1998               60/109,124   Nov. 19, 1998               60/109,127   Nov. 19, 1998               60/109,267   Nov. 20, 1998               60/109,594   Nov. 23, 1998               60/110,053   Nov. 25, 1998               60/110,050   Nov. 25, 1998               60/110,158   Nov. 27, 1998               60/110,263   Nov. 30, 1998           5.   09/451,320   Dec. 1, 1999   which claims                   priority to           60/110,495   Dec. 1, 1998               60/110,626   Dec. 2, 1998               60/110,701   Dec. 3, 1998               60/111,339   Dec. 7, 1998               60/111,589   Dec. 9, 1998               60/111,782   Dec. 10, 1998               60/111,812   Dec. 11, 1998               60/112,096   Dec. 14, 1998               60/112,224   Dec. 15, 1998               60/112,624   Dec. 16, 1998               60/112,862   Dec. 17, 1998               60/112,912   Dec. 18, 1998               60/113,248   Dec. 21, 1998               60/113,522   Dec. 22, 1998               60/113,826   Dec. 23, 1998               60/113,998   Dec. 28, 1998               60/114,384   Dec. 29, 1998               60/114,455   Dec. 30, 1998               60/115,153   Jan. 7, 1999               60/115,152   Jan. 7, 1999               60/115,151   Jan. 7, 1999               60/115,155   Jan. 7, 1999               60/115,156   Jan. 7, 1999               60/115,364   Jan. 8, 1999               60/116,960   Jan. 22, 1999           6.   09/478,081   Jan. 4, 2000   which claims                   priority to           60/116,674   Jan. 21, 1999               60/115,518   Jan. 12, 1999               60/115,154   Jan. 7, 1999               60/115,365   Jan. 8, 1999               60/116,384   Jan. 15, 1999               60/115,339   Jan. 11, 1999               60/116,340   Jan. 19, 1999               60/114,866   Jan. 6, 1999               60/116,962   Jan. 22, 1999               60/114,740   Jan. 4, 1999               60/115,905   Jan. 14, 1999               60/115,847   Jan. 13, 1999               60/116,672   Jan. 21, 1999               60/116,383   Jan. 15, 1999               60/116,329   Jan. 19, 1999               60/117,756   Jan. 28, 1999           7.   09/497,191   Feb. 3, 2000   which claims                   priority to           60/120,196   Feb. 16, 1999               60/121,470   Feb. 24, 1999               60/122,107   Feb. 26, 1999               60/121,334   Feb. 23, 1999               60/119,462   Feb. 10, 1999               60/120,583   Feb. 18, 1999               60/121,704   Feb. 25, 1999               60/120,198   Feb. 16, 1999               60/121,072   Feb. 22, 1999               60/119,922   Feb. 12, 1999               60/118,672   Feb. 3, 1999               60/118,808   Feb. 4, 1999               60/118,778   Feb. 5, 1999               60/119,029   Feb. 8, 1999               60/119,332   Feb. 9, 1999           8.   09/517,537   Mar. 1, 2000   which claims                   priority to           60/123,534   Mar. 5, 1999               60/122,266   Mar. 1, 1999               60/123,941   Mar. 12, 1999               60/124,263   Mar. 11, 1999               60/123,726   Mar. 10, 1999               60/122,568   Mar. 2, 1999               60/123,680   Mar. 9, 1999               60/123,715   Mar. 10, 1999               60/121,775   Mar. 4, 1999               60/122,611   Mar. 3, 1999           9.   09/637,820   Aug. 11, 2000   which claims                   priority to           60/148,347   Aug. 12, 1999           10.   09/637,565   Aug. 11, 2000   which claims                   priority to           60/148,342   Aug. 12, 1999           11.   09/637,564   Aug. 11, 2000   which claims                   priority to           60/148,340   Aug. 12, 1999           12.   09/637,792   Aug. 11, 2000   which claims                   priority to           60/148,337   Aug. 12, 1999           36.   09/790,663   Feb. 23, 2001   which claims                   priority to           60/185,398   Feb. 28, 2000               60/185,140   Feb. 25, 2000               60/185,750   Feb. 29, 2000           37.   09/795,347   Mar. 1, 2001   which claims                   priority to           60/186,296   Mar. 1, 2000               60/186,748   Mar. 3, 2000               60/186,283   Mar. 1, 2000               60/191,825   Mar. 24, 2000               60/190,069   Mar. 20, 2000               60/189,959   Mar. 16, 2000               60/190,070   Mar. 20, 2000               60/190,545   Mar. 20, 2000               60/190,089   Mar. 20, 2000               60/191,084   Mar. 22, 2000               60/191,097   Mar. 22, 2000               60/191,543   Mar. 23, 2000               60/189,953   Mar. 16, 2000               60/191,823   Mar. 24, 2000               60/192,421   Mar. 27, 2000               60/186,390   Mar. 2, 2000               60/192,308   Mar. 27, 2000               60/187,178   Mar. 2, 2000               60/192,941   Mar. 29, 2000               60/193,244   Mar. 30, 2000               60/193,245   Mar. 30, 2000               60/193,453   Mar. 31, 2000               60/193,455   Mar. 31, 2000               60/191,545   Mar. 23, 2000               60/187,888   Mar. 8, 2000               60/186,386   Mar. 2, 2000               60/192,940   Mar. 29, 2000               60/189,462   Mar. 15, 2000               60/186,669   Mar. 3, 2000               60/187,896   Mar. 8, 2000               60/186,387   Mar. 2, 2000               60/188,187   Mar. 10, 2000               60/188,186   Mar. 10, 2000               60/188,185   Mar. 10, 2000               60/188,175   Mar. 10, 2000               60/189,080   Mar. 14, 2000               60/189,052   Mar. 14, 2000               60/189,461   Mar. 15, 2000               60/187,378   Mar. 7, 2000           38.   09/795,359   Mar. 1, 2001   which claims                   priority to           60/189,460   Mar. 15, 2000               60/190,090   Mar. 20, 2000               60/189,965   Mar. 17, 2000               60/189,958   Mar. 16, 2000               60/188,687   Mar. 13, 2000               60/188,174   Mar. 10, 2000               60/187,985   Mar. 9, 2000               60/187,379   Mar. 7, 2000               60/186,277   Mar. 1, 2000               60/192,855   Mar. 29, 2000               60/186,670   Mar. 3, 2000               60/192,420   Mar. 27, 2000               60/193,469   Mar. 31, 2000               60/193,243   Mar. 30, 2000               60/191,826   Mar. 24, 2000               60/191,549   Mar. 23, 2000           39.   09/804,470   Mar. 16, 2001   which claims                   priority to           60/189,948   Mar. 16, 2000               60/190,121   Mar. 16, 2000               60/189,947   Mar. 16, 2000               60/190,120   Mar. 16, 2000           41.   09/824,790   Apr. 4, 2001   which claims                   priority to           60/199,123   Apr. 24, 2000               60/194,698   Apr. 5, 2000               60/196,168   Apr. 11, 2000               60/197,397   Apr. 14, 2000               60/195,258   Apr. 7, 2000               60/194,884   Apr. 6, 2000               60/196,483   Apr. 12, 2000               60/194,682   Apr. 5, 2000               60/194,385   Apr. 4, 2000               60/198,400   Apr. 19, 2000               60/198,765   Apr. 21, 2000               60/198,629   Apr. 20, 2000               60/198,268   Apr. 17, 2000           42.   09/824,882   Apr. 4, 2001   which claims                   priority to           60/195,045   Apr. 6, 2000               60/196,089   Apr. 11, 2000               60/198,373   Apr. 19, 2000               60/198,386   Apr. 19, 2000               60/197,687   Apr. 17, 2000               60/198,133   Apr. 17, 2000               60/197,671   Apr. 17, 2000               60/195,283   Apr. 7, 2000               60/196,289   Apr. 12, 2000               60/196,486   Apr. 12, 2000               60/198,763   Apr. 21, 2000               60/196,169   Apr. 11, 2000               60/197,678   Apr. 17, 2000               60/194,874   Apr. 6, 2000               60/194,885   Apr. 6, 2000               60/194,872   Apr. 6, 2000               60/195,257   Apr. 7, 2000               60/194,697   Apr. 5, 2000               60/194,683   Apr. 5, 2000               60/194,398   Apr. 4, 2000               60/194,404   Apr. 4, 2000               60/196,487   Apr. 12, 2000               60/200,102   Apr. 27, 2000               60/198,623   Apr. 20, 2000               60/198,767   Apr. 21, 2000               60/199,122   Apr. 24, 2000               60/199,124   Apr. 24, 2000               60/196,485   Apr. 12, 2000               60/199,828   Apr. 26, 2000               60/199,818   Apr. 26, 2000               60/200,103   Apr. 27, 2000               60/198,619   Apr. 20, 2000           43.   09/832,192   Apr. 11, 2001   which claims                   priority to           60/200,773   Apr. 28, 2000               60/196,212   Apr. 12, 2000               60/197,869   Apr. 14, 2000               60/196,213   Apr. 13, 2000               60/197,870   Apr. 17, 2000               60/197,871   Apr. 17, 2000               60/200,373   Apr. 28, 2000               60/196,211   Apr. 11, 2000           44.   09/832,934   Apr. 12, 2001   is a continuation                   of           09/637,820   Aug. 11, 2000   which claims                   priority to           60/148,347   Aug. 12/99           45.   09/842,088   Apr. 26, 2001   which claims                   priority to           60/200,031   Apr. 26, 2000           46.   09/842,246   Apr. 26, 2001   which claims                   priority to           60/200,034   Apr. 26, 2000           47.   09/845,208   May 1, 2001   which claims                   priority to           60/203,622   May 11, 2000               60/200,763   May 1, 2000               60/201,016   May 1, 2000               60/200,762   May 1, 2000               60/200,761   May 1, 2000               60/203,671   May 11, 2000               60/203,669   May 11, 2000               60/203,672   May 11, 2000           48.   09/845,206   May 1, 2001   which claims                   priority to           60/204,122   May 15, 2000               60/207,452   May 30, 2000               60/207,329   May 30, 2000               60/205,243   May 19, 2000               60/204,388   May 15, 2000               60/204,568   May 16, 2000               60/204,830   May 17, 2000               60/204,829   May 17, 2000               60/205,201   May 18, 2000               60/207,367   May 26, 2000               60/205,242   May 19, 2000               60/203,279   May 11, 2000               60/205,572   May 22, 2000               60/205,576   May 22, 2000               60/206,316   May 23, 2000               60/206,319   May 23, 2000               60/206,553   May 24, 2000               60/206,545   May 24, 2000               60/205,058   May 18, 2000               60/202,180   May 5, 2000               60/207,354   May 26, 2000               60/204,569   May 16, 2000               60/201,275   May 2, 2000               60/200,879   May 1, 2000               60/201,305   May 2, 2000               60/201,740   May 4, 2000               60/203,915   May 12, 2000               60/202,112   May 5, 2000               60/203,916   May 12, 2000               60/202,914   May 9, 2000               60/202,636   May 9, 2000               60/202,634   May 9, 2000               60/202,963   May 10, 2000               60/203,457   May 11, 2000               60/202,968   May 10, 2000               60/201,750   May 4, 2000               60/207,239   May 26, 2000               60/207,243   May 26, 2000               60/202,919   May 9, 2000           49.   09/845,318   May 1, 2001   which claims                   priority to           60/205,325   May 17, 2000               60/201,018   May 1, 2000           50.   09/845,209   May 1, 2001   which claims                   priority to           60/205,233   May 17, 2000               60/201,017   May 1, 2000           51.   09/870,713   Jun. 1, 2001   which claims                   priority to           60/209,338   Jun. 2, 2000           52.   09/870,699   Jun. 1, 2001   which claims                   priority to           60/208,421   Jun. 1, 2000           53.   09/870,675   Jun. 1, 2001   which claims                   priority to           60/208,649   Jun. 2, 2000           54.   09/870,646   Jun. 1, 2001   which claims                   priority to           60/208,648   Jun. 1, 2000           55.   09/870,476   Jun. 1, 2001   which claims                   priority to           60/208,324   Jun. 1, 2000               60/210,008   Jun. 8, 2000               60/208,917   Jun. 5, 2000               60/208,919   Jun. 5, 2000           56.   09/870,664   Jun. 1, 2001   which claims                   priority to           60/208,918   Jun. 5, 2000               60/214,535   Jun. 27, 2000               60/208,920   Jun. 5, 2000               60/215,127   Jun. 30, 2000               60/214,799   Jun. 28, 2000               60/213,249   Jun. 22, 2000               60/210,564   Jun. 9, 2000               60/210,006   Jun. 8, 2000               60/208,312   Jun. 1, 2000               60/211,214   Jun. 13, 2000           57.   09/878,974   Jun. 13, 2001   which claims                   priority to           60/211,539   Jun. 15, 2000               60/214,760   Jun. 27, 2000               60/213,195   Jun. 22, 2000               60/213,221   Jun. 22, 2000               60/212,677   Jun. 20, 2000               60/212,414   Jun. 19, 2000               60/211,210   Jun. 13, 2000               60/212,713   Jun. 20, 2000           58.   09/881,096   Jun. 15, 2001   which claims                   priority to           60/213,270   Jun. 22, 2000               60/212,727   Jun. 20, 2000               60/212,623   Jun. 19, 2000               60/211,538   Jun. 15, 2000               60/214,524   Jun. 27, 2000           59.   09/898,063   Jul. 5, 2001   which claims                   priority to           60/216,362   Jul. 5, 2000               60/220,811   Jul. 25, 2000               60/220,652   Jul. 25, 2000               60/217,384   Jul. 11, 2000               60/219,033   Jul. 18, 2000           60.   09/898,064   Jul. 5, 2001   which claims                   priority to           60/217,476   Jul. 11, 2000               60/216,361   Jul. 5, 2000               60/220,647   Jul. 25, 2000               60/220,484   Jul. 25, 2000               60/219,004   Jul. 18, 2000           61.   09/902,093   Jul. 11, 2001   which claims                   priority to           60/226,725   Aug. 21, 2000               60/225,302   Aug. 15, 2000               60/228,897   Aug. 30, 2000               60/227,026   Aug. 23, 2000               60/217,385   Jul. 11, 2000               60/219,021   Jul. 18, 2000               60/224,516   Aug. 14, 2000               60/220,814   Jul. 25, 2000           62.   09/902,613   Jul. 12, 2001   which claims                   priority to           60/217,754   Jul. 12, 2000               60/223,114   Aug. 1, 2000           63.   09/902,614   Jul. 12, 2001   which claims                   priority to           60/223,116   Aug. 3, 2000               60/218,548   Jul. 12, 2000           64.   09/903,497   Jul. 13, 2001   which claims                   priority to           60/217,846   Jul. 13, 2000               60/223,099   Aug. 3, 2000           65.   09/903,988   Jul. 13, 2001   which claims                   priority to           60/218,566   Jul. 14, 2000               60/223,098   Aug. 3, 2000           66.   09/918,556   Aug. 1, 2001   which claims                   priority to           60/223,115   Aug. 1, 2000           67.   09/920,626   Aug. 3, 2001   which claims                   priority to           60/223,100   Aug. 3, 2000               60/237,361   Aug. 31, 2000               60/226,325   Aug. 18, 2000           68.   09/921,135   Aug. 3, 2001   which claims                   priority to           60/223,101   Aug. 3, 2000               60/226,323   Aug. 18, 2000               60/229,519   Aug. 31, 2000           69.   09/922,661   Aug. 7, 2001   which claims                   priority to           60/229,521   Aug. 31, 2000               60/226,381   Aug. 18, 2000               60/223,329   Aug. 7, 2000           70.   09/924,702   Aug. 9, 2001   claims priority of           60/224,390   Aug. 9, 2000           71.   09/924,701   Aug. 9, 2001   which claims                   priority to           60/224,391   Aug. 9, 2000           72.   09/928,372   Aug. 14, 2001   which claims                   priority to           60/227,024   Aug. 23, 2000               60/228,898   Aug. 30, 2000               60/225,303   Aug. 15, 2000               60/224,517   Aug. 14, 2000               60/226,452   Aug. 21, 2000           73.   09/930,244   Aug. 16, 2001   which claims                   priority to           60/237,362   Aug. 31, 2000               60/225,848   Aug. 16, 2000           74.   09/930,231   Aug. 16, 2001   which claims                   priority to           60/225,849   Aug. 16, 2000           75.   09/930,214   Aug. 16, 2001   which claims                   priority to           60/225,850   Aug. 16, 2000               60/229,520   Aug. 31, 2000           76.   09/930,223   Aug. 16, 2001   which claims                   priority to           60/225,847   Aug. 16, 2000           77.   09/931,043   Aug. 17, 2001   which claims                   priority to           60/226,324   Aug. 18, 2000           78.   09/931,911   Aug. 20, 2001   which claims                   priority to           60/229,520   Aug. 31, 2000               09/940,255   Aug. 24, 2001   which claims                   priority to       1.   60/228,025   Aug. 25, 2000           2.   60/227,781   Aug. 25, 2000           3.   60/227,783   Aug. 25, 2000           4.   60/227,731   Aug. 25, 2000           5.   60/227,732   Aug. 25, 2000           6.   60/227,729   Aug. 25, 2000           7.   60/228,167   Aug. 25, 2000           8.   60/227,734   Aug. 25, 2000           9.   60/227,792   Aug. 25, 2000           10.   60/227,733   Aug. 25, 2000           11.   60/227,730   Aug. 25, 2000           12.   60/227,770   Aug. 25, 2000           13.   60/227,728   Aug. 25, 2000           14.   60/227,773   Aug. 25, 2000           15.   60/228,033   Aug. 25, 2000           16.   60/228,024   Aug. 25, 2000           17.   60/227,769   Aug. 25, 2000           18.   60/227,780   Aug. 25, 2000           19.   60/227,725   Aug. 25, 2000           20.   60/227,774   Aug. 25, 2000           21.   60/231,840   Sep. 6, 2000           22.   60/231,837   Sep. 6, 2000           23.   60/231,833   Sep. 6, 2000           34.   60/231,835   Sep. 6, 2000           25.   60/231,834   Sep. 6, 2000           26.   60/228,163   Aug. 25, 2000           27.   60/228,046   Aug. 25, 2000           28.   60/228,098   Aug. 25, 2000           29.   60/228,047   Aug. 25, 2000           30.   60/228,052   Aug. 25, 2000           31.   60/228,049   Aug. 25, 2000           32.   60/228,132   Aug. 25, 2000           33.   60/228,152   Aug. 25, 2000           34.   60/228,135   Aug. 25, 2000           35.   60/228,322   Aug. 25, 2000           36.   60/228,156   Aug. 25, 2000           37.   60/228,323   Aug. 25, 2000           38.   60/228,133   Aug. 25, 2000           39.   60/228,320   Aug. 25, 2000           40.   60/228,159   Aug. 25, 2000           41.   60/228,151   Aug. 25, 2000           42.   60/228,202   Aug. 25, 2000           43.   60/228,208   Aug. 25, 2000           44.   60/228,153   Aug. 25, 2000           45.   60/228,179   Aug. 25, 2000           46.   60/228,180   Aug. 25, 2000           47.   60/228,209   Aug. 25, 2000           48.   60/228,178   Aug. 25, 2000           49.   60/228,177   Aug. 25, 2000           50.   60/227,976   Aug. 25, 2000           51.   60/228,207   Aug. 25, 2000           52.   60/228,048   Aug. 25, 2000           53.   60/228,096   Aug. 25, 2000           54.   60/227,932   Aug. 25, 2000           55.   60/227,936   Aug. 25, 2000           56.   60/228,044   Aug. 25, 2000           57.   60/228,216   Aug. 25, 2000           58.   60/228,065   Aug. 25, 2000           59.   60/227,975   Aug. 25, 2000           60.   60/228,181   Aug. 25, 2000           61.   60/228,063   Aug. 25, 2000           62.   60/228,064   Aug. 25, 2000           63.   60/228,055   Aug. 25, 2000           64.   60/228,074   Aug. 25, 2000           65.   60/227,939   Aug. 25, 2000           66.   60/227,955   Aug. 25, 2000           67.   60/228,053   Aug. 25, 2000           68.   60/227,978   Aug. 25, 2000           69.   60/227,982   Aug. 25, 2000           70.   60/228,189   Aug. 25, 2000           71.   60/228,054   Aug. 25, 2000           72.   60/228,164   Aug. 25, 2000           73.   60/228,161   Aug. 25, 2000           74.   60/228,165   Aug. 25, 2000           75.   60/228,221   Aug. 25, 2000           76.   60/228,240   Aug. 25, 2000           77.   60/227,979   Aug. 25, 2000           78.   60/227,954   Aug. 25, 2000           79.   60/228,217   Aug. 25, 2000           80.   60/227,929   Aug. 25, 2000           81.   60/228,043   Aug. 25, 2000           82.   60/227,931   Aug. 25, 2000           83.   60/228,187   Aug. 25, 2000           84.   60/228,061   Aug. 25, 2000           85.   60/228,150   Aug. 25, 2000           86.                   87.   60/230,430   Sep. 6, 2000           88.   60/230,434   Sep. 6, 2000           89.   60/232,044   Sep. 13, 2000           90.   60/232,043   Sep. 13, 2000           91.   60/232,858   Sep. 15, 2000           92.   60/232,865   Sep. 15, 2000           93.   60/233,621   Sep. 18, 2000           94.   60/233,634   Sep. 18, 2000           95.   60/246,732   Nov. 9, 2000           96.   60/247,010   Nov. 13, 2000           97.   60/247,051   Nov. 13, 2000           98.   60/247,050   Nov. 13, 2000           99.   60/247,049   Nov. 13, 2000           100.   60/234,179   Sep. 20, 2000           101.   60/234,178   Sep. 20, 2000           102.   60/234,233   Sep. 21, 2000           103.   60/234,217   Sep. 21, 2000           104.   60/234,220   Sep. 21, 2000           105.   60/234,968   Sep. 25, 2000           106.   60/234,979   Sep. 25, 2000           107.   60/234,974   Sep. 25, 2000           108.   60/235,118   Sep. 25, 2000           109.   60/234,949   Sep. 26, 2000           110.   60/235,577   Sep. 27, 2000           111.   60/235,934   Sep. 28, 2000           112.   60/236,380   Sep. 29, 2000           113.   60/236,732   Oct. 2, 2000           114.   60/237,035   Oct. 2, 2000           115.   60/237,379   Oct. 4, 2000           116.   60/237,505   Oct. 4, 2000           117.   60/237,686   Oct. 5, 2000           118.   60/238,473   Oct. 10, 2000           119.   60/238,472   Oct. 10, 2000           120.   60/238,456   Oct. 10, 2000           121.   60/238,421   Oct. 10, 2000           122.   60/239,091   Oct. 11, 2000           123.   60/239,245   Oct. 11, 2000           124.   60/240,862   Oct. 17, 2000           125.   60/240,863   Oct. 17, 2000           126.   60/241,368   Oct. 19, 2000           127.   60/241,367   Oct. 19, 2000           128.   60/241,751   Oct. 20, 2000           129.   60/241,750   Oct. 20, 2000           130.   60/242,065   Oct. 23, 2000           131.   60/242,072   Oct. 23, 2000           132.   60/242,686   Oct. 24, 2000           133.   60/242,705   Oct. 25, 2000           134.   60/242,706   Oct. 25, 2000           135.   60/243,289   Oct. 26, 2000           136.   60/243,288   Oct. 26, 2000           137.   60/243,398   Oct. 27, 2000           138.   60/243,478   Oct. 27, 2000           139.   60/243,723   Oct. 30, 2000           140.   60/243,735   Oct. 30, 2000           141.   60/244,691   Nov. 1, 2000           142.   60/244,747   Nov. 1, 2000           143.   60/244,923   Nov. 2, 2000           144.   60/244,920   Nov. 2, 2000           145.   60/245,164   Nov. 3, 2000           146.   60/245,165   Nov. 3, 2000           147.   60/248,198   Nov. 15, 2000           148.   60/248,197   Nov. 15, 2000           149.   60/248,555   Nov. 16, 2000           150.   60/249,256   Nov. 17, 2000           151.   60/249,257   Nov. 17, 2000           152.   60/249,454   Nov. 20, 2000           153.   60/249,453   Nov. 20, 2000           154.   60/252,080   Nov. 21, 2000           155.   60/252,464   Nov. 22, 2000           156.   60/252,465   Nov. 22, 2000           157.   60/252,598   Nov. 24, 2000           158.   60/245,676   Nov. 6, 2000           159.   60/245,576   Nov. 6, 2000           160.   60/252,590   Nov. 24, 2000           161.   60/253,140   Nov. 28, 2000           162.   60/253,722   Nov. 29, 2000           163.   60/253,748   Nov. 29, 2000           164.   60/250,356   Nov. 1, 2000           165.   60/250,464   Nov. 4, 2000           166.   60/251,387   Nov. 6, 2000           167.   60/251,504   Nov. 7, 2000           168.   60/251,508   Nov. 7, 2000           169.   60/251,853   Nov. 8, 2000           170.   60/251,854   Nov. 8, 2000           171.   60/254,174   Nov. 11, 2000           172.   60/254,196   Nov. 11, 2000           173.   60/254,891   Nov. 13, 2000           174.   60/256,503   Nov. 15, 2000           175.   60/255,415   Nov. 15, 2000           176.   60/255,891   Nov. 18, 2000           177.   60/255,892   Nov. 18, 2000           178.   60/256,306   Nov. 19, 2000           179.   60/256,929   Nov. 21, 2000           180.   60/257,978   Nov. 27, 2000           181.   60/258,880   Jan. 2, 2001           182.   60/262,389   Jan. 19, 2001           183.   60/262,359   Jan. 19, 2001           184.   60/264,026   Jan. 26, 2001           185.   60/264,027   Jan. 26, 2001           186.   60/264,282   Jan. 29, 2001           187.   60/264,257   Jan. 29, 2001           188.   60/266,468   Feb. 6, 2001           189.   60/266,469   Feb. 6, 2001           190.   60/266,863   Feb. 7, 2001           191.   60/267,425   Feb. 9, 2001           192.   60/267,430   Feb. 9, 2001           193.   60/267,426   Feb. 9, 2001           194.   60/267,707   Feb. 12, 2001           195.   60/267,706   Feb. 12, 2001           196.   60/268,366   Feb. 14, 2001           197.   60/268,921   Feb. 16, 2001           198.   60/269,890   Feb. 21, 2001           199.   60/269,891   Feb. 21, 2001           200.   60/269,892   Feb. 21, 2001           201.   60/269,893   Feb. 21, 2001           202.   60/270,122   Feb. 22, 2001           203.   60/270,913   Feb. 26, 2001           204.   60/270,912   Feb. 26, 2001           205.   60/271,724   Feb. 28, 2001           206.   60/271,725   Feb. 28, 2001           207.   60/272,467   Mar. 2, 2001           208.   60/272,783   Mar. 5, 2001           209.   60/273,554   Mar. 7, 2001           210.   60/273,553   Mar. 7, 2001           211.   60/273,552   Mar. 7, 2001           212.   60/227,793   Aug. 25, 2000           213.   60/228,031   Aug. 25, 2000           214.   60/228,028   Aug. 25, 2000           215.   60/228,027   Aug. 25, 2000           216.   60/228,026   Aug. 25, 2000           217.   60/228,038   Aug. 25, 2000           218.   60/228,036   Aug. 25, 2000           219.   60/227,790   Aug. 25, 2000           220.   60/228,039   Aug. 25, 2000           221.   60/228,030   Aug. 25, 2000           222.   60/228,032   Aug. 25, 2000           223.   60/228,149   Aug. 25, 2000           224.   60/228,040   Aug. 25, 2000           225.   60/227,777   Aug. 25, 2000           226.   60/228,037   Aug. 25, 2000           227.   60/227,791   Aug. 25, 2000           228.   60/228,041   Aug. 25, 2000                    
Number 27
 
     Application Ser. No. 10/282,058 listed above is a continuation-in-part of application Ser. No. 09/940,258 filed on Aug. 24, 2001, and application Ser. No. 10/162,726 filed on Jun. 6, 2002, the entire contents of both of these applications are hereby incorporated by reference. 
     Through application Ser. Nos. 09/940,258 and 10/162,726, the present application also claims priority under 35 USC § 119(e) and/or § 120 of the following applications, the entire contents of which are also hereby incorporated by reference: 
                                                     Application                       No.   Filing Date                                                        1.   09/391,631   Sep. 3, 1999   which claims                       priority to           2.   60/099,671   Sep. 4, 1998   and           3.   60/099,672   Sep. 4, 1998   and           4.   60/099,933   Sep. 11, 1998   and           5.   60/100,864   Sep. 17, 1998   and           6.   60/101,042   Sep. 18, 1998   and           7.   60/101,682   Sep. 24, 1998   and           8.   60/102,533   Sep. 30, 1998   and           9.   60/102,460   Sep. 30, 1998   and           10.   60/103,116   Oct. 5, 1998   and           11.   60/103,141   Oct. 5, 1998   and           12.   60/103,574   Oct. 9, 1998   and           13.   60/103,907   Oct. 13, 1998   and           14.   60/106,105   Oct. 29, 1998   and           15.   60/106,218   Oct. 30, 1998   and           16.   60/107,282   Nov. 6, 1998   and           17.   60/107,836   Nov. 10, 1998   and           18.   60/108,526   Nov. 16, 1998   and           19.   60/108,901   Nov. 17, 1998   and           20.   60/109,267   Nov. 20, 1998   and           21.   60/109,594   Nov. 23, 1998   and           22.   60/110,263   Nov. 30, 1998   and           23.   60/110,495   Dec. 1, 1998   and           24.   60/110,626   Dec. 2, 1998   and           25.   60/110,701   Dec. 3, 1998   and           26.   60/111,339   Dec. 7, 1998   and           27.   60/111,589   Dec. 9, 1998   and           28.   60/112,096   Dec. 14, 1998   and           29.   60/112,224   Dec. 15, 1998   and           30.   60/112,624   Dec. 16, 1998   and           31.   60/112,862   Dec. 17, 1998   and           32.   60/115,152   Jan. 7, 1999   and           33.   60/115,156   Jan. 7, 1999   and           34.   60/115,365   Jan. 8, 1999   and           35.   60/115,339   Jan. 11, 1999   and           36.   60/115,847   Jan. 13, 1999   and           37.   60/116,674   Jan. 21, 1999   and           38.   60/116,962   Jan. 22, 1999   and           39.   60/120,583   Feb. 18, 1999   and           40.   60/121,072   Feb. 22, 1999   and           41.   60/122,568   Mar. 2, 1999   and           42.   60/123,941   Mar. 12, 1999               43.   09/413,198   Oct. 5, 1999   which claims                       priority to           44.   60/103,116   Oct. 5, 1998   and           45.   60/103,141   Oct. 5, 1998   and           46.   60/103,215   Oct. 6, 1998   and           47.   60/103,554   Oct. 8, 1998   and           48.   60/103,574   Oct. 9, 1998   and           49.   60/103,907   Oct. 13, 1998   and           50.   60/104,268   Oct. 14, 1998   and           51.   60/104,680   Oct. 16, 1998   and           52.   60/104,828   Oct. 19, 1998   and           53.   60/105,008   Oct. 20, 1998   and           54.   60/105,142   Oct. 21, 1998   and           55.   60/105,533   Oct. 22, 1998   and           56.   60/105,571   Oct. 26, 1998   and           57.   60/105,815   Oct. 27, 1998   and           58.   60/106,105   Oct. 29, 1998   and           59.   60/106,218   Oct. 30, 1998               60.   09/412,922   Oct. 5, 1999   which claims                       priority to           61.   60/103,116   Oct. 5, 1998   and           62.   60/103,141   Oct. 5, 1998   and           63.   60/103,215   Oct. 6, 1998   and           64.   60/103,554   Oct. 8, 1998   and           65.   60/103,574   Oct. 9, 1998   and           66.   60/103,907   Oct. 13, 1998   and           67.   60/104,268   Oct. 14, 1998   and           68.   60/104,680   Oct. 16, 1998   and           69.   60/104,828   Oct. 19, 1998   and           70.   60/105,008   Oct. 20, 1998   and           71.   60/105,142   Oct. 21, 1998   and           72.   60/105,533   Oct. 22, 1998   and           73.   60/105,571   Oct. 26, 1998   and           74.   60/105,815   Oct. 27, 1998   and           75.   60/106,105   Oct. 29, 1998   and           76.   60/106,218   Oct. 30, 1998   and           77.   60/106,685   Nov. 2, 1998   and           78.   60/107,282   Nov. 6, 1998   and           79.   60/107,720   Nov. 9, 1998   and           80.   60/107,719   Nov. 9, 1998   and           81.   60/107,836   Nov. 10, 1998   and           82.   60/108,190   Nov. 12, 1998   and           83.   60/108,526   Nov. 16, 1998   and           84.   60/108,901   Nov. 17, 1998   and           85.   60/109,124   Nov. 19, 1998   and           86.   60/109,127   Nov. 19, 1998   and           87.   60/109,267   Nov. 20, 1998   and           88.   60/109,594   Nov. 23, 1998   and           89.   60/110,053   Nov. 25, 1998   and           90.   60/110,050   Nov. 25, 1998   and           91.   60/110,158   Nov. 27, 1998   and           92.   60/110,263   Nov. 30, 1998   and           93.   60/110,495   Dec. 1, 1998   and           94.   60/110,626   Dec. 2, 1998   and           95.   60/110,701   Dec. 3, 1998   and           96.   60/111,339   Dec. 7, 1998   and           97.   60/111,589   Dec. 9, 1998   and           98.   60/111,782   Dec. 10, 1998   and           99.   60/111,812   Dec. 11, 1998   and           100.   60/112,096   Dec. 14, 1998   and           101.   60/112,224   Dec. 15, 1998   and           102.   60/112,624   Dec. 16, 1998   and           103.   60/112,862   Dec. 17, 1998   and           104.   60/112,912   Dec. 18, 1998   and           105.   60/113,248   Dec. 21, 1998   and           106.   60/113,522   Dec. 22, 1998   and           107.   60/113,826   Dec. 23, 1998   and           108.   60/113,998   Dec. 28, 1998   and           109.   60/114,384   Dec. 29, 1998   and           110.   60/114,455   Dec. 30, 1998   and           111.   60/114,740   Jan. 4, 1999   and           112.   60/114,866   Jan. 6, 1999   and           113.   60/115,153   Jan. 7, 1999   and           114.   60/115,152   Jan. 7, 1999   and           115.   60/115,151   Jan. 7, 1999   and           116.   60/115,155   Jan. 7, 1999   and           117.   60/115,156   Jan. 7, 1999   and           118.   60/115,154   Jan. 7, 1999   and           119.   60/115,364   Jan. 8, 1999   and           120.   60/115,365   Jan. 8, 1999   and           121.   60/115,339   Jan. 11, 1999   and           122.   60/115,518   Jan. 12, 1999   and           123.   60/115,847   Jan. 13, 1999   and           124.   60/115,905   Jan. 14, 1999   and           125.   60/116,383   Jan. 15, 1999   and           126.   60/116,384   Jan. 15, 1999   and           127.   60/116,329   Jan. 19, 1999   and           128.   60/116,340   Jan. 19, 1999   and           129.   60/116,674   Jan. 21, 1999   and           130.   60/116,672   Jan. 21, 1999   and           131.   60/116,960   Jan. 22, 1999   and           132.   60/116,962   Jan. 22, 1999   and           133.   60/117,756   Jan. 28, 1999   and           134.   60/118,672   Feb. 3, 1999   and           135.   60/118,808   Feb. 4, 1999   and           136.   60/118,778   Feb. 5, 1999   and           137.   60/119,029   Feb. 8, 1999   and           138.   60/119,332   Feb. 9, 1999   and           139.   60/119,462   Feb. 10, 1999   and           140.   60/119,922   Feb. 12, 1999   and           141.   60/120,196   Feb. 16, 1999   and           142.   60/120,198   Feb. 16, 1999   and           143.   60/120,583   Feb. 18, 1999   and           144.   60/121,072   Feb. 22, 1999   and           145.   60/121,334   Feb. 23, 1999   and           146.   60/121,470   Feb. 24, 1999   and           147.   60/121,704   Feb. 25, 1999   and           148.   60/122,107   Feb. 26, 1999   and           149.   60/122,266   Mar. 1, 1999   and           150.   60/122,568   Mar. 2, 1999   and           151.   60/122,611   Mar. 3, 1999   and           152.   60/121,775   Mar. 4, 1999   and           153.   60/123,534   Mar. 5, 1999   and           154.   60/123,680   Mar. 9, 1999   and           155.   60/123,715   Mar. 10, 1999   and           156.   60/123,726   Mar. 10, 1999   and           157.   60/124,263   Mar. 11, 1999   and           158.   60/123,941   Mar. 12, 1999               159.   09/428,944   Oct. 28, 1999   which claims                       priority to           160.   60/106,685   Nov. 2, 1998   and           161.   60/107,282   Nov. 6, 1998   and           162.   60/107,720   Nov. 9, 1998   and           163.   60/107,719   Nov. 9, 1998   and           164.   60/107,836   Nov. 10, 1998   and           165.   60/108,190   Nov. 12, 1998   and           166.   60/108,526   Nov. 16, 1998   and           167.   60/108,901   Nov. 17, 1998   and           168.   60/109,124   Nov. 19, 1998   and           169.   60/109,127   Nov. 19, 1998   and           170.   60/109,267   Nov. 20, 1998   and           171.   60/109,594   Nov. 23, 1998   and           172.   60/110,053   Nov. 25, 1998   and           173.   60/110,050   Nov. 25, 1998   and           174.   60/110,158   Nov. 27, 1998   and           175.   60/110,263   Nov. 30, 1998               176.   09/451,320   Dec. 1, 1999   which claims                       priority to           177.   60/110,495   Dec. 1, 1998   and           178.   60/110,626   Dec. 2, 1998   and           179.   60/110,701   Dec. 3, 1998   and           180.   60/111,339   Dec. 7, 1998   and           181.   60/111,589   Dec. 9, 1998   and           182.   60/111,782   Dec. 10, 1998   and           183.   60/111,812   Dec. 11, 1998   and           184.   60/112,096   Dec. 14, 1998   and           185.   60/112,224   Dec. 15, 1998   and           186.   60/112,624   Dec. 16, 1998   and           187.   60/112,862   Dec. 17, 1998   and           188.   60/112,912   Dec. 18, 1998   and           189.   60/113,248   Dec. 21, 1998   and           190.   60/113,522   Dec. 22, 1998   and           191.   60/113,826   Dec. 23, 1998   and           192.   60/113,998   Dec. 28, 1998   and           193.   60/114,384   Dec. 29, 1998   and           194.   60/114,455   Dec. 30, 1998   and           195.   60/115,153   Jan. 7, 1999   and           196.   60/115,152   Jan. 7, 1999   and           197.   60/115,151   Jan. 7, 1999   and           198.   60/115,155   Jan. 7, 1999   and           199.   60/115,156   Jan. 7, 1999   and           200.   60/115,364   Jan. 8, 1999   and           201.   60/116,960   Jan. 22, 1999               202.   09/497,191   Feb. 3, 2000   which claims                       priority to           203.   60/118,672   Feb. 3, 1999   and           204.   60/118,808   Feb. 4, 1999   and           205.   60/118,778   Feb. 5, 1999   and           206.   60/119,029   Feb. 8, 1999   and           207.   60/119,332   Feb. 9, 1999   and           208.   60/119,462   Feb. 10, 1999   and           209.   60/119,922   Feb. 12, 1999   and           210.   60/120,196   Feb. 16, 1999   and           211.   60/120,198   Feb. 16, 1999   and           212.   60/120,583   Feb. 18, 1999   and           213.   60/121,072   Feb. 22, 1999   and           214.   60/121,334   Feb. 23, 1999   and           215.   60/121,470   Feb. 24, 1999   and           216.   60/121,704   Feb. 25, 1999   and           217.   60/122,107   Feb. 26, 1999               218.   09/517,537   Mar. 1, 2000   which claims                       priority to           219.   60/122,266   Mar. 1, 1999   and           220.   60/122,568   Mar. 2, 1999   and           221.   60/122,611   Mar. 3, 1999   and           222.   60/121,775   Mar. 4, 1999   and           223.   60/123,534   Mar. 5, 1999   and           224.   60/123,680   Mar. 9, 1999   and           225.   60/123,715   Mar. 10, 1999   and           226.   60/123,726   Mar. 10, 1999   and           227.   60/124,263   Mar. 11, 1999   and           228.   60/123,941   Mar. 12, 1999               229.   09/637,565   Aug. 11, 2000   which claims                       priority to           230.   60/148,342   Aug. 12, 1999               231.   09/637,564   Aug. 11, 2000   which claims                       priority to           232.   60/148,340   Aug. 12, 1999               233.   09/637,792   Aug. 11, 2000   which claims                       priority to           234.   60/148,337   Aug. 12, 1999               235.   09/790,663   Feb. 23, 2001   which claims                       priority to           236.   60/185,140   Feb. 25, 2000   and           237.   60/185,398   Feb. 28, 2000   and           238.   60/185,750   Feb. 29, 2000               239.   09/795,359   Mar. 1, 2001   which claims                       priority to           240.   60/186,277   Mar. 1, 2000   and           241.   60/186,670   Mar. 3, 2000   and           242.   60/187,379   Mar. 7, 2000   and           243.   60/187,985   Mar. 9, 2000   and           244.   60/188,174   Mar. 10, 2000   and           245.   60/188,687   Mar. 13, 2000   and           246.   60/189,460   Mar. 15, 2000   and           247.   60/189,958   Mar. 16, 2000   and           248.   60/189,965   Mar. 17, 2000   and           249.   60/190,090   Mar. 20, 2000   and           250.   60/191,549   Mar. 23, 2000   and           251.   60/191,826   Mar. 24, 2000   and           252.   60/192,420   Mar. 27, 2000   and           253.   60/192,855   Mar. 29, 2000   and           254.   60/193,243   Mar. 30, 2000   and           255.   60/193,469   Mar. 31, 2000               256.   09/804,470   Mar. 16, 2001   which claims                       priority to           257.   60/190,120   Mar. 16, 2000   and           258.   60/189,947   Mar. 16, 2000   and           259.   60/189,948   Mar. 16, 2000   and           260.   60/190,121   Mar. 16, 2000               261.   09/824,790   Apr. 4, 2001   which claims                       priority to           262.   60/194,884   Apr. 6, 2000   and           263.   60/194,385   Apr. 4, 2000   and           264.   60/194,682   Apr. 5, 2000   and           265.   60/194,698   Apr. 5, 2000   and           266.   60/195,258   Apr. 7, 2000   and           267.   60/196,168   Apr. 11, 2000   and           268.   60/196,483   Apr. 12, 2000   and           269.   60/197,397   Apr. 14, 2000   and           270.   60/198,268   Apr. 17, 2000   and           271.   60/198,400   Apr. 19, 2000   and           272.   60/198,629   Apr. 20, 2000   and           273.   60/198,765   Apr. 21, 2000   and           274.   60/199,123   Apr. 24, 2000               275.   09/832,192   Apr. 11, 2001   which claims                       priority to           276.   60/196,212   Apr. 12, 2000   and           277.   60/196,211   Apr. 11, 2000   and           278.   60/197,869   Apr. 14, 2000   and           279.   60/196,213   Apr. 13, 2000   and           280.   60/197,870   Apr. 17, 2000   and           281.   60/197,871   Apr. 17, 2000   and           282.   60/200,373   Apr. 28, 2000   and           283.   60/200,773   Apr. 28, 2000               284.   09/842,246   Apr. 26, 2001   which claims                       priority to           285.   60/200,034   Apr. 26, 2000               286.   09/845,208   May 1, 2001   which claims                       priority to           287.   60/200,763   May 1, 2000   and           288.   60/201,016   May 1, 2000   and           289.   60/200,762   May 1, 2000   and           290.   60/200,761   May 1, 2000   and           291.   60/203,671   May 11, 2000   and           292.   60/203,672   May 11, 2000   and           293.   60/203,669   May 11, 2000   and           294.   60/203,622   May 11, 2000               295.   09/845,318   May 1, 2001   which claims                       priority to           296.   60/201,018   May 1, 2000   and           297.   60/205,325   May 17, 2000               298.   09/845,209   May 1, 2001   which claims                       priority to           299.   60/201,017   May 1, 2000   and           300.   60/205,233   May 17, 2000               301.   09/870,646   Jun. 1, 2001   which claims                       priority to           302.   60/208,648   Jun. 1, 2000               303.   09/870,476   Jun. 1, 2001   which claims                       priority to           304.   60/208,324   Jun. 1, 2000   and           305.   60/208,919   Jun. 5, 2000   and           306.   60/208,917   Jun. 5, 2000   and           307.   60/210,008   Jun. 8, 2000               308.   09/870,664   Jun. 1, 2001   which claims                       priority to           309.   60/208,312   Jun. 1, 2000   and           310.   60/208,918   Jun. 5, 2000   and           311.   60/208,920   Jun. 5, 2000   and           312.   60/210,006   Jun. 8, 2000   and           313.   60/210,564   Jun. 9, 2000   and           314.   60/211,214   Jun. 13, 2000   and           315.   60/213,249   Jun. 22, 2000   and           316.   60/214,535   Jun. 27, 2000   and           317.   60/214,799   Jun. 28, 2000   and           318.   60/215,127   Jun. 30, 2000               319.   09/878,974   Jun. 13, 2001   which claims                       priority to           320.   60/211,210   Jun. 13, 2000   and           321.   60/211,539   Jun. 15, 2000   and           322.   60/212,414   Jun. 19, 2000   and           323.   60/212,677   Jun. 20, 2000   and           324.   60/212,713   Jun. 20, 2000   and           325.   60/213,195   Jun. 22, 2000   and           326.   60/213,221   Jun. 22, 2000   and           327.   60/214,760   Jun. 27, 2000               328.   09/902,613   Jul. 12, 2001   which claims                       priority to           329.   60/223,114   Aug. 1, 2000               330.   09/903,497   Jul. 13, 2001   which claims                       priority to           331.   60/217,846   Jul. 13, 2000   and           332.   60/223,099   Aug. 3, 2000               333.   09/918,556   Aug. 1, 2001   which claims                       priority to           334.   60/223,115   Aug. 1, 2000               335.   09/920,626   Aug. 3, 2001   which claims                       priority to           336.   60/223,100   Aug. 3, 2000   and           337.   60/226,325   Aug. 18, 2000   and           338.   60/237,361   Aug. 31, 2000               339.   09/922,661   Aug. 7, 2001   which claims                       priority to           340.   60/223,329   Aug. 7, 2000   and           341.   60/229,521   Aug. 31, 2000   and           342.   60/226,381   Aug. 18, 2000               343.   09/924,702   Aug. 9, 2001   which claims                       priority to           344.   60/224,390   Aug. 9, 2000               345.   09/930,244   Aug. 16, 2001   which claims                       priority to           346.   60/237,362   Aug. 31, 2000   and           347.   60/225,848   Aug. 16, 2000               348.   09/930,231   Aug. 16, 2001   which claims                       priority to           349.   60/225,849   Aug. 16, 2000               350.   09/930,223   Aug. 16, 2001   which claims                       priority to           351.   60/225,847   Aug. 16, 2000               352.   09/931,911   Aug. 20, 2001   which claims                       priority to           353.   60/229,520   Aug. 31, 2000               354.   10/082,096   Feb. 26, 2002   which is a 1.53(b)                       continuation of           355.   09/795,347   Mar. 1, 2001   which claims                       priority to           356.   60/186,390   Mar. 2, 2000   and           357.   60/186,283   Mar. 1, 2000   and           358.   60/186,296   Mar. 1, 2000   and           359.   60/187,178   Mar. 2, 2000   and           360.   60/186,386   Mar. 2, 2000   and           361.   60/186,387   Mar. 2, 2000   and           362.   60/186,748   Mar. 3, 2000   and           363.   60/186,669   Mar. 3, 2000   and           364.   60/187,378   Mar. 7, 2000   and           365.   60/187,896   Mar. 8, 2000   and           366.   60/187,888   Mar. 8, 2000   and           367.   60/188,187   Mar. 10, 2000   and           368.   60/188,186   Mar. 10, 2000   and           369.   60/188,185   Mar. 10, 2000   and           370.   60/188,175   Mar. 10, 2000   and           371.   60/189,080   Mar. 14, 2000   and           372.   60/189,052   Mar. 14, 2000   and           373.   60/189,461   Mar. 15, 2000   and           374.   60/189,462   Mar. 15, 2000   and           375.   60/189,953   Mar. 16, 2000   and           376.   60/189,959   Mar. 16, 2000   and           377.   60/190,069   Mar. 20, 2000   and           378.   60/190,070   Mar. 20, 2000   and           379.   60/190,545   Mar. 20, 2000   and           380.   60/190,089   Mar. 20, 2000   and           381.   60/191,084   Mar. 22, 2000   and           382.   60/191,097   Mar. 22, 2000   and           383.   60/191,543   Mar. 23, 2000   and           384.   60/191,545   Mar. 23, 2000   and           385.   60/191,823   Mar. 24, 2000   and           386.   60/191,825   Mar. 24, 2000   and           387.   60/192,421   Mar. 27, 2000   and           388.   60/192,308   Mar. 27, 2000   and           389.   60/192,940   Mar. 29, 2000   and           390.   60/192,941   Mar. 29, 2000   and           391.   60/193,244   Mar. 30, 2000   and           392.   60/193,245   Mar. 30, 2000   and           393.   60/193,453   Mar. 31, 2000   and           394.   60/193,455   Mar. 31, 2000               395.   10/084,376   Feb. 28, 2002   which is a 1.53(b)                       continuation of           396.   09/924,701   Aug. 9, 2001   which claims                       priority to           397.   60/224,391   Aug. 9, 2000               398.   10/086,239   Mar. 4, 2002   which is a 1.53(b)                       continuation of           399.   09/845,206   May 1, 2001   which claims                       priority to           400.   60/201,275   May 2, 2000   and           401.   60/200,879   May 1, 2000   and           402.   60/201,305   May 2, 2000   and           403.   60/201,740   May 4, 2000   and           404.   60/201,750   May 4, 2000   and           405.   60/202,112   May 5, 2000   and           406.   60/202,180   May 5, 2000   and           407.   60/202,914   May 9, 2000   and           408.   60/202,636   May 9, 2000   and           409.   60/202,919   May 9, 2000   and           410.   60/202,634   May 9, 2000   and           411.   60/202,968   May 10, 2000   and           412.   60/202,963   May 10, 2000   and           413.   60/203,457   May 11, 2000   and           414.   60/203,279   May 11, 2000   and           415.   60/203,916   May 12, 2000   and           416.   60/203,915   May 12, 2000   and           417.   60/204,388   May 15, 2000   and           418.   60/204,122   May 15, 2000   and           419.   60/204,568   May 16, 2000   and           420.   60/204,569   May 16, 2000   and           421.   60/204,830   May 17, 2000   and           422.   60/204,829   May 17, 2000   and           423.   60/205,201   May 18, 2000   and           424.   60/205,058   May 18, 2000   and           425.   60/205,242   May 19, 2000   and           426.   60/205,243   May 19, 2000   and           427.   60/205,572   May 22, 2000   and           428.   60/205,576   May 22, 2000   and           429.   60/206,316   May 23, 2000   and           430.   60/206,319   May 23, 2000   and           431.   60/206,553   May 24, 2000   and           432.   60/206,545   May 24, 2000   and           433.   60/207,367   May 26, 2000   and           434.   60/207,243   May 26, 2000   and           435.   60/207,239   May 26, 2000   and           436.   60/207,354   May 26, 2000   and           437.   60/207,452   May 30, 2000   and           438.   60/207,329   May 30, 2000               439.   10/091,527   Mar. 7, 2002   which is a 1.53(b)                       continuation of           440.   09/842,088   Apr. 26, 2001   which claims                       priority to           441.   60/200,031   Apr. 26, 2000               442.   10/095,465   Mar. 13, 2002   which is a 1.53(b)                       continuation of           443.   09/824,882   Apr. 4, 2001   which claims                       priority to           444.   60/194,404   Apr. 4, 2000   and           445.   60/194,398   Apr. 4, 2000   and           446.   60/194,683   Apr. 5, 2000   and           447.   60/194,697   Apr. 5, 2000   and           448.   60/194,874   Apr. 6, 2000   and           449.   60/194,872   Apr. 6, 2000   and           450.   60/194,885   Apr. 6, 2000   and           451.   60/195,045   Apr. 6, 2000   and           452.   60/195,283   Apr. 7, 2000   and           453.   60/195,257   Apr. 7, 2000   and           454.   60/196,169   Apr. 11, 2000   and           455.   60/196,089   Apr. 11, 2000   and           456.   60/196,487   Apr. 12, 2000   and           457.   60/196,289   Apr. 12, 2000   and           458.   60/196,485   Apr. 12, 2000   and           459.   60/196,486   Apr. 12, 2000   and           460.   60/197,687   Apr. 17, 2000   and           461.   60/197,678   Apr. 17, 2000   and           462.   60/198,133   Apr. 17, 2000   and           463.   60/197,671   Apr. 17, 2000   and           464.   60/198,386   Apr. 19, 2000   and           465.   60/198,373   Apr. 19, 2000   and           466.   60/198,619   Apr. 20, 2000   and           467.   60/198,623   Apr. 20, 2000   and           468.   60/198,767   Apr. 21, 2000   and           469.   60/198,763   Apr. 21, 2000   and           470.   60/199,124   Apr. 24, 2000   and           471.   60/199,122   Apr. 24, 2000   and           472.   60/199,828   Apr. 26, 2000   and           473.   60/199,818   Apr. 26, 2000   and           474.   60/200,103   Apr. 27, 2000   and           475.   60/200,102   Apr. 27, 2000               476.   10/097,600   Mar. 15, 2002   which is a 1.53(b)                       continuation of           477.   09/832,934   Apr. 12, 2001   which is a 1.53(b)                       continuation of           478.   09/637,820   Aug. 11, 2000   which claims                       priority to           479.   60/148,347   Aug. 12, 1999               480.   10/097,295   Mar. 15, 2002   which is a 1.53(b)                       continuation of           481.   09/881,096   Jun. 15, 2001   which claims                       priority to           482.   60/211,538   Jun. 15, 2000   and           483.   60/212,623   Jun. 19, 2000   and           484.   60/212,727   Jun. 20, 2000   and           485.   60/213,270   Jun. 22, 2000   and           486.   60/214,524   Jun. 27, 2000               487.   10/198,315   Mar. 18, 2002   which is a 1.53(b)                       continuation of           488.   09/870,699   Jun. 1, 2001   which claims                       priority to           489.   60/208,421   Jun. 1, 2000               490.   10/098,506   Mar. 18, 2002   which is a 1.53(b)                       continuation of           491.   09/870,713   Jun. 1, 2001   which claims                       priority to           492.   60/209,338   Jun. 2, 2000               493.   10/103,845   Mar. 25, 2002   which is a 1.53(b)                       continuation of           494.   09/898,063   Jul. 5, 2001   which claims                       priority to           495.   60/216,362   Jul. 5, 2000   and           496.   60/217,384   Jul. 11, 2000   and           497.   60/219,033   Jul. 18, 2000   and           498.   60/220,811   Jul. 25, 2000   and           499.   60/220,652   Jul. 25, 2000               500.   10/106,718   Mar. 27, 2002   which is a 1.53(b)                       continuation of           501.   09/898,064   Jul. 5, 2001   which claims                       priority to           502.   60/216,361   Jul. 5, 2000   and           503.   60/217,476   Jul. 11, 2000   and           504.   60/219,004   Jul. 18, 2000   and           505.   60/220,647   Jul. 25, 2000   and           506.   60/220,484   Jul. 25, 2000               507.   10/109,638   Apr. 1, 2002   which is a 1.53(b)                       continuation of           508.   09/902,614   Jul. 12, 2001   which claims                       priority to           509.   60/218,548   Jul. 12, 2000   and           510.   60/223,116   Aug. 3, 2000               511.   10/109,638   Apr. 10, 2002   which is a 1.53(b)                       continuation of           512.   09/930,214   Aug. 16, 2001   which claims                       priority to           513.   60/229,520   Aug. 31, 2000   and           514.   60/225,850   Aug. 16, 2000               515.   10/123,117   Apr. 17, 2002   which is a 1.53(b)                       continuation of           516.   09/921,135   Aug. 3, 2001   which claims                       priority to           517.   60/223,101   Aug. 3, 2000   and           518.   60/229,519   Aug. 31, 2000   and           519.   60/226,323   Aug. 18, 2000               520.   10/123,222   Apr. 17, 2002   which is a 1.53(b)                       continuation of           521.   09/902,093   Jul. 11, 2001   which claims                       priority to           522.   60/217,385   Jul. 11, 2000   and           523.   60/219,021   Jul. 18, 2000   and           524.   60/220,814   Jul. 25, 2000   and           525.   60/224,516   Aug. 14, 2000   and           526.   60/225,302   Aug. 15, 2000   and           527.   60/226,725   Aug. 21, 2000   and           528.   60/227,026   Aug. 23, 2000   and           529.   60/228,897   Aug. 30, 2000               530.   10/123,159   Apr. 17, 2002   which is a 1.53(b)                       continuation of           531.   09/903,988   Jul. 13, 2001   which claims                       priority to           532.   60/218,566   Jul. 14, 2000   and           533.   60/223,098   Aug. 3, 2000               534.   10/123,111   Apr. 17, 2002   which is a 1.53(b)                       continuation of           535.   09/928,372   Aug. 14, 2001   which claims                       priority to           536.   60/224,517   Aug. 14, 2000   and           537.   60/225,303   Aug. 15, 2000   and           538.   60/226,452   Aug. 21, 2000   and           539.   60/227,024   Aug. 23, 2000   and           540.   60/228,898   Aug. 30, 2000               541.   10/124,666   Apr. 18, 2002   which is a 1.53(b)                       continuation of           542.   09/931,043   Aug. 17, 2001   which claims                       priority to           543.   60/226,324   Aug. 18, 2000               544.   10/133,891   Apr. 29, 2002   which is a 1.53(b)                       continuation of           545.   09/774,340   Jan. 31, 2001               546.   10/133,893   Apr. 29, 2002   which is a 1.53(b)                       continuation of           547.   09/691,039   Oct. 19, 2000               548.   10/134/014   Apr. 29, 2002   which is a 1.53(b)                       continuation of           549.   09/741,043   Dec. 21, 2000               550.   10/133,373   Apr. 29, 2002   which is a 1.53(b)                       continuation of           551.   09/691,045   Oct. 19, 2000               552.   10/133,905   Apr. 29, 2002   which is a 1.53(b)                       continuation of           553.   09/691,019   Oct. 19, 2000               554.   10/133,376   Apr. 29, 2002   which is a 1.53(b)                       continuation of           555.   09/870,675   Jun. 1, 2001   which claims                       priority to           556.   60/208,649   Jun. 2, 2000               557.   10/138,320   May 6, 2002   which is a 1.53(b)                       continuation of           558.   09/478,081   Jan. 4, 2000   which claims                       priority to           559.   60/114,740   Jan. 4, 1999   and           560.   60/114,866   Jan. 6, 1999   and           561.   60/115,154   Jan. 7, 1999   and           562.   60/115,365   Jan. 8, 1999   and           563.   60/115,339   Jan. 11, 1999   and           564.   60/115,518   Jan. 12, 1999   and           565.   60/115,847   Jan. 13, 1999   and           566.   60/115,905   Jan. 14, 1999   and           567.   60/116,383   Jan. 15, 1999   and           568.   60/116,384   Jan. 15, 1999   and           569.   60/116,329   Jan. 19, 1999   and           570.   60/116,340   Jan. 19, 1999   and           571.   60/116,674   Jan. 21, 1999   and           572.   60/116,672   Jan. 21, 1999   and           573.   60/116,962   Jan. 22, 1999   and           574.   60/117,756   Jan. 28, 1999               575.   60/228,025   Aug. 25, 2000               576.   60/227,781   Aug. 25, 2000               577.   60/227,783   Aug. 25, 2000               578.   60/227,731   Aug. 25, 2000               579.   60/227,732   Aug. 25, 2000               580.   60/227,729   Aug. 25, 2000               581.   60/228,167   Aug. 25, 2000               582.   60/227,734   Aug. 25, 2000               583.   60/227,792   Aug. 25, 2000               584.   60/227,733   Aug. 25, 2000               585.   60/227,730   Aug. 25, 2000               586.   60/227,770   Aug. 25, 2000               587.   60/227,728   Aug. 25, 2000               588.   60/227,773   Aug. 25, 2000               589.   60/228,033   Aug. 25, 2000               590.   60/228,024   Aug. 25, 2000               591.   60/227,769   Aug. 25, 2000               592.   60/227,780   Aug. 25, 2000               593.   60/227,725   Aug. 25, 2000               594.   60/227,774   Aug. 25, 2000               595.   60/228,163   Aug. 25, 2000               596.   60/228,046   Aug. 25, 2000               597.   60/228,098   Aug. 25, 2000               598.   60/228,047   Aug. 25, 2000               599.   60/228,052   Aug. 25, 2000               600.   60/228,049   Aug. 25, 2000               601.   60/228,132   Aug. 25, 2000               602.   60/228,152   Aug. 25, 2000               603.   60/228,135   Aug. 25, 2000               604.   60/228,322   Aug. 25, 2000               605.   60/228,156   Aug. 25, 2000               606.   60/228,323   Aug. 25, 2000               607.   60/228,133   Aug. 25, 2000               608.   60/228,320   Aug. 25, 2000               609.   60/228,159   Aug. 25, 2000               610.   60/228,151   Aug. 25, 2000               611.   60/228,202   Aug. 25, 2000               612.   60/228,208   Aug. 25, 2000               613.   60/228,153   Aug. 25, 2000               614.   60/228,179   Aug. 25, 2000               615.   60/228,180   Aug. 25, 2000               616.   60/228,209   Aug. 25, 2000               617.   60/228,178   Aug. 25, 2000               618.   60/228,177   Aug. 25, 2000               619.   60/227,976   Aug. 25, 2000               620.   60/228,207   Aug. 25, 2000               621.   60/228,048   Aug. 25, 2000               622.   60/228,096   Aug. 25, 2000               623.   60/227,932   Aug. 25, 2000               624.   60/227,936   Aug. 25, 2000               625.   60/228,044   Aug. 25, 2000               626.   60/228,216   Aug. 25, 2000               627.   60/228,065   Aug. 25, 2000               628.   60/227,975   Aug. 25, 2000               629.   60/228,181   Aug. 25, 2000               630.   60/228,063   Aug. 25, 2000               631.   60/228,064   Aug. 25, 2000               632.   60/228,055   Aug. 25, 2000               633.   60/228,074   Aug. 25, 2000               634.   60/227,939   Aug. 25, 2000               635.   60/227,955   Aug. 25, 2000               636.   60/228,053   Aug. 25, 2000               637.   60/227,978   Aug. 25, 2000               638.   60/227,982   Aug. 25, 2000               639.   60/228,189   Aug. 25, 2000               640.   60/228,054   Aug. 25, 2000               641.   60/228,164   Aug. 25, 2000               642.   60/228,161   Aug. 25, 2000               643.   60/228,165   Aug. 25, 2000               644.   60/228,221   Aug. 25, 2000               645.   60/228,240   Aug. 25, 2000               646.   60/227,979   Aug. 25, 2000               647.   60/227,954   Aug. 25, 2000               648.   60/228,217   Aug. 25, 2000               649.   60/227,929   Aug. 25, 2000               650.   60/228,043   Aug. 25, 2000               651.   60/227,931   Aug. 25, 2000               652.   60/228,187   Aug. 25, 2000               653.   60/228,061   Aug. 25, 2000               654.   60/228,150   Aug. 25, 2000               655.                       656.   60/227,793   Aug. 25, 2000               657.   60/228,031   Aug. 25, 2000               658.   60/228,028   Aug. 25, 2000               659.   60/228,027   Aug. 25, 2000               660.   60/228,026   Aug. 25, 2000               661.   60/228,038   Aug. 25, 2000               662.   60/228,036   Aug. 25, 2000               663.   60/227,790   Aug. 25, 2000               664.   60/228,039   Aug. 25, 2000               665.   60/228,030   Aug. 25, 2000               666.   60/228,032   Aug. 25, 2000               667.   60/228,149   Aug. 25, 2000               668.   60/228,040   Aug. 25, 2000               669.   60/227,777   Aug. 25, 2000               670.   60/228,037   Aug. 25, 2000               671.   60/227,791   Aug. 25, 2000               672.   60/228,041   Aug. 25, 2000               673.   60/231,840   Sep. 6, 2000               674.   60/231,837   Sep. 6, 2000               675.   60/231,833   Sep. 6, 2000               676.   60/231,835   Sep. 6, 2000               677.   60/231,834   Sep. 6, 2000               678.   60/230,430   Sep. 6, 2000               679.   60/230,434   Sep. 6, 2000               680.   60/232,044   Sep. 13, 2000               681.   60/232,043   Sep. 13, 2000               682.   60/232,858   Sep. 15, 2000               683.   60/232,865   Sep. 15, 2000               684.   60/233,621   Sep. 18, 2000               685.   60/233,634   Sep. 18, 2000               686.   60/234,179   Sep. 20, 2000               687.   60/234,178   Sep. 20, 2000               688.   60/234,233   Sep. 21, 2000               689.   60/234,217   Sep. 21, 2000               690.   60/234,220   Sep. 21, 2000               691.   60/234,968   Sep. 25, 2000               692.   60/234,979   Sep. 25, 2000               693.   60/234,974   Sep. 25, 2000               694.   60/235,118   Sep. 25, 2000               695.   60/234,949   Sep. 26, 2000               696.   60/235,577   Sep. 27, 2000               697.   60/235,934   Sep. 28, 2000               698.   60/236,380   Sep. 29, 2000               699.   60/236,732   Oct. 2, 2000               700.   60/237,035   Oct. 2, 2000               701.   60/237,379   Oct. 4, 2000               702.   60/237,505   Oct. 4, 2000               703.   60/237,686   Oct. 5, 2000               704.   60/238,473   Oct. 10, 2000               705.   60/238,472   Oct. 10, 2000               706.   60/238,456   Oct. 10, 2000               707.   60/238,421   Oct. 10, 2000               708.   60/239,091   Oct. 11, 2000               709.   60/239,245   Oct. 11, 2000               710.   60/240,862   Oct. 17, 2000               711.   60/240,863   Oct. 17, 2000               712.   60/241,368   Oct. 19, 2000               713.   60/241,367   Oct. 19, 2000               714.   09/691,020   Oct. 19, 2000               715.   09/691,044   Oct. 19, 2000               716.   09/691,028   Oct. 19, 2000               717.   09/691,056   Oct. 19, 2000               718.   09/691,038   Oct. 19, 2000               719.   09/691,031   Oct. 19, 2000               720.   09/691,018   Oct. 19, 2000               721.   60/241,751   Oct. 20, 2000               722.   60/241,750   Oct. 20, 2000               723.   60/242,065   Oct. 23, 2000               724.   60/242,072   Oct. 23, 2000               725.   60/242,686   Oct. 24, 2000               726.   60/242,705   Oct. 25, 2000               727.   60/242,706   Oct. 25, 2000               728.   60/243,289   Oct. 26, 2000               729.   60/243,288   Oct. 26, 2000               730.   60/243,398   Oct. 27, 2000               731.   60/243,478   Oct. 27, 2000               732.   60/243,723   Oct. 30, 2000               733.   60/243,735   Oct. 30, 2000               734.   60/244,691   Nov. 1, 2000               735.   60/244,747   Nov. 1, 2000               736.   60/244,923   Nov. 2, 2000               737.   60/244,920   Nov. 2, 2000               738.   60/245,164   Nov. 3, 2000               739.   60/245,165   Nov. 3, 2000               740.   60/245,676   Nov. 6, 2000               741.   60/245,576   Nov. 6, 2000               742.   60/246,732   Nov. 9, 2000               743.   60/247,010   Nov. 13, 2000               744.   60/247,051   Nov. 13, 2000               745.   60/247,050   Nov. 13, 2000               746.   60/247,049   Nov. 13, 2000               747.   60/248,198   Nov. 15, 2000               748.   60/248,197   Nov. 15, 2000               749.   60/248,555   Nov. 16, 2000               750.   60/249,256   Nov. 17, 2000               751.   60/249,257   Nov. 17, 2000               752.   60/249,454   Nov. 20, 2000               753.   60/249,453   Nov. 20, 2000               754.   60/252,080   Nov. 21, 2000               755.   60/252,464   Nov. 22, 2000               756.   60/252,465   Nov. 22, 2000               757.   60/252,598   Nov. 24, 2000               758.   60/252,590   Nov. 24, 2000               759.   60/253,140   Nov. 28, 2000               760.   60/253,722   Nov. 29, 2000               761.   60/253,748   Nov. 29, 2000               762.   60/250,356   Dec. 1, 2000               763.   60/250,464   Dec. 4, 2000               764.   60/251,387   Dec. 6, 2000               765.   60/251,504   Dec. 7, 2000               766.   60/251,508   Dec. 7, 2000               767.   60/251,853   Dec. 8, 2000               768.   60/251,854   Dec. 8, 2000               769.   60/254,174   Dec. 11, 2000               770.   60/254,196   Dec. 11, 2000               771.   60/254,891   Dec. 13, 2000               772.   60/256,503   Dec. 15, 2000               773.   60/255,415   Dec. 15, 2000               774.   60/255,891   Dec. 18, 2000               775.   60/255,892   Dec. 18, 2000               776.   60/256,306   Dec. 19, 2000               777.   60/256,929   Dec. 21, 2000               778.   60/257,978   Dec. 27, 2000               779.   09/750,044   Dec. 29, 2000               780.   60/258,880   Jan. 2, 2001               781.   09/750,910   Jan. 2, 2001               782.   09/752,823   Jan. 3, 2001               783.   09/754,184   Jan. 5, 2001               784.   09/754,185   Jan. 5, 2001               785.   60/262,389   Jan. 19, 2001               786.   60/262,359   Jan. 19, 2001               787.   60/264,026   Jan. 26, 2001               788.   60/264,027   Jan. 26, 2001               789.   60/264,282   Jan. 29, 2001               790.   60/264,257   Jan. 29, 2001               791.   09/774,106   Jan. 31, 2001               792.   09/774,089   Jan. 31, 2001               793.   09/774,090   Jan. 31, 2001               794.   09/775,870   Feb. 1, 2001               795.   09/776,014   Feb. 1, 2001               796.   60/266,468   Feb. 6, 2001               797.   60/266,469   Feb. 6, 2001               798.   60/266,863   Feb. 7, 2001               799.   09/778,734   Feb. 8, 2001               800.   60/267,425   Feb. 9, 2001               801.   60/267,430   Feb. 9, 2001               802.   60/267,426   Feb. 9, 2001               803.   60/267,707   Feb. 12, 2001               804.   60/267,706   Feb. 12, 2001               805.   60/268,366   Feb. 14, 2001               806.   60/268,921   Feb. 16, 2001               807.   60/269,890   Feb. 21, 2001               808.   60/269,891   Feb. 21, 2001               809.   60/269,892   Feb. 21, 2001               810.   60/269,893   Feb. 21, 2001               811.   60/270,122   Feb. 22, 2001               812.   60/270,913   Feb. 26, 2001               813.   60/270,912   Feb. 26, 2001               814.   60/271,724   Feb. 28, 2001               815.   60/271,725   Feb. 28, 2001               816.   60/272,467   Mar. 2, 2001               817.   60/272,783   Mar. 5, 2001               818.   60/273,554   Mar. 7, 2001               819.   60/273,553   Mar. 7, 2001               820.   60/273,552   Mar. 7, 2001               821.   09/823,082   Apr. 2, 2001               822.   09/940,230   Aug. 24, 2001                    
Number 28
 
     Application Ser. No. 10/376,785 listed above claims priority under 35 USC § 119(e) of the following application, the entire contents of which are also hereby incorporated by reference: 
                                             Application No.   Filed                          60/361,089   Mar. 1, 2002                        
Number 29
 
     Application Ser. No. 10/376,797 listed above claims priority under 35 USC § 119(e) of the following application, the entire contents of which are also hereby incorporated by reference: 
                                             Application No.   Filed                          60/361,110   Mar. 1, 2002                        
Number 30
 
     Application Ser. No. 09/513,996 listed above is a continuation-in-part of the following provisional applications, the entire contents of which are hereby incorporated by reference, and the present application also claims priority of these provisional applications under 35 USC § 119(e): 
                                             Client No.   Filing Date   Application No.                      80090.001   Feb. 25, 1999   60/121,825           80105.001   Mar. 5, 1999   60/123,180           80107.001   Mar. 9, 1999   60/123,548           80112.001   Mar. 23, 1999   60/125,788           80113.001   Mar. 25, 1999   60/126,264           80114.001   Mar. 29, 1999   60/126,785           80115.001   Apr. 1, 1999   60/127,462           91000.001   Apr. 6, 1999   60/128,234           91001.001   Apr. 8, 1999   60/128,714           80118.001   Apr. 16, 1999   60/129,845           80120.001   Apr. 19, 1999   60/130,077           80121.001   Apr. 21, 1999   60/130,449           80122.001   Apr. 23, 1999   60/130,891           80115.002   Apr. 23, 1999   60/130,510           80123.001   Apr. 28, 1999   60/131,449           80124.001   Apr. 30, 1999   60/132,407           80125.001   Apr. 30, 1999   60/132,048           80126.001   May 4, 1999   60/132,484           80127.001   May 5, 1999   60/132,485           91002.001   May 6, 1999   60/132,487           80129.001   May 6, 1999   60/132,486           80130.001   May 7, 1999   60/132,863           80131.001   May 11, 1999   60/134,256           00025.001   May 14, 1999   60/134,221           80117.001   May 14, 1999   60/134,218           91006.001   May 14, 1999   60/134,370           80116.001   May 14, 1999   60/134,219           91007.001   May 18, 1999   60/134,768           91008.001   May 19, 1999   60/134,941           91009.001   May 20, 1999   60/135,124           91010.001   May 21, 1999   60/135,353           91011.001   May 24, 1999   60/135,629           91012.001   May 25, 1999   60/136,021           91013.001   May 27, 1999   60/136,392           91014.001   May 28, 1999   60/136,782           91015.001   Jun. 1, 1999   60/137,222           91016.001   Jun. 3, 1999   60/137,528           91017.001   Jun. 4, 1999   60/137,502           91018.001   Jun. 7, 1999   60/137,724           91019.001   Jun. 8, 1999   60/138,094           00033.001   Jun. 10, 1999   60/138,540           00033.002   Jun. 10, 1999   60/138,847           00034.001   Jun. 14, 1999   60/139,119           80132.012   Jun. 16, 1999   60/139,452           80132.011   Jun. 16, 1999   60/139,453           00037.001   Jun. 17, 1999   60/139,492           80132.004   Jun. 18, 1999   60/139,461           00039.001   Jun. 18, 1999   60/139,750           80132.009   Jun. 18, 1999   60/139,463           80132.006   Jun. 18, 1999   60/139,457           80132.003   Jun. 18, 1999   60/139,459           80132.005   Jun. 18, 1999   60/139,462           80132.010   Jun. 18, 1999   60/139,455           80132.001   Jun. 18, 1999   60/139,458           80132.002   Jun. 18, 1999   60/139,454           80132.008   Jun. 18, 1999   60/139,456           80132.007   Jun. 18, 1999   60/139,460           00038.001   Jun. 18, 1999   60/139,763           00042.001   Jun. 21, 1999   60/139,817           00043.001   Jun. 22, 1999   60/139,899           00044.001   Jun. 23, 1999   60/140,354           00042.002   Jun. 23, 1999   60/140,353           00045.001   Jun. 24, 1999   60/140,695           00046.001   Jun. 28, 1999   60/140,823           00048.001   Jun. 29, 1999   60/140,991           00049.001   Jun. 30, 1999   60/141,287           00051.001   Jul. 1, 1999   60/142,154           00050.001   Jul. 1, 1999   60/141,842           00052.001   Jul. 2, 1999   60/142,055           00053.001   Jul. 6, 1999   60/142,390           00054.001   Jul. 8, 1999   60/142,803           00058.001   Jul. 9, 1999   60/142,920           00059.001   Jul. 12, 1999   60/142,977           00060.001   Jul. 13, 1999   60/143,542           00061.001   Jul. 14, 1999   60/143,624           00062.001   Jul. 15, 1999   60/144,005           80134.004   Jul. 16, 1999   60/144,085           80134.003   Jul. 16, 1999   60/144,086           80134.010   Jul. 19, 1999   60/144,333           80134.013   Jul. 19, 1999   60/144,335           00064.001   Jul. 19, 1999   60/144,325           80134.014   Jul. 19, 1999   60/144,334           80134.006   Jul. 19, 1999   60/144,332           80134.008   Jul. 19, 1999   60/144,331           80135.002   Jul. 20, 1999   60/144,884           80134.012   Jul. 20, 1999   60/144,352           00065.001   Jul. 20, 1999   60/144,632           00066.001   Jul. 21, 1999   60/144,814           80134.002   Jul. 21, 1999   60/145,086           80134.001   Jul. 21, 1999   60/145,088           00067.001   Jul. 22, 1999   60/145,192           80134.007   Jul. 22, 1999   60/145,085           80134.005   Jul. 22, 1999   60/145,089           80134.009   Jul. 22, 1999   60/145,087           80134.011   Jul. 23, 1999   60/145,145           80135.001   Jul. 23, 1999   60/145,224           00069.001   Jul. 23, 1999   60/145,218           00070.001   Jul. 26, 1999   60/145,276           80136.002   Jul. 27, 1999   60/145,919           00071.001   Jul. 27, 1999   60/145,913           80136.001   Jul. 27, 1999   60/145,918           00072.001   Jul. 28, 1999   60/145,951           80137.001   Aug. 2, 1999   60/146,388           80137.002   Aug. 2, 1999   60/146,389           00073.001   Aug. 2, 1999   60/146,386           00074.001   Aug. 3, 1999   60/147,038           80138.002   Aug. 4, 1999   60/147,302           00076.001   Aug. 4, 1999   60/147,204           00077.001   Aug. 5, 1999   60/147,260           80136.003   Aug. 5, 1999   60/147,192           80138.001   Aug. 6, 1999   60/147,303           00079.001   Aug. 6, 1999   60/147,416           00080.001   Aug. 9, 1999   60/147,493           80139.002   Aug. 9, 1999   60/147,935           80139.001   Aug. 10, 1999   60/148,171           00081.001   Aug. 11, 1999   60/148,319           00082.001   Aug. 12, 1999   60/148,341           00083.001   Aug. 13, 1999   60/148,565           80142.002   Aug. 13, 1999   60/148,684           80142.001   Aug. 16, 1999   60/149,368           00084.001   Aug. 17, 1999   60/149,175           00085.001   Aug. 18, 1999   60/149,426           00086.001   Aug. 20, 1999   60/149,722           80143.002   Aug. 20, 1999   60/149,929           00087.001   Aug. 20, 1999   60/149,723           00088.001   Aug. 23, 1999   60/149,902           80143.001   Aug. 23, 1999   60/149,930           00089.001   Aug. 25, 1999   60/150,566           00090.001   Aug. 26, 1999   60/150,884           80144.001   Aug. 27, 1999   60/151,065           80144.002   Aug. 27, 1999   60/151,066           00091.001   Aug. 27, 1999   60/151,080           00092.001   Aug. 30, 1999   60/151,303           00093.001   Aug. 31, 1999   60/151,438           00094.001   Sep. 1, 1999   60/151,930           00095.001   Sep. 7, 1999   60/152,363           00096.001   Sep. 10, 1999   60/153,070           00098.001   Sep. 13, 1999   60/153,758           00099.001   Sep. 15, 1999   60/154,018           00101.001   Sep. 16, 1999   60/154,039           00102.001   Sep. 20, 1999   60/154,779           00103.001   Sep. 22, 1999   60/155,139           00104.001   Sep. 23, 1999   60/155,486           00105.001   Sep. 24, 1999   60/155,659           00106.001   Sep. 28, 1999   60/156,458           00107.001   Sep. 29, 1999   60/156,596           00108.001   Oct. 4, 1999   60/157,117           00109.001   Oct. 5, 1999   60/157,753           00110.001   Oct. 6, 1999   60/157,865           00111.001   Oct. 7, 1999   60/158,029           00112.001   Oct. 8, 1999   60/158,232           00113.001   Oct. 12, 1999   60/158,369           80148.002   Oct. 13, 1999   60/159,294           80145.002   Oct. 13, 1999   60/159,295           80146.002   Oct. 13, 1999   60/159,293           80147.001   Oct. 14, 1999   60/159,638           80147.002   Oct. 14, 1999   60/159,637           80148.001   Oct. 14, 1999   60/159,329           80146.001   Oct. 14, 1999   60/159,331           80145.001   Oct. 14, 1999   60/159,330           00116.001   Oct. 18, 1999   60/159,584           00118.001   Oct. 21, 1999   60/160,815           80150.002   Oct. 21, 1999   60/160,767           80150.001   Oct. 21, 1999   60/160,768           00119.001   Oct. 21, 1999   60/160,741           80149.002   Oct. 21, 1999   60/160,770           80149.001   Oct. 21, 1999   60/160,814           80151.002   Oct. 22, 1999   60/160,981           00120.001   Oct. 22, 1999   60/160,980           80151.001   Oct. 22, 1999   60/160,989           00121.001   Oct. 25, 1999   60/161,405           80152.002   Oct. 25, 1999   60/161,404           80152.001   Oct. 25, 1999   60/161,406           00122.001   Oct. 26, 1999   60/161,361           80153.001   Oct. 26, 1999   60/161,360           80153.002   Oct. 26, 1999   60/161,359           00123.001   Oct. 28, 1999   60/161,920           80154.001   Oct. 28, 1999   60/161,992           80154.002   Oct. 28, 1999   60/161,993           00124.001   Oct. 29, 1999   60/162,143           80155.001   Oct. 29, 1999   60/162,142           80155.002   Oct. 29, 1999   60/162,228           80156.002   Nov. 1, 1999   60/162,895           80156.001   Nov. 1, 1999   60/162,891           00125.001   Nov. 1, 1999   60/162,894           00126.001   Nov. 2, 1999   60/163,093           80157.001   Nov. 2, 1999   60/163,092           80157.002   Nov. 2, 1999   60/163,091           00127.001   Nov. 3, 1999   60/163,249           80158.001   Nov. 3, 1999   60/163,248           80158.002   Nov. 3, 1999   60/163,281           80159.002   Nov. 4, 1999   60/163,380           80159.001   Nov. 4, 1999   60/163,381           00128.001   Nov. 4, 1999   60/163,379           80160.001   Nov. 8, 1999   60/164,151           80160.002   Nov. 8, 1999   60/164,150           00129.001   Nov. 8, 1999   60/164,146           80161.002   Nov. 9, 1999   60/164,260           80162.002   Nov. 9, 1999   60/164,259           80164.002   Nov. 10, 1999   60/164,548           80162.001   Nov. 10, 1999   60/164,317           80163.001   Nov. 10, 1999   60/164,321           80163.002   Nov. 10, 1999   60/164,318           00131.001   Nov. 10, 1999   60/164,544           80164.001   Nov. 10, 1999   60/164,545           80161.001   Nov. 10, 1999   60/164,319           00133.001   Nov. 12, 1999   60/164,870           80166.001   Nov. 12, 1999   60/164,959           80166.002   Nov. 12, 1999   60/164,962           80165.002   Nov. 12, 1999   60/164,960           80165.001   Nov. 12, 1999   60/164,871           00132.001   Nov. 12, 1999   60/164,961           00134.001   Nov. 15, 1999   60/164,927           80167.001   Nov. 15, 1999   60/164,929           80167.002   Nov. 15, 1999   60/164,926           00135.001   Nov. 16, 1999   60/165,669           80168.001   Nov. 16, 1999   60/165,671           80168.002   Nov. 16, 1999   60/165,661           00136.001   Nov. 17, 1999   60/165,919           80169.001   Nov. 17, 1999   60/165,918           80169.002   Nov. 17, 1999   60/165,911           80170.002   Nov. 18, 1999   60/166,158           00137.001   Nov. 18, 1999   60/166,157           80170.001   Nov. 18, 1999   60/166,173           80171.002   Nov. 19, 1999   60/166,412           00139.001   Nov. 19, 1999   60/166,419           80171.001   Nov. 19, 1999   60/166,411           00140.001   Nov. 22, 1999   60/166,733           80172.001   Nov. 22, 1999   60/166,750           80173.002   Nov. 23, 1999   60/167,362           80173.001   Nov. 24, 1999   60/167,382           00141.001   Nov. 24, 1999   60/167,233           80174.001   Nov. 24, 1999   60/167,234           80174.002   Nov. 24, 1999   60/167,235           00142.001   Nov. 30, 1999   60/167,904           80175.001   Nov. 30, 1999   60/167,908           80175.002   Nov. 30, 1999   60/167,902           00143.001   Dec. 1, 1999   60/168,232           80176.001   Dec. 1, 1999   60/168,233           80176.002   Dec. 1, 1999   60/168,231           00144.001   Dec. 2, 1999   60/168,546           80177.001   Dec. 2, 1999   60/168,549           80177.002   Dec. 2, 1999   60/168,548           80178.001   Dec. 3, 1999   60/168,673           00145.001   Dec. 3, 1999   60/168,675           80178.002   Dec. 3, 1999   60/168,674           80179.001   Dec. 7, 1999   60/169,278           80179.002   Dec. 7, 1999   60/169,302           00147.001   Dec. 7, 1999   60/169,298           80180.001   Dec. 8, 1999   60/169,692           80180.002   Dec. 8, 1999   60/169,691           00149.001   Dec. 16, 1999   60/171,107           80181.002   Dec. 16, 1999   60/171,098           80181.001   Dec. 16, 1999   60/171,114           80182.002   Jan. 19, 2000   60/176,866           80183.002   Jan. 19, 2000   60/176,867           80184.002   Jan. 19, 2000   60/176,910           00152.001   Jan. 26, 2000   60/178,166           00153.002   Jan. 27, 2000   60/178,547           80185.001   Jan. 27, 2000   60/177,666           80183.001   Jan. 27, 2000   60/178,546           80182.001   Jan. 27, 2000   60/178,544           80184.001   Jan. 27, 2000   60/178,545           80186.001   Jan. 28, 2000   60/178,755           00155.001   Jan. 28, 2000   60/178,754           00157.001   Feb. 1, 2000   60/179,395           80187.001   Feb. 1, 2000   60/179,388           00158.001   Feb. 3, 2000   60/180,039           80188.001   Feb. 3, 2000   60/180,139           80189.001   Feb. 4, 2000   60/180,207           00159.001   Feb. 4, 2000   60/180,206           00160.001   Feb. 7, 2000   60/180,695           80190.001   Feb. 7, 2000   60/180,696           00161.001   Feb. 9, 2000   60/181,228           80191.001   Feb. 9, 2000   60/181,214           00162.001   Feb. 10, 2000   60/181,476           80192.002   Feb. 10, 2000   60/181,551           00163.001   Feb. 15, 2000   60/182,477           80193.001   Feb. 15, 2000   60/182,516           00164.001   Feb. 15, 2000   60/182,512           80194.001   Feb. 15, 2000   60/182,478           80195.001   Feb. 17, 2000   60/183,165           00165.001   Feb. 17, 2000   60/183,166                    
Number 31
 
     Application Ser. No. 09/935,625 listed above is a continuation-in-part of the following applications, the entire contents of which are also hereby incorporated by reference: 
                                         Application No.   Filed                      60/228,279   Aug. 25, 2000           60/228,248   Aug. 25, 2000           60/228,247   Aug. 25, 2000           60/228,246   Aug. 25, 2000           60/228,224   Aug. 25, 2000                    
Number 32
 
     Application Ser. No. 10/375,265 listed above is a continuation of application Ser. No. 10/156,052, filed May 29, 2002, which is a continuation of application Ser. No. 09/935,350, filed on Aug. 23, 2001. The entire contents of the two above-mentioned applications are hereby incorporated by reference. 
     Moreover, application Ser. No. 09/935,350 is a conversion of the following provisional applications, to which the present application claims priority under 35 USC § 119(e), the entire contents of which are hereby incorporated by reference: 
                                         Application No.   Filed                      60/228,095   Aug. 23, 2000           60/228,094   Aug. 23, 2000           60/228,126   Aug. 23, 2000           60/228,029   Aug. 23, 2000           60/227,779   Aug. 23, 2000           60/227,782   Aug. 23, 2000           60/228,092   Aug. 23, 2000           60/228,125   Aug. 23, 2000           60/228,127   Aug. 23, 2000           60/228,091   Aug. 23, 2000           60/227,771   Aug. 23, 2000           60/227,727   Aug. 23, 2000           60/227,726   Aug. 23, 2000           60/228,090   Aug. 23, 2000           60/227,776   Aug. 23, 2000           60/228,093   Aug. 23, 2000           60/227,778   Aug. 23, 2000                    
Number 33
 
     Application Ser. No. 10/376,766 listed above claims priority under 35 USC § 119(e) of the following application, the entire contents of which are also hereby incorporated by reference: 
                                             Application No.   Filed                          60/361,109   Mar. 1, 2002                        
Number 34
 
     Application Ser. No. 09/686,093 listed above claims priority under 35 USC § 119(e) of the following application, the entire contents of which are hereby incorporated by reference: 
                                             Application No.   Filing Date                          60/158,369   Oct. 12, 1999                        
Number 35
 
     Application Ser. No. 09/680,498 listed above claims priority under 35 USC § 119(e) of the following application, the entire contents of which are hereby incorporated by reference: 
                                             Application No.   Filing Date                          60/158,232   Oct. 8, 1999                        
Number 36
 
     Application Ser. No. 09/671,635 listed above claims priority under 35 USC § 119(e) of the following application, the entire contents of which are hereby incorporated by reference: 
                                             Application No.   Filing Date                          60/156,458   Sep. 28, 1999                        
Number 37
 
     Application Ser. No. 09/667,517 listed above claims priority under 35 USC § 119(e) of the following application, the entire contents of which are hereby incorporated by reference: 
                                             Application No.   Filing Date                          60/155,486   Sep. 23, 1999                        
Number 38
 
     Application Ser. No. 09/665,714 listed above claims priority under 35 USC § 119(e) of the following application, the entire contents of which are hereby incorporated by reference: 
                                             Application No.   Filing Date                          60/154,779   Sep. 20, 1999                        
Number 39
 
     Application Ser. No. 09/621,323 listed above claims priority under 35 USC § 119(e) of the following application, the entire contents of which are hereby incorporated by reference: 
                                             Application No.   Filing Date                          60/144,632   Jul. 20, 1999                        
Number 40
 
     Application Ser. No. 09/633,191 listed above claims priority under 35 USC § 119(e) of the following application, the entire contents of which are hereby incorporated by reference: 
                                             Application No.   Filing Date                          60/147,260   Aug. 5, 1999                        
Number 41
 
     Application Ser. No. 09/651,370 listed above claims priority under 35 USC § 119(e) of the following application, the entire contents of which are hereby incorporated by reference: 
                                             Application No.   Filing Date                          60/151,303   Aug. 30, 1999                        
Number 42
 
     Application Ser. No. 10/426,837 listed above claims priority under 35 USC § 119(e) of the following application, the entire contents of which are hereby incorporated by reference: 
                                             Application No.   Filing Date                          60/376,553   May 1, 2002           60/376,517   May 1, 2002                        
Number 43
 
     Application Ser. No. 09/702,841 listed above claims priority under 35 USC § 119(e) of the following application, the entire contents of which are hereby incorporated by reference: 
                                             Application No.   Filing Date                          60/162,891   Nov. 1, 1999                        
Number 44
 
     Application Ser. No. 09/696,751 listed above claims priority under 35 USC § 119(e) of the following application, the entire contents of which are hereby incorporated by reference: 
                                             Application No.   Filing Date                          60/161,406   Oct. 25, 1999                        
Number 45
 
     Application Ser. No. 10/356,562 is a continuation of application Ser. No. 10/132,279, filed Apr. 26, 2002, the entire contents of which are hereby incorporated by reference. 
     Application Ser. No. 10/132,279 is a continuation-in-part of the following nonprovisional applications, to which the present application claims priority under § 120, the entire contents of which are also hereby incorporated by reference: 
     
       
         
           
               
               
               
               
             
               
                   
               
               
                   
                 Client No. 
                 Application No. 
                 Filed 
               
               
                   
               
             
            
               
                   
               
            
           
           
               
               
               
               
            
               
                 1. 
                 80001.006 
                 09/391,631 
                 Sep. 3, 1999 
               
               
                 2. 
                 80010.003 
                 09/412,922 
                 Oct. 5, 1999 
               
               
                 3. 
                 80010.002 
                 09/413,198 
                 Oct. 5, 1999 
               
               
                 4. 
                 80026.002 
                 09/428,944 
                 Oct. 28, 1999 
               
               
                 5. 
                 80042.002 
                 09/451,320 
                 Dec. 1, 1999 
               
               
                 6. 
                 80060.002 
                 09/478,081 
                 Jan. 4, 2000 
               
               
                 7. 
                 80084.002 
                 09/497,191 
                 Feb. 3, 2000 
               
               
                 8. 
                 80141.008 
                 09/637,792 
                 Aug. 11, 2000 
               
               
                 9. 
                 80141.007 
                 09/637,564 
                 Aug. 11, 2000 
               
               
                 10. 
                 80141.006 
                 09/637,565 
                 Aug. 11, 2000 
               
               
                 11. 
                 80141.010 
                 10/097,600 
                 Mar. 15 2002 
               
               
                   
               
            
           
         
       
     
     Through the eleven nonprovisional applications listed above, the present application also claims priority under 35 USC § 119(e) of the following provisional applications, the entire contents of which are hereby incorporated by reference: 
     1. Appln. Ser. No. 09/391,631 filed Sep. 3, 1999 claims priority under 35 USC § 119(e) of the following provisional applications: 
                                                 Application No.   Filing Date                                                    1.   60/099,671   Sep. 4, 1998           2.   60/099,672   Sep. 4, 1998           3.   60/099,933   Sep. 11, 1998           4.   60/100,864   Sep. 17, 1998           5.   60/101,042   Sep. 18, 1998           6.   60/101,682   Sep. 24, 1998           7.   60/102,533   Sep. 30, 1998           8.   60/102,460   Sep. 30, 1998           9.   60/103,116   Oct. 5, 1998           10.   60/103,141   Oct. 5, 1998           11.   60/103,574   Oct. 9, 1998           12.   60/103,907   Oct. 13, 1998           13.   60/106,105   Oct. 29, 1998           14.   60/106,218   Oct. 30, 1998           15.   60/107,282   Nov. 6, 1998           16.   60/107,836   Nov. 10, 1998           17.   60/108,526   Nov. 16, 1998           18.   60/108,901   Nov. 17, 1998           19.   60/109,267   Nov. 20, 1998           20.   60/109,594   Nov. 23, 1998           21.   60/110,263   Nov. 30, 1998           22.   60/110,495   Dec. 1, 1998           23.   60/110,626   Dec. 2, 1998           24.   60/110,701   Dec. 3, 1998           25.   60/111,339   Dec. 7, 1998           26.   60/111,589   Dec. 9, 1998           27.   60/112,096   Dec. 14, 1998           28.   60/112,224   Dec. 15, 1998           29.   60/112,624   Dec. 16, 1998           30.   60/112,862   Dec. 17, 1998           31.   60/115,152   Jan. 7, 1999           32.   60/115,156   Jan. 7, 1999           33.   60/115,365   Jan. 8, 1999           34.   60/115,339   Jan. 11, 1999           35.   60/115,847   Jan. 13, 1999           36.   60/116,674   Jan. 21, 1999           37.   60/116,962   Jan. 22, 1999           38.   60/120,583   Feb. 18, 1999           39.   60/121,072   Feb. 22, 1999           40.   60/122,568   Mar. 2, 1999           41.   60/123,941   Mar. 12, 1999                    
2. Appln. Ser. No. 09/412,922 filed Oct. 5, 1999 claims priority under 35 USC § 119(e) of the following provisional applications:
 
                                                 Application No.   Filing Date                                                    1.   60/103,116   Oct. 5, 1998           2.   60/103,141   Oct. 5, 1998           3.   60/103,215   Oct. 6, 1998           4.   60/103,554   Oct. 8, 1998           5.   60/103,574   Oct. 9, 1998           6.   60/103,907   Oct. 13, 1998           7.   60/104,268   Oct. 14, 1998           8.   60/104,680   Oct. 16, 1998           9.   60/104,828   Oct. 19, 1998           10.   60/105,008   Oct. 20, 1998           11.   60/105,142   Oct. 21, 1998           12.   60/105,533   Oct. 22, 1998           13.   60/105,571   Oct. 26, 1998           14.   60/105,815   Oct. 27, 1998           15.   60/106,105   Oct. 29, 1998           16.   60/106,218   Oct. 30, 1998           17.   60/106,685   Nov. 2, 1998           18.   60/107,282   Nov. 6, 1998           19.   60/107,720   Nov. 9, 1998           20.   60/107,719   Nov. 9, 1998           21.   60/107,836   Nov. 10, 1998           22.   60/108,190   Nov. 12, 1998           23.   60/108,526   Nov. 16, 1998           24.   60/108,901   Nov. 17, 1998           25.   60/109,124   Nov. 19, 1998           26.   60/109,127   Nov. 19, 1998           27.   60/109,267   Nov. 20, 1998           28.   60/109,594   Nov. 23, 1998           29.   60/110,053   Nov. 25, 1998           30.   60/110,050   Nov. 25, 1998           31.   60/110,158   Nov. 27, 1998           32.   60/110,263   Nov. 30, 1998           33.   60/110,495   Dec. 1, 1998           34.   60/110,626   Dec. 2, 1998           35.   60/110,701   Dec. 3, 1998           36.   60/111,339   Dec. 7, 1998           37.   60/111,589   Dec. 9, 1998           38.   60/111,782   Dec. 10, 1998           39.   60/111,812   Dec. 11, 1998           40.   60/112,096   Dec. 14, 1998           41.   60/112,224   Dec. 15, 1998           42.   60/112,624   Dec. 16, 1998           43.   60/112,862   Dec. 17, 1998           44.   60/112,912   Dec. 18, 1998           45.   60/113,248   Dec. 21, 1998           46.   60/113,522   Dec. 22, 1998           47.   60/113,826   Dec. 23, 1998           48.   60/113,998   Dec. 28, 1998           49.   60/114,384   Dec. 29, 1998           50.   60/114,455   Dec. 30, 1998           51.   60/114,740   Jan. 4, 1999           52.   60/114,866   Jan. 6, 1999           53.   60/115,153   Jan. 7, 1999           54.   60/115,152   Jan. 7, 1999           55.   60/115,151   Jan. 7, 1999           56.   60/115,155   Jan. 7, 1999           57.   60/115,156   Jan. 7, 1999           58.   60/115,154   Jan. 7, 1999           59.   60/115,364   Jan. 8, 1999           60.   60/115,365   Jan. 8, 1999           61.   60/115,339   Jan. 11, 1999           62.   60/115,518   Jan. 12, 1999           63.   60/115,847   Jan. 13, 1999           64.   60/115,905   Jan. 14, 1999           65.   60/116,383   Jan. 15, 1999           66.   60/116,384   Jan. 15, 1999           67.   60/116,329   Jan. 19, 1999           68.   60/116,340   Jan. 19, 1999           69.   60/116,674   Jan. 21, 1999           70.   60/116,672   Jan. 21, 1999           71.   60/116,960   Jan. 22, 1999           72.   60/116.962   Jan. 22, 1999           73.   60/117,756   Jan. 28, 1999           74.   60/118,672   Feb. 3, 1999           75.   60/118,808   Feb. 4, 1999           76.   60/118,778   Feb. 5, 1999           77.   60/119,029   Feb. 8, 1999           78.   60/119,332   Feb. 9, 1999           79.   60/119,462   Feb. 10, 1999           80.   60/119,922   Feb. 12, 1999           81.   60/120,196   Feb. 16, 1999           82.   60/120,198   Feb. 16, 1999           83.   60/120,583   Feb. 18, 1999           84.   60/121,072   Feb. 22, 1999           85.   60/121,334   Feb. 23, 1999           86.   60/121,470   Feb. 24, 1999           87.   60/121,704   Feb. 25, 1999           88.   60/122,107   Feb. 26, 1999           89.   60/122,266   Mar. 1, 1999           90.   60/122,568   Mar. 2, 1999           91.   60/122,611   Mar. 3, 1999           92.   60/121,775   Mar. 4, 1999           93.   60/123,534   Mar. 5, 1999           94.   60/123,680   Mar. 9, 1999           95.   60/123,715   Mar. 10, 1999           96.   60/123,726   Mar. 10, 1999           97.   60/124,263   Mar. 11, 1999           98.   60/123,941   Mar. 12, 1999                    
3. Appln. Ser. No. 09/413,198 filed Oct. 5, 1999 claims priority under 35 USC § 119(e) of the following provisional applications:
 
                                                     Application No.   Filing Date                                                        1.   60/103,116   Oct. 5, 1998           2.   60/103,141   Oct. 5, 1998           3.   60/103,215   Oct. 6, 1998           4.   60/103,554   Oct. 8, 1998           5.   60/103,574   Oct. 9, 1998           6.   60/103,907   Oct. 13, 1998           7.   60/104,268   Oct. 14, 1998           8.   60/104,680   Oct. 16, 1998           9.   60/104,828   Oct. 19, 1998           10.   60/105,008   Oct. 20, 1998           11.   60/105,142   Oct. 21, 1998           12.   60/105,533   Oct. 22, 1998           13.   60/105,571   Oct. 26, 1998           14.   60/105,815   Oct. 27, 1998           15.   60/106,105   Oct. 29, 1998           16.   60/106,218   Oct. 30, 1998                        
4. Appln. Ser. No. 09/428,944 filed Oct. 28, 1999 claims priority under 35 USC § 119(e) of the following provisional applications:
 
                                                     Appln. No.   Filing Date                                                        1.   60/106,685   Nov. 2, 1998           2.   60/107,282   Nov. 6, 1998           3.   60/107,720   Nov. 9, 1998           4.   60/107,719   Nov. 9, 1998           5.   60/107,836   Nov. 10, 1998           6.   60/108,190   Nov. 12, 1998           7.   60/108,526   Nov. 16, 1998           8.   60/108,901   Nov. 17, 1998           9.   60/109,124   Nov. 19, 1998           10.   60/109,127   Nov. 19, 1998           11.   60/109,267   Nov. 20, 1998           12.   60/109,594   Nov. 23, 1998           13.   60/110,053   Nov. 25, 1998           14.   60/110,050   Nov. 25, 1998           15.   60/110,158   Nov. 27, 1998           16.   60/110,263   Nov. 30, 1998                        
5. Appln. Ser. No. 09/451,320 filed Dec. 1, 1999 claims priority under 35 USC § 119(e) of the following provisional applications:
 
                                                     Appln. No.   Filing Date                                                        1.   60/110,495   Dec. 1, 1998           2.   60/110,626   Dec. 2, 1998           3.   60/110,701   Dec. 3, 1998           4.   60/111,339   Dec. 7, 1998           5.   60/111,589   Dec. 9, 1998           6.   60/111,782   Dec. 10, 1998           7.   60/111,812   Dec. 11, 1998           8.   60/112,096   Dec. 14, 1998           9.   60/112,224   Dec. 15, 1998           10.   60/112,624   Dec. 16, 1998           11.   60/112,862   Dec. 17, 1998           12.   60/112,912   Dec. 18, 1998           13.   60/113,248   Dec. 21, 1998           14.   60/113,522   Dec. 22, 1998           15.   60/113,826   Dec. 23, 1998           16.   60/113,998   Dec. 28, 1998           17.   60/114,384   Dec. 29, 1998           18.   60/114,455   Dec. 30, 1998           19.   60/115,153   Jan. 7, 1999           20.   60/115,152   Jan. 7, 1999           21.   60/115,151   Jan. 7, 1999           22.   60/115,155   Jan. 7, 1999           23.   60/115,156   Jan. 7, 1999           24.   60/115,364   Jan. 8, 1999           25   60/116.960   Jan. 22, 1999                        
6. Appln. Ser. No. 09/478,081 filed Jan. 4, 2000 claims priority under 35 USC § 119(e) of the following provisional applications:
 
                                                     Appln. No.   Filing Date                                                        1.   60/114,740   Jan. 4, 1999           2.   60/114,866   Jan. 6, 1999           3.   60/115,154   Jan. 7, 1999           4.   60/115,365   Jan. 8, 1999           5.   60/115,339   Jan. 11, 1999           6.   60/115,518   Jan. 12, 1999           7.   60/115,847   Jan. 13, 1999           8.   60/115,905   Jan. 14, 1999           9.   60/116,383   Jan. 15, 1999           10.   60/116,384   Jan. 15, 1999           11.   60/116,329   Jan. 19, 1999           12.   60/116,340   Jan. 19, 1999           13.   60/116,674   Jan. 21, 1999           14.   60/116,672   Jan. 21, 1999           15.   60/116,962   Jan. 22, 1999           16.   60/117,756   Jan. 28, 1999                        
7. Appln. Ser. No. 09/497,191 filed Feb. 3, 2000 claims priority under 35 USC § 119(e) of the following provisional applications:
 
                                                 Appln. No.   Filing Date                                                    1.   60/118,672   Feb. 3, 1999           2.   60/118,808   Feb. 4, 1999           3.   60/118,778   Feb. 5, 1999           4.   60/119,029   Feb. 8, 1999           5.   60/119,332   Feb. 9, 1999           6.   60/119,462   Feb. 10, 1999           7.   60/119,922   Feb. 12, 1999           8.   60/120,196   Feb. 16, 1999           9.   60/120,198   Feb. 16, 1999           10.   60/120,583   Feb. 18, 1999           11.   60/121,072   Feb. 22, 1999           12.   60/121,334   Feb. 23, 1999           13.   60/121,470   Feb. 24, 1999           14.   60/121,704   Feb. 25, 1999           15.   60/122,107   Feb. 26, 1999                    
8. Appln. Ser. No. 09/637,792 filed Aug. 11, 2000 claims priority under 35 USC § 119(e) of the following provisional applications:
 
                                             Appln. No.   Filing Date                          60/148,337   Aug. 12, 1999                        
9. Appln. Ser. No. 09/637,564 filed Aug. 11, 2000 claims priority under 35 USC § 119(e) of the following provisional applications:
 
                                             Appln. No.   Filing Date                          60/148,340   Aug. 12, 1999                        
10. Appln. Ser. No. 09/637,565 filed Aug. 11, 2000 claims priority under 35 USC § 119(e) of the following provisional applications:
 
                                             Appln. No.   Filing Date                          60/148,342   Aug. 12, 1999                        
11. Appln. Ser. No. 10/097,600 filed Mar. 15, 2002 is a continuation of application Ser. No. 09/832,934 filed Apr. 12, 2001, which is a continuation of application Ser. No. 09/637,820 filed Aug. 11, 2000, through which it claims priority under 35 USC § 119(e) of the following provisional application:
 
                                             Appln. No.   Filing Date                          60/148,347   Aug. 12, 1999                        
Number 46
 
     Application Ser. No. 10/336,799 listed above is a continuation of application Ser. No. 10/132,257, filed on Apr. 26, 2002, the entire contents of which are hereby incorporated by reference. 
     Through application Ser. No. 10/132,257, the present application claims priority under 35 USC § 119(e) and § 120 of the following applications, the entire contents of which are hereby incorporated by reference: 
     
       
         
           
               
               
               
               
               
             
               
                   
               
               
                   
                   
                 Client No. 
                 Application No. 
                 Filed 
               
               
                   
               
             
            
               
                   
               
            
           
           
               
               
               
               
               
            
               
                   
                 1. 
                 91000.002 
                 09/543,680 
                 Apr. 6, 2000 
               
               
                   
                 2. 
                 91002.002 
                 09/565,308 
                 May 5, 2000 
               
               
                   
                 3. 
                 91007.002 
                 09/573,655 
                 May 18, 2000 
               
               
                   
                 4. 
                 00033.003 
                 09/592,459 
                 Jun. 9, 2000 
               
               
                   
                 5. 
                 00034.002 
                 09/593,710 
                 Jun. 14, 2000 
               
               
                   
                 6. 
                 00045.002 
                 09/602,016 
                 Jun. 23, 2000 
               
               
                   
                 7. 
                 00048.002 
                 09/606,181 
                 Jun. 29, 2000 
               
               
                   
                 8. 
                 00050.002 
                 09/607,081 
                 Jun. 30, 2000 
               
               
                   
                 9. 
                 00051.002 
                 09/610,157 
                 Jun. 30, 2000 
               
               
                   
                 10. 
                 00052.002 
                 09/609,198 
                 Jun. 30, 2000 
               
               
                   
                 11. 
                 00053.002 
                 09/611,409 
                 Jul. 6, 2000 
               
               
                   
                 12. 
                 00054.002 
                 09/612,645 
                 Jul. 7, 2000 
               
               
                   
                 13. 
                 00058.002 
                 09/613,547 
                 Jul. 7, 2000 
               
               
                   
               
            
           
         
       
     
     Through the applications listed above, the present application also claims priority under 35 USC § 119(e) of the following applications, the entire contents of which are hereby incorporated by reference: 
                                                     Clent No.   Application No.   Filed                                                        14.   91000.001   60/128,234   Apr. 6, 1999           15.   91001.001   60/128,714   Apr. 8, 1999           16.   91002.001   60/132,487   May 6, 1999           17.   91007.001   60/134,768   May 18, 1999           18.   91008.001   60/134,941   May 19, 1999           19.   91009.001   60/135,124   May 20, 1999           20.   91010.001   60/135,353   May 21, 1999           21.   91011.001   60/135,629   May 24, 1999           22.   91012.001   60/136,021   May 25, 1999           23.   91013.001   60/136,392   May 27, 1999           24.   91014.001   60/136,782   May 28, 1999           25.   91015.001   60/137,222   Jun. 1, 1999           26.   91016.001   60/137,528   Jun. 3, 1999           27.   91017.001   60/137,502   Jun. 4, 1999           28.   91018.001   60/137,724   Jun. 7, 1999           29.   91019.001   60/138,094   Jun. 8, 1999           30.   00033.001   60/138,540   Jun. 10, 1999           31.   00033.002   60/138,847   Jun. 10, 1999           32.   00034.001   60/139,119   Jun. 14, 1999           33.   00045.001   60/140,695   Jun. 24, 1999           34.   00048.001   60/140,991   Jun. 29, 1999           35.   00050.001   60/141,842   Jul. 1, 1999           36.   00051.001   60/142,154   Jul. 1, 1999           37.   00052.001   60/142,055   Jul. 2, 1999           38.   00053.001   60/142,390   Jul. 6, 1999           39.   00054.001   60/142,803   Jul. 8, 1999           40.   00058.001   60/142,920   Jul. 9, 1999                    
Number 47
 
     Application Ser. No. 10/347,322 is a continuation of application Ser. No. 10/132,256, filed on Apr. 26, 2002, the entire contents of which are hereby incorporated by reference. 
     Application Ser. No. 10/132,256 is a continuation-in-part of the following nonprovisional applications, to which the present application claims priority under § 120, the entire contents of which are hereby incorporated by reference: 
     
       
         
           
               
               
               
               
             
               
                   
               
               
                   
                   
                 Application No. 
                 Filed 
               
               
                   
               
             
            
               
                   
               
            
           
           
               
               
               
               
            
               
                   
                 1. 
                 09/595,326 
                 Jun. 16, 2000 
               
               
                   
                 2. 
                 09/692,696 
                 Oct. 20, 2000 
               
               
                   
                 3. 
                 09/692,154 
                 Oct. 20, 2000 
               
               
                   
                 4. 
                 09/692,714 
                 Oct. 20, 2000 
               
               
                   
                 5. 
                 09/692,148 
                 Oct. 20, 2000 
               
               
                   
                 6. 
                 09/692,717 
                 Oct. 20, 2000 
               
               
                   
                 7. 
                 09/692,152 
                 Oct. 20, 2000 
               
               
                   
                 8. 
                 09/696,751 
                 Oct. 25, 2000 
               
               
                   
                 9. 
                 09/695,387 
                 Oct. 25, 2000 
               
               
                   
                 10. 
                 09/696,284 
                 Oct. 26, 2000 
               
               
                   
                 11. 
                 09/696,017 
                 Oct. 26, 2000 
               
               
                   
                 12. 
                 09/697,056 
                 Oct. 27, 2000 
               
               
                   
                 13. 
                 09/697,145 
                 Oct. 27, 2000 
               
               
                   
                 14. 
                 09/697,081 
                 Oct. 27, 2000 
               
               
                   
                 15. 
                 09/697,076 
                 Oct. 27, 2000 
               
               
                   
                 16. 
                 09/702,873 
                 Nov. 1, 2000 
               
               
                   
                 17. 
                 09/702,841 
                 Nov. 1, 2000 
               
               
                   
                 18. 
                 09/703,619 
                 Nov. 2, 2000 
               
               
                   
                 19. 
                 09/703,627 
                 Nov. 2, 2000 
               
               
                   
                 20. 
                 09/704,550 
                 Nov. 3, 2000 
               
               
                   
                 21. 
                 09/704,836 
                 Nov. 3, 2000 
               
               
                   
                 22. 
                 09/704,541 
                 Nov. 3, 2000 
               
               
                   
                 23. 
                 09/704,540 
                 Nov. 3, 2000 
               
               
                   
                 24. 
                 09/708,092 
                 Nov. 8, 2000 
               
               
                   
                 25. 
                 09/726,578 
                 Dec. 1, 2000 
               
               
                   
                 26. 
                 09/769,525 
                 Jan. 26, 2001 
               
               
                   
                 27. 
                 09/774,806 
                 Feb. 1, 2001 
               
               
                   
                 28. 
                 09/870,664 
                 Jun. 1, 2001 
               
               
                   
                 29. 
                 10/082,096 
                 Feb. 26, 2002 
               
               
                   
                 30. 
                 10/086,239 
                 Mar. 4, 2002 
               
               
                   
                 31. 
                 10/094,538 
                 Mar. 11, 2002 
               
               
                   
                 32. 
                 10/095,465 
                 Mar. 13, 2002 
               
               
                   
                 33. 
                 10/097,295 
                 Mar. 15, 2002 
               
               
                   
                 34. 
                 10/103,845 
                 Mar. 25, 2002 
               
               
                   
                 35. 
                 10/123,111 
                 Apr. 17, 2002 
               
               
                   
               
            
           
         
       
     
     Through the thirty-five nonprovisional applications listed above, the present application also claims priority under 35 USC § 119(e) of the following provisional applications, the entire contents of which are hereby incorporated by reference: 
     1. Appln. Ser. No. 09/595,326 filed Jun. 16, 2000 claims priority under 35 USC § 119(e) of the following provisional applications: 
                                             Application No.   Filing Date                          60/139,763   Jun. 18, 1999                        
2. Appln. Ser. No. 09/692,696 filed Oct. 20, 2000 claims priority under 35 USC § 119(e) of the following provisional applications:
 
                                             Appln. No.   Filing Date                          60/160,981   Oct. 22, 1999                        
3. Appln. Ser. No. 09/692,154 filed Oct. 20, 2000 claims priority under 35 USC § 119(e) of the following provisional applications:
 
                                             Appln. No.   Filing Date                          60/160,814   Oct. 21, 1999                        
4. Appln. Ser. No. 09/692,714 filed Oct. 20, 2000 claims priority under 35 USC § 119(e) of the following provisional applications:
 
                                             Appln. No.   Filing Date                          60/160,770   Oct. 21, 1999                        
5. Appln. Ser. No. 09/692,148 filed Oct. 20, 2000 claims priority under 35 USC § 119(e) of the following provisional applications:
 
                                             Appln. No.   Filing Date                          60/160,768   Oct. 21, 1999                        
6. Appln. Ser. No. 09/692,717 filed Oct. 20, 2000 claims priority under 35 USC § 119(e) of the following provisional applications:
 
                                             Appln. No.   Filing Date                          60/160,767   Oct. 21, 1999                        
7. Appln. Ser. No. 09/692,152 filed Oct. 20, 2000 claims priority under 35 USC § 119(e) of the following provisional applications:
 
                                             Appln. No.   Filing Date                          60/160,989   Oct. 22, 1999                        
8. Appln. Ser. No. 09/696,751 filed Oct. 25, 2000 claims priority under 35 USC § 119(e) of the following provisional applications:
 
                                             Appln. No.   Filing Date                          60/161,406   Oct. 25, 1999                        
9. Appln. Ser. No. 09/695,387 filed Oct. 25, 2000 claims priority under 35 USC § 119(e) of the following provisional applications:
 
                                             Appln. No.   Filing Date                          60/161,404   Oct. 25, 1999                        
10. Appln. Ser. No. 09/696,284 filed Oct. 26, 2000 claims priority under 35 USC § 119(e) of the following provisional applications:
 
                                             Appln. No.   Filing Date                          60/161,360   Oct. 26, 1999                        
11. Appln. Ser. No. 09/696,017 filed Oct. 26, 2000 claims priority under 35 USC § 119(e) of the following provisional applications:
 
                                             Appln. No.   Filing Date                          60/161,359   Oct. 26, 1999                        
12. Appln. Ser. No. 09/697,056 filed Oct. 27, 2000 claims priority under 35 USC § 119(e) of the following provisional applications:
 
                                             Appln. No.   Filing Date                          60/161,992   Oct. 28, 1999                        
13. Appln. Ser. No. 09/697,145 filed Oct. 27, 2000 claims priority under 35 USC § 119(e) of the following provisional applications:
 
                                             Appln. No.   Filing Date                          60/161,993   Oct. 28, 1999                        
14. Appln. Ser. No. 09/697,081 filed Oct. 27, 2000 claims priority under 35 USC § 119(e) of the following provisional applications:
 
                                             Appln. No.   Filing Date                          60/162,142   Oct. 29, 1999                        
15. Appln. Ser. No. 09/697,076 filed Oct. 27, 2000 claims priority under 35 USC § 119(e) of the following provisional applications:
 
                                             Appln. No.   Filing Date                          60/162,228   Oct. 29, 1999                        
16. Appln. Ser. No. 09/702,873 filed Nov. 1, 2000 claims priority under 35 USC § 119(e) of the following provisional applications:
 
                                             Appln. No.   Filing Date                          60/162,895   Nov. 1, 1999                        
17. Appln. Ser. No. 09/702,841 filed Nov. 1, 2000 claims priority under 35 USC § 119(e) of the following provisional applications:
 
                                             Appln. No.   Filing Date                          60/162,891   Nov. 1, 1999                        
18. Appln. Ser. No. 09/703,619 filed Nov. 2, 2000 claims priority under 35 USC § 119(e) of the following provisional applications:
 
                                             Appln. No.   Filing Date                          60/163,091   Nov. 2, 1999                        
19. Appln. Ser. No. 09/703,627 filed Nov. 2, 2000 claims priority under 35 USC § 119(e) of the following provisional applications:
 
                                             Appln. No.   Filing Date                          60/163,092   Nov. 2, 1999                        
20. Appln. Ser. No. 09/704,550 filed Nov. 3, 2000 claims priority under 35 USC § 119(e) of the following provisional applications:
 
                                             Appln. No.   Filing Date                          60/163,248   Nov. 3, 1999                        
21. Appln. Ser. No. 09/704,836 filed Nov. 3, 2000 claims priority under 35 USC § 119(e) of the following provisional applications:
 
                                             Appln. No.   Filing Date                          60/163,281   Nov. 3, 1999                        
22. Appln. Ser. No. 09/704,541 filed Nov. 3, 2000 claims priority under 35 USC § 119(e) of the following provisional applications:
 
                                             Appln. No.   Filing Date                          60/163,381   Nov. 4, 1999                        
23. Appln. Ser. No. 09/704,540 filed Nov. 3, 2000 claims priority under 35 USC § 119(e) of the following provisional applications:
 
                                             Appln. No.   Filing Date                          60/163,380   Nov. 4, 1999                        
24. Appln. Ser. No. 09/708,092 filed Nov. 8, 2000 claims priority under 35 USC § 119(e) of the following provisional applications:
 
                                                     Appln. No.   Filing Date                                                        1.   60/165,918   Nov. 17, 1999           2.   60/166,733   Nov. 22, 1999           3.   60/165,661   Nov. 16, 1999           4.   60/165,919   Nov. 17, 1999           5.   60/165,911   Nov. 17, 1999           6.   60/166,173   Nov. 18, 1999           7.   60/166,158   Nov. 18, 1999           8.   60/166,419   Nov. 19, 1999           9.   60/166,157   Nov. 18, 1999           10.   60/166,412   Nov. 19, 1999           11.   60/165,669   Nov. 16, 1999           12.   60/166,750   Nov. 22, 1999           13.   60/167,233   Nov. 24, 1999           14.   60/167,234   Nov. 24, 1999           15.   60/167,235   Nov. 24, 1999           16.   60/167,904   Nov. 30, 1999           17.   60/167,908   Nov. 30, 1999           18.   60/166,411   Nov. 19, 1999           19.   60/164,960   Nov. 12, 1999           20.   60/164,146   Nov. 8, 1999           21.   60/164,151   Nov. 8, 1999           22.   60/164,150   Nov. 8, 1999           23.   60/164,544   Nov. 10, 1999           24.   60/164,545   Nov. 10, 1999           25.   60/164,548   Nov. 10, 1999           26.   60/165,671   Nov. 16, 1999           27.   60/164,871   Nov. 12, 1999           28.   60/167,902   Nov. 30, 1999           29.   60/164,870   Nov. 12, 1999           30.   60/164,959   Nov. 12, 1999           31.   60/164,962   Nov. 12, 1999           32.   60/164,927   Nov. 15, 1999           33.   60/164,929   Nov. 15, 1999           34.   60/164,926   Nov. 15, 1999           35.   60/164,961   Nov. 12, 1999                        
25. Appln. Ser. No. 09/726,578 filed Dec. 1, 2000 claims priority under 35 USC § 119(e) of the following provisional applications:
 
                                                     Appln. No.   Filing Date                                                        1.   60/169,302   Dec. 7, 1999           2.   60/168,231   Dec. 1, 1999           3.   60/168,549   Dec. 2, 1999           4.   60/168,548   Dec. 2, 1999           5.   60/168,675   Dec. 3, 1999           6.   60/168,673   Dec. 3, 1999           7.   60/168,674   Dec. 3, 1999           8.   60/168,232   Dec. 1, 1999           9.   60/169,278   Dec. 7, 1999           10.   60/168,233   Dec. 1, 1999           11.   60/171,107   Dec. 16, 1999           12.   60/171,114   Dec. 16, 1999           13.   60/171,098   Dec. 16, 1999           14.   60/169,298   Dec. 7, 1999           15.   60/168,546   Dec. 2, 1999                        
26. Appln. Ser. No. 09/769,525 filed Jan. 26, 2001 claims priority under 35 USC § 119(e) of the following provisional applications:
 
                                                     Appln. No.   Filing Date                                                        1.   60/178,547   Jan. 27, 2000           2.   60/178,755   Jan. 28, 2000           3.   60/177,666   Jan. 27, 2000           4.   60/178,754   Jan. 28, 2000                        
27. Appln. Ser. No. 09/774,806 filed Feb. 1, 2001 claims priority under 35 USC § 119(e) of the following provisional applications:
 
                                                     Appln. No.   Filing Date                                                        1.   60/182,477   Feb. 15, 2000           2.   60/180,696   Feb. 7, 2000           3.   60/183,166   Feb. 17, 2000           4.   60/183,165   Feb. 17, 2000           5.   60/182,512   Feb. 15, 2000           6.   60/182,516   Feb. 15, 2000           7.   60/181,551   Feb. 10, 2000           8.   60/181,476   Feb. 10, 2000           9.   60/184,667   Feb. 24, 2000           10.   60/181,228   Feb. 9, 2000           11.   60/185,397   Feb. 28, 2000           12.   60/180,695   Feb. 7, 2000           13.   60/180,207   Feb. 4, 2000           14.   60/181,214   Feb. 9, 2000           15.   60/180,139   Feb. 3, 2000           16.   60/179,388   Feb. 1, 2000           17.   60/179,395   Feb. 1, 2000           18.   60/185,119   Feb. 25, 2000           19.   60/180,039   Feb. 3, 2000           20.   60/184,658   Feb. 24, 2000           21.   60/185,396   Feb. 28, 2000           22.   60/180,206   Feb. 4, 2000           23.   60/185,118   Feb. 25, 2000                        
28. Appln. Ser. No. 09/870,664 filed Jun. 1, 2001 claims priority under 35 USC § 119(e) of the following provisional applications:
 
                                                     Appln. No.   Filing Date                                                        1.   60/208,918   Jun. 5, 2000           2.   60/214,535   Jun. 27, 2000           3.   60/208,920   Jun. 5, 2000           4.   60/215,127   Jun. 30, 2000           5.   60/214,799   Jun. 28, 2000           6.   60/213,249   Jun. 22, 2000           7.   60/210,564   Jun. 9, 2000           8.   60/210,006   Jun. 8, 2000           9.   60/208,312   Jun. 1, 2000           10.   60/211,214   Jun. 13, 2000                        
29. Appln. Ser. No. 10/082,096 filed Feb. 26, 2002 is a continuation of application Ser. No. 09/795,347 filed Mar. 1, 2001 and claims priority under 35 USC § 119(e) of the following provisional applications claims priority under 35 USC § 119(e) of the following provisional applications:
 
                                                     Appln. No.   Filing Date                                                        1.   60/192,308   Mar. 27, 2000           2.   60/189,959   Mar. 16, 2000           3.   60/190,069   Mar. 20, 2000           4.   60/190,070   Mar. 20, 2000           5.   60/190,545   Mar. 20, 2000           6.   60/190,089   Mar. 20, 2000           7.   60/191,084   Mar. 22, 2000           8.   60/191,097   Mar. 22, 2000           9.   60/191,543   Mar. 23, 2000           10.   60/191,545   Mar. 23, 2000           11.   60/191,823   Mar. 24, 2000           12.   60/192,421   Mar. 27, 2000           13.   60/189,461   Mar. 15, 2000           14.   60/192,940   Mar. 29, 2000           15.   60/192,941   Mar. 29, 2000           16.   60/193,244   Mar. 30, 2000           17.   60/193,245   Mar. 30, 2000           18.   60/193,453   Mar. 31, 2000           19.   60/193,455   Mar. 31, 2000           20.   60/191,825   Mar. 24, 2000           21.   60/187,378   Mar. 7, 2000           22.   60/186,390   Mar. 2, 2000           23.   60/186,283   Mar. 1, 2000           24.   60/186,296   Mar. 1, 2000           25.   60/187,178   Mar. 2, 2000           26.   60/186,386   Mar. 2, 2000           27.   60/186,387   Mar. 2, 2000           28.   60/189,953   Mar. 16, 2000           29.   60/186,669   Mar. 3, 2000           30.   60/189,462   Mar. 15, 2000           31.   60/187,896   Mar. 8, 2000           32.   60/187,888   Mar. 8, 2000           33.   60/188,187   Mar. 10, 2000           34.   60/188,186   Mar. 10, 2000           35.   60/188,185   Mar. 10, 2000           36.   60/188,175   Mar. 10, 2000           37.   60/189,080   Mar. 14, 2000           38.   60/189,052   Mar. 14, 2000           39.   60/186,748   Mar. 3, 2000                        
30. Appln. Ser. No. 10/086,239 filed Mar. 4, 2002 is a continuation of application Ser. No. 09/845,206 filed May 1, 2001 and claims priority under 35 USC § 119(e) of the following provisional applications:
 
                                                     Appln. No.   Filing Date                                                        1.   60/201,305   May 2, 2000           2.   60/206,319   May 23, 2000           3.   60/204,829   May 17, 2000           4.   60/201,275   May 2, 2000           5.   60/205,058   May 18, 2000           6.   60/205,242   May 19, 2000           7.   60/205,243   May 19, 2000           8.   60/205,572   May 22, 2000           9.   60/204,569   May 16, 2000           10.   60/206,316   May 23, 2000           11.   60/204,830   May 17, 2000           12.   60/206,553   May 24, 2000           13.   60/206,545   May 24, 2000           14.   60/207,367   May 26, 2000           15.   60/207,243   May 26, 2000           16.   60/207,239   May 26, 2000           17.   60/207,354   May 26, 2000           18.   60/207,452   May 30, 2000           19.   60/207,329   May 30, 2000           20.   60/205,576   May 22, 2000           21.   60/202,636   May 9, 2000           22.   60/200,879   May 1, 2000           23.   60/201,740   May 4, 2000           24.   60/201,750   May 4, 2000           25.   60/202,112   May 5, 2000           26.   60/205,201   May 18, 2000           27.   60/202,914   May 9, 2000           28.   60/204,568   May 16, 2000           29.   60/202,919   May 9, 2000           30.   60/202,634   May 9, 2000           31.   60/202,968   May 10, 2000           32.   60/202,963   May 10, 2000           33.   60/203,457   May 11, 2000           34.   60/203,279   May 11, 2000           35.   60/203,916   May 12, 2000           36.   60/203,915   May 12, 2000           37.   60/204,388   May 15, 2000           38.   60/204,122   May 15, 2000           39.   60/202,180   May 5, 2000                        
31. Appln. Ser. No. 10/094,538 filed Mar. 11, 2002 is a continuation of application Ser. No. 09/783,606 filed Feb. 15, 2001 and claims priority under 35 USC § 119(e) of the following provisional applications:
 
                                             Appln. No.   Filing Date                          60/182,478   Feb. 15, 2000                        
32. Appln. Ser. No. 10/095,465 filed Mar. 13, 2002 is a continuation of application Ser. No. 09/824,882 filed Apr. 4, 2001 and claims priority under 35 USC § 119(e) of the following provisional applications:
 
                                                     Appln. No.   Filing Date                                                        1.   60/199,828   Apr. 26, 2000           2.   60/198,619   Apr. 20, 2000           3.   60/195,045   Apr. 6, 2000           4.   60/194,404   Apr. 4, 2000           5.   60/196,486   Apr. 12, 2000           6.   60/196,487   Apr. 12, 2000           7.   60/196,169   Apr. 11, 2000           8.   60/196,089   Apr. 11, 2000           9.   60/196,485   Apr. 12, 2000           10.   60/194,874   Apr. 6, 2000           11.   60/197,671   Apr. 17, 2000           12.   60/194,872   Apr. 6, 2000           13.   60/194,697   Apr. 5, 2000           14.   60/194,683   Apr. 5, 2000           15.   60/199,122   Apr. 24, 2000           16.   60/198,623   Apr. 20, 2000           17.   60/197,678   Apr. 17, 2000           18.   60/198,133   Apr. 17, 2000           19.   60/197,687   Apr. 17, 2000           20.   60/198,386   Apr. 19, 2000           21.   60/198,373   Apr. 19, 2000           22.   60/194,398   Apr. 4, 2000           23.   60/200,102   Apr. 27, 2000           24.   60/195,283   Apr. 7, 2000           25.   60/196,289   Apr. 12, 2000           26.   60/199,124   Apr. 24, 2000           27.   60/195,257   Apr. 7, 2000           28.   60/199,818   Apr. 26, 2000           29.   60/200,103   Apr. 27, 2000           30.   60/198,767   Apr. 21, 2000           31.   60/198,763   Apr. 21, 2000           32.   60/194,885   Apr. 6, 2000                        
33. Appln. Ser. No. 10/097,295 filed Mar. 15, 2002 is a continuation of application Ser. No. 09/881,096 filed Jun. 15, 2001 and claims priority under 35 USC § 119(e) of the following provisional applications:
 
                                                     Appln. No.   Filing Date                                                        1.   60/212,727   Jun. 20, 2000           2.   60/212,623   Jun. 19, 2000           3.   60/213,270   Jun. 22, 2000           4.   60/214,524   Jun. 27, 2000           5.   60/211,538   Jun. 15, 2000                        
34. Appln. Ser. No. 10/103,845 filed Mar. 25, 2002 is a continuation of application Ser. No. 09/898,063 filed Jul. 5, 2001 and claims priority under 35 USC § 119(e) of the following provisional applications:
 
                                                     Appln. No.   Filing Date                                                        1.   60/219,033   Jul. 18, 2000           2.   60/216,362   Jul. 5, 2000           3.   60/217,384   Jul. 11, 2000           4.   60/220,811   Jul. 25, 2000           5.   60/220,652   Jul. 25, 2000                        
35. Appln. Ser. No. 10/123,111 filed Apr. 17, 2002 is a continuation of application Ser. No. 09/928,372 filed Aug. 14, 2001 and claims priority under 35 USC § 119(e) of the following provisional applications:
 
                                                     Appln. No.   Filing Date                                                        1.   60/225,303   Aug. 15, 2000           2.   60/227,024   Aug. 23, 2000           3.   60/228,898   Aug. 30, 2000           4.   60/224,517   Aug. 14, 2000           5.   60/226,452   Aug. 21, 2000                        
Number 48
 
     Application Ser. No. 10/406,556 listed above is a continuation application Ser. No. 10/132,277, filed on Apr. 26, 2002, the entire contents of which are hereby incorporated by reference. 
     Application Ser. No. 10/132,277 is a continuation-in-part of the following nonprovisional applications, to which the present application also claims priority, the entire contents of which are hereby incorporated by reference: 
     
       
         
           
               
               
               
               
               
             
               
                   
               
               
                   
                   
                 Client No. 
                 Appln. No. 
                 Filed 
               
               
                   
               
             
            
               
                   
               
            
           
           
               
               
               
               
               
            
               
                   
                 1. 
                 91006.002 
                 09/570,581 
                 May 12, 2000 
               
               
                   
                 2. 
                 00037.002 
                 09/595,334 
                 Jun. 16, 2000 
               
               
                   
                 3. 
                 00039.002 
                 09/596,577 
                 Jun. 16, 2000 
               
               
                   
                 4. 
                 00042.003 
                 09/602,660 
                 Jun. 21, 2000 
               
               
                   
                 5. 
                 00043.002 
                 09/602,152 
                 Jun. 22, 2000 
               
               
                   
                 6. 
                 00044.002 
                 09/602,025 
                 Jun. 23, 2000 
               
               
                   
                 7. 
                 00046.002 
                 09/605,843 
                 Jun. 28, 2000 
               
               
                   
                 8. 
                 00049.002 
                 09/608,960 
                 Jun. 30, 2000 
               
               
                   
                 9. 
                 00059.002 
                 09/615,007 
                 Jul. 12, 2000 
               
               
                   
                 10. 
                 00060.002 
                 09/615,748 
                 Jul. 13, 2000 
               
               
                   
                 11. 
                 00061.002 
                 09/617,525 
                 Jul. 14, 2000 
               
               
                   
                 12. 
                 00062.002 
                 09/617,203 
                 Jul. 14, 2000 
               
               
                   
                 13. 
                 00064.002 
                 09/620,421 
                 Jul. 19, 2000 
               
               
                   
                 14. 
                 00065.002 
                 09/621,323 
                 Jul. 20, 2000 
               
               
                   
                 15. 
                 00066.002 
                 09/621,630 
                 Jul. 21, 2000 
               
               
                   
                 16. 
                 00067.002 
                 09/621,660 
                 Jul. 21, 2000 
               
               
                   
                 17. 
                 00069.002 
                 09/621,902 
                 Jul. 21, 2000 
               
               
                   
                 18. 
                 00070.002 
                 09/616,628 
                 Jul. 26, 2000 
               
               
                   
                 19. 
                 00071.002 
                 09/628,986 
                 Jul. 27, 2000 
               
               
                   
                 20. 
                 00072.002 
                 09/628,552 
                 Jul. 28, 2000 
               
               
                   
                 21. 
                 00073.002 
                 09/632,340 
                 Aug. 2, 2000 
               
               
                   
                 22. 
                 00074.002 
                 09/632,349 
                 Aug. 3, 2000 
               
               
                   
                 23. 
                 00076.002 
                 09/633,051 
                 Aug. 4, 2000 
               
               
                   
                 24. 
                 00077.002 
                 09/633,191 
                 Aug. 4, 2000 
               
               
                   
                 25. 
                 00079.002 
                 09/633,239 
                 Aug. 4, 2000 
               
               
                   
                 26. 
                 00080.002 
                 09/635,277 
                 Aug. 9, 2000 
               
               
                   
                 27. 
                 00081.002 
                 09/637,837 
                 Aug. 11, 2000 
               
               
                   
                 28. 
                 00082.002 
                 09/636,555 
                 Aug. 11, 2000 
               
               
                   
                 29. 
                 00083.002 
                 09/637,563 
                 Aug. 11, 2000 
               
               
                   
                 30. 
                 00084.002 
                 09/641,198 
                 Aug. 17, 2000 
               
               
                   
                 31. 
                 00087.002 
                 09/640,695 
                 Aug. 18, 2000 
               
               
                   
                 32. 
                 00085.002 
                 09/641,359 
                 Aug. 18, 2000 
               
               
                   
                 33. 
                 00086.002 
                 09/641,375 
                 Aug. 18, 2000 
               
               
                   
                 34. 
                 00088.002 
                 09/643,854 
                 Aug. 23, 2000 
               
               
                   
                 35. 
                 00089.002 
                 09/645,440 
                 Aug. 25, 2000 
               
               
                   
                 36. 
                 00090.002 
                 09/648,708 
                 Aug. 25, 2000 
               
               
                   
                 37. 
                 00091.002 
                 09/645,441 
                 Aug. 25, 2000 
               
               
                   
                 38. 
                 00092.002 
                 09/651,370 
                 Aug. 30, 2000 
               
               
                   
                 39. 
                 00093.002 
                 09/653,466 
                 Aug. 31, 2000 
               
               
                   
                 40. 
                 00094.002 
                 09/654,547 
                 Sep. 1, 2000 
               
               
                   
                 41. 
                 00095.002 
                 09/657,454 
                 Sep. 7, 2000 
               
               
                   
                 42. 
                 00096.002 
                 09/657,569 
                 Sep. 8, 2000 
               
               
                   
                 43. 
                 00098.002 
                 09/660,883 
                 Sep. 13, 2000 
               
               
                   
                 44. 
                 00099.002 
                 09/663,196 
                 Sep. 15, 2000 
               
               
                   
                 45. 
                 00101.002 
                 09/663,195 
                 Sep. 15, 2000 
               
               
                   
                 46. 
                 00102.002 
                 09/665,714 
                 Sep. 20, 2000 
               
               
                   
                 47. 
                 00103.002 
                 09/667,597 
                 Sep. 22, 2000 
               
               
                   
                 48. 
                 00104.002 
                 09/667,517 
                 Sep. 22, 2000 
               
               
                   
                 49. 
                 00105.002 
                 09/667,229 
                 Sep. 22, 2000 
               
               
                   
                 50. 
                 00106.002 
                 09/671,635 
                 Sep. 28, 2000 
               
               
                   
                 51. 
                 00107.002 
                 09/672,075 
                 Sep. 29, 2000 
               
               
                   
                 52. 
                 00108.002 
                 09/679,203 
                 Oct. 4, 2000 
               
               
                   
                 53. 
                 00109.002 
                 09/678,223 
                 Oct. 5, 2000 
               
               
                   
                 54. 
                 00110.002 
                 09/680,499 
                 Oct. 6, 2000 
               
               
                   
                 55. 
                 00111.002 
                 09/680,490 
                 Oct. 6, 2000 
               
               
                   
                 56. 
                 00112.002 
                 09/680,498 
                 Oct. 6, 2000 
               
               
                   
                 57. 
                 00113.002 
                 09/686,093 
                 Oct. 12, 2000 
               
               
                   
                 58. 
                 00116.002 
                 09/690,745 
                 Oct. 18, 2000 
               
               
                   
                 59. 
                 00120.002 
                 09/692,108 
                 Oct. 20, 2000 
               
               
                   
                 60. 
                 00119.002 
                 09/692,153 
                 Oct. 20, 2000 
               
               
                   
                 61. 
                 00118.002 
                 09/692,157 
                 Oct. 20, 2000 
               
               
                   
                 62. 
                 00121.002 
                 09/695,391 
                 Oct. 25, 2000 
               
               
                   
                 63. 
                 00122.002 
                 09/696,305 
                 Oct. 26, 2000 
               
               
                   
                 64. 
                 00123.002 
                 09/697,080 
                 Oct. 27, 2000 
               
               
                   
                 65. 
                 00124.002 
                 09/697,718 
                 Oct. 27, 2000 
               
               
                   
                 66. 
                 00125.002 
                 09/702,840 
                 Nov. 1, 2000 
               
               
                   
                 67. 
                 00126.002 
                 09/703,932 
                 Nov. 2, 2000 
               
               
                   
                 68. 
                 00127.002 
                 09/704,559 
                 Nov. 3, 2000 
               
               
                   
                 69. 
                 00128.002 
                 09/704,542 
                 Nov. 3, 2000 
               
               
                   
                 70. 
                 00129.002 
                 09/708,092 
                 Nov. 8, 2000 
               
               
                   
                 71. 
                 00143.002 
                 09/726,578 
                 Dec. 1, 2000 
               
               
                   
                 72. 
                 00153.002 
                 09/769,525 
                 Jan. 26, 2001 
               
               
                   
                 73. 
                 00157.002 
                 09/774,806 
                 Feb. 1, 2001 
               
               
                   
                 74. 
                 00231.002 
                 09/870,652 
                 Jun. 1, 2001 
               
               
                   
                 75. 
                 91072.002 
                 09/878,974 
                 Jun. 13, 2001 
               
               
                   
                 76. 
                 00170.003 
                 10/082,096 
                 Feb. 26, 2002 
               
               
                   
                 77. 
                 00211.003 
                 10/086,239 
                 Mar. 4, 2002 
               
               
                   
                 78. 
                 00191.003 
                 10/095,465 
                 Mar. 13, 2002 
               
               
                   
                 79. 
                 00252.003 
                 10/106,718 
                 Mar. 27, 2002 
               
               
                   
                 80. 
                 80298.003 
                 10/123,111 
                 Apr. 17, 2002 
               
               
                   
               
            
           
         
       
     
     Through the applications listed above, the present application also claims priority under 35 USC § 119(e), § 119(a-d) and § 120 of the following applications, the entire contents of which are hereby incorporated by reference: 
                                             Client No.   Appln. No.   Filed                                                81.   91006.001   60/134,370   May 14, 1999       82.   00037.001   60/139,492   Jun. 17, 1999       83.   00038.001   60/139,763   Jun. 18, 1999       84.   00039.001   60/139,750   Jun. 18, 1999       85.   00042.001   60/139,817   Jun. 21, 1999       86.   00043.001   60/139,899   Jun. 22, 1999       87.   00042.002   60/140,353   Jun. 23, 1999       88.   00044.001   60/140,354   Jun. 23, 1999       89.   00046.001   60/140,823   Jun. 28, 1999       90.   00049.001   60/141,287   Jun. 30, 1999       91.   00059.001   60/142,977   Jul. 12, 1999       92.   00060.001   60/143,542   Jul. 13, 1999       93.   00061.001   60/143,624   Jul. 14, 1999       94.   00062.001   60/144,005   Jul. 15, 1999       95.   00064.001   60/144,325   Jul. 19, 1999       96.   00065.001   60/144,632   Jul. 20, 1999       97.   00066.001   60/144,814   Jul. 21, 1999       98.   00067.001   60/145,192   Jul. 22, 1999       99.   00069.001   60/145,218   Jul. 23, 1999       100.   00070.001   60/145,276   Jul. 26, 1999       101.   00071.001   60/145,913   Jul. 27, 1999       102.   00072.001   60/145,951   Jul. 28, 1999       103.   00073.001   60/146,386   Aug. 2, 1999       104.   00074.001   60/147,038   Aug. 3, 1999       105.   00076.001   60/147,204   Aug. 4, 1999       106.   00077.001   60/147,260   Aug. 5, 1999       107.   00079.001   60/147,416   Aug. 6, 1999       108.   00080.001   60/147,493   Aug. 9, 1999       109.   00081.001   60/148,319   Aug. 11, 1999       110.   00082.001   60/148,341   Aug. 12, 1999       111.   00083.001   60/148,565   Aug. 13, 1999       112.   00084.001   60/149,175   Aug. 17, 1999       113.   00085.001   60/149,426   Aug. 18, 1999       114.   00086.001   60/149,722   Aug. 20, 1999       115.   00087.001   60/149,723   Aug. 20, 1999       116.   00088.001   60/149,902   Aug. 23, 1999       117.   00089.001   60/150,566   Aug. 25, 1999       118.   00090.001   60/150,884   Aug. 26, 1999       119.   00091.001   60/151,080   Aug. 27, 1999       120.   00092.001   60/151,303   Aug. 30, 1999       121.   00093.001   60/151,438   Aug. 31, 1999       122.   00094.001   60/151,930   Sep. 1, 1999       123.   00095.001   60/152,363   Sep. 7, 1999       124.   00096.001   60/153,070   Sep. 10, 1999       125.   00098.001   60/153,758   Sep. 13, 1999       126.   00099.001   60/154,018   Sep. 15, 1999       127.   00101.001   60/154,039   Sep. 16, 1999       128.   00102.001   60/154,779   Sep. 20, 1999       129.   00103.001   60/155,139   Sep. 22, 1999       130.   00104.001   60/155,486   Sep. 23, 1999       131.   00105.001   60/155,659   Sep. 24, 1999       132.   00106.001   60/156,458   Sep. 28, 1999       133.   00107.001   60/156,596   Sep. 29, 1999       134.   00108.001   60/157,117   Oct. 4, 1999       135.   00109.001   60/157,753   Oct. 5, 1999       136.   00110.001   60/157,865   Oct. 6, 1999       137.   00111.001   60/158,029   Oct. 7, 1999       138.   00112.001   60/158,232   Oct. 8, 1999       139.   00113.001   60/158,369   Oct. 12, 1999       140.   00116.001   60/159,584   Oct. 18, 1999       141.   00119.001   60/160,741   Oct. 21, 1999       142.   00118.001   60/160,815   Oct. 21, 1999       143.   00120.001   60/160,980   Oct. 22, 1999       144.   00121.001   60/161,405   Oct. 25, 1999       145.   00122.001   60/161,361   Oct. 26, 1999       146.   00123.001   60/161,920   Oct. 28, 1999       147.   00124.001   60/162,143   Oct. 29, 1999       148.   00125.001   60/162,894   Nov. 1, 1999       149.   00126.001   60/163,093   Nov. 2, 1999       150.   00127.001   60/163,249   Nov. 3, 1999       151.   00128.001   60/163,379   Nov. 4, 1999       152.   00129.001   60/164,146   Nov. 8, 1999       153.   00131.001   60/164,544   Nov. 10, 1999       154.   00133.001   60/164,870   Nov. 12, 1999       155.   00132.001   60/164,961   Nov. 12, 1999       156.   00134.001   60/164,927   Nov. 15, 1999       157.   00135.001   60/165,669   Nov. 16, 1999       158.   00136.001   60/165,919   Nov. 17, 1999       159.   00137.001   60/166,157   Nov. 18, 1999       160.   00139.001   60/166,419   Nov. 19, 1999       161.   00140.001   60/166,733   Nov. 22, 1999       162.   00141.001   60/167,233   Nov. 24, 1999       163.   00142.001   60/167,904   Nov. 30, 1999       164.   00143.001   60/168,232   Dec. 1, 1999       165.   00144.001   60/168,546   Dec. 2, 1999       166.   00145.001   60/168,675   Dec. 3, 1999       167.   00147.001   60/169,298   Dec. 7, 1999       168.   00149.001   60/171,107   Dec. 16, 1999       169.   00153.001   60/178,547   Jan. 27, 2000       170.   00155.001   60/178,754   Jan. 28, 2000       171.   00157.001   60/179,395   Feb. 1, 2000       172.   00158.001   60/180,039   Feb. 3, 2000       173.   00159.001   60/180,206   Feb. 4, 2000       174.   00160.001   60/180,695   Feb. 7, 2000       175.   00161.001   60/181,228   Feb. 9, 2000       176.   00162.001   60/181,476   Feb. 10, 2000       177.   00163.001   60/182,477   Feb. 15, 2000       178.   00164.001   60/182,512   Feb. 15, 2000       179.   00165.001   60/183,166   Feb. 17, 2000       180.   00167.001   60/184,667   Feb. 24, 2000       181.   00168.001   60/185,118   Feb. 25, 2000       182.   00169.001   60/185,396   Feb. 28, 2000       183.   00170.001   60/186,283   Mar. 1, 2000       184.   00172.001   60/186,386   Mar. 2, 2000       185.   00171.001   60/186,390   Mar. 2, 2000       186.   00173.001   60/186,748   Mar. 3, 2000       187.   00174.001   60/187,378   Mar. 7, 2000       188.   00175.001   60/187,896   Mar. 8, 2000       189.   00177.001   60/188,187   Mar. 10, 2000       190.   00178.001   60/188,185   Mar. 10, 2000       191.   00179.001   60/189,080   Mar. 14, 2000       192.   00180.001   60/189,461   Mar. 15, 2000       193.   00181.001   60/189,953   Mar. 16, 2000       194.   00182.001   60/190,069   Mar. 20, 2000       195.   00183.001   60/190,545   Mar. 20, 2000       196.   00184.001   60/191,084   Mar. 22, 2000       197.   00185.001   60/191,543   Mar. 23, 2000       198.   00186.001   60/191,823   Mar. 24, 2000       199.   00187.001   60/192,421   Mar. 27, 2000       200.   00188.001   60/192,940   Mar. 29, 2000       201.   00189.001   60/193,244   Mar. 30, 2000       202.   00190.001   60/193,453   Mar. 31, 2000       203.   00191.001   60/194,404   Apr. 4, 2000       204.   00192.001   60/194,683   Apr. 5, 2000       205.   00193.001   60/194,874   Apr. 6, 2000       206.   00194.001   60/194,885   Apr. 6, 2000       207.   00195.001   60/195,283   Apr. 7, 2000       208.   00196.001   60/196,169   Apr. 11, 2000       209.   00197.001   60/196,487   Apr. 12, 2000       210.   00200.001   60/196,485   Apr. 12, 2000       211.   00201.001   60/197,687   Apr. 17, 2000       212.   00202.001   60/198,133   Apr. 17, 2000       213.   00203.001   60/198,386   Apr. 19, 2000       214.   00204.001   60/198,619   Apr. 20, 2000       215.   00206.001   60/198,767   Apr. 21, 2000       216.   00207.001   60/199,124   Apr. 24, 2000       217.   00208.001   60/199,828   Apr. 26, 2000       218.   00210.001   60/200,103   Apr. 27, 2000       219.   00211.001   60/201,275   May 2, 2000       220.   00212.001   60/201,740   May 4, 2000       221.   00213.001   60/202,112   May 5, 2000       222.   00214.001   60/202,914   May 9, 2000       223.   00215.001   60/202,919   May 9, 2000       224.   00216.001   60/202,968   May 10, 2000       225.   00217.001   60/203,457   May 11, 2000       226.   00219.001   60/203,916   May 12, 2000       227.   00220.001   60/204,388   May 15, 2000       228.   00221.001   60/204,568   May 16, 2000       229.   00222.001   60/204,830   May 17, 2000       230.   00223.001   60/205,201   May 18, 2000       231.   00224.001   60/205,242   May 19, 2000       232.   00225.001   60/205,572   May 22, 2000       233.   00226.001   60/206,316   May 23, 2000       234.   00227.001   60/206,553   May 24, 2000       235.   00228.001   60/207,367   May 26, 2000       236.   00229.001   60/207,239   May 26, 2000       237.   00230.001   60/207,452   May 30, 2000       238.   00231.001   60/208,329   Jun. 1, 2000       239.   00232.001   60/208,910   Jun. 5, 2000       240.   00233.001   60/208,921   Jun. 5, 2000       241.   00234.001   60/210,012   Jun. 8, 2000       242.   00235.001   60/210,670   Jun. 9, 2000       243.   00237.001   60/211,213   Jun. 13, 2000       244.   80274.001   60/211,540   Jun. 15, 2000       245.   80275.001   60/212,649   Jun. 19, 2000       246.   80276.001   60/212,713   Jun. 20, 2000       247.   80276.001   60/212,713   Jun. 20, 2000       248.   80278.001   60/213,220   Jun. 22, 2000       249.   00242.001   60/213,271   Jun. 22, 2000       250.   00248.001   60/214,534   Jun. 27, 2000       251.   80279.001   60/214,762   Jun. 27, 2000       252.   00249.001   60/214,800   Jun. 28, 2000       253.   00250.001   60/215,775   Jun. 30, 2000       254.   00252.001   60/216,361   Jul. 5, 2000       255.   00253.001   60/217,476   Jul. 11, 2000       256.   00254.001   60/219,004   Jul. 18, 2000       257.   00255.001   60/220,647   Jul. 25, 2000       258.   00256.001   60/220,484   Jul. 25, 2000       259.   80298.001   60/224,517   Aug. 14, 2000       260.   80300.001   60/225,303   Aug. 15, 2000       261.   80301.001   60/226,452   Aug. 21, 2000       262.   80307.001   60/227,024   Aug. 23, 2000       263.   80308.001   60/228,898   Aug. 30, 2000       264.   80309.001   60/230,430   Sep. 6, 2000       265.   80310.001   60/232,044   Sep. 13, 2000       266.   80311.001   60/232,858   Sep. 15, 2000       267.   80312.001   60/233,621   Sep. 18, 2000       268.   80313.001   60/234,179   Sep. 20, 2000       269.   80314.001   60/234,233   Sep. 21, 2000       270.   80315.001   60/234,968   Sep. 25, 2000       271.   80316.001   60/234,974   Sep. 25, 2000       272.   80317.001   60/234,949   Sep. 26, 2000       273.   80318.001   60/236,732   Oct. 2, 2000       274.   80319.001   60/237,379   Oct. 4, 2000       275.   80320.001   60/237,686   Oct. 5, 2000       276.   80321.001   60/238,473   Oct. 10, 2000       277.   80322.001   60/238,456   Oct. 10, 2000       278.   80323.001   60/239,091   Oct. 11, 2000       279.   80324.001   60/240,862   Oct. 17, 2000       280.   80325.001   60/241,368   Oct. 19, 2000       281.   80331.001   60/241,751   Oct. 20, 2000       282.   80332.001   60/242,065   Oct. 23, 2000       283.   80334.001   60/242,686   Oct. 24, 2000       284.   80335.001   60/242,705   Oct. 25, 2000       285.   80336.001   60/243,289   Oct. 26, 2000       286.   80337.001   60/243,398   Oct. 27, 2000       287.   80338.001   60/243,723   Oct. 30, 2000       288.   80339.001   60/244,691   Nov. 1, 2000       289.   80340.001   60/244,923   Nov. 2, 2000       290.   80341.001   60/245,164   Nov. 3, 2000       291.   80342.001   60/245,676   Nov. 6, 2000       292.   80343.001   60/246,732   Nov. 9, 2000       293.   80344.001   60/247,010   Nov. 13, 2000       294.   80346.001   60/247,050   Nov. 13, 2000       295.   80347.001   60/248,198   Nov. 15, 2000       296.   80348.001   60/249,256   Nov. 17, 2000       297.   80349.001   60/249,454   Nov. 20, 2000       298.   80350.001   60/252,464   Nov. 22, 2000       299.   80351.001   60/252,598   Nov. 24, 2000       300.   80352.001   60/253,722   Nov. 29, 2000       301.   80353.001   60/251,504   Dec. 7, 2000       302.   80354.001   60/251,853   Dec. 8, 2000       303.   80355.001   60/254,174   Dec. 11, 2000       304.   80356.001   60/256,503   Dec. 15, 2000       305.   80357.001   60/255,891   Dec. 18, 2000       306.   80359.001   60/258,880   Jan. 2, 2001       307.   80362.001   60/262,389   Jan. 19, 2001       308.   80363.001   60/264,026   Jan. 26, 2001       309.   80364.001   60/264,282   Jan. 29, 2001       310.   3001-55300-US-P-   60/266,468   Feb. 6, 2001           30946.01               311.   3001-55300-US-P-   60/267,425   Feb. 9, 2001           31053.01               312.   3001-55300-US-P-   60/267,707   Feb. 12, 2001           31070.01               313.   3001-55300-US-P-   60/269,890   Feb. 21, 2001           31112.01               314.   3001-55300-US-P-   60/269,892   Feb. 21, 2001           31130.01               315.   3001-55300-US-P-   60/271,724   Feb. 28, 2001           31162.01               316.   00170.002   09/795,347   Mar. 1, 2001       317.   3001-55300-US-P-   60/273,553   Mar. 7, 2001           31197.01               318.   00191.002   09/824,882   Apr. 4, 2001       319.   00211.002   09/845,206   May 1, 2001       320.   00252.002   09/898,064   Jul. 5, 2001       321.   80298.002   09/928,372   Aug. 14, 2001                    
Number 49
 
     Application Ser. No. 10/340,820 listed above is a continuation of application Ser. No. 10/132,287, filed on Apr. 26, 2002, the entire contents of which are hereby incorporated by reference. 
     Application Ser. No. 10/132,287 is a continuation-in-part of the following nonprovisional applications, to which the present application claims priority under 35 U.S.C. § 120, the entire contents of which are hereby incorporated by reference: 
     
       
         
           
               
               
               
               
               
             
               
                   
               
               
                   
                   
                 Client No. 
                 Appln. 
                 Filed 
               
               
                   
               
             
            
               
                   
                 1.  
                 91022.002 
                 09/790,663 
                 Feb. 23, 2001 
               
               
                   
                 2.  
                 91025.002  
                 09/795,359  
                 Mar. 1, 2001 
               
               
                   
                 3.  
                 91042.002  
                 09/824,790  
                 Apr. 4, 2001 
               
               
                   
                 4.  
                 91055.002  
                 09/845,311  
                 May 1, 2001 
               
               
                   
                 5.  
                 91068.002 
                 09/870,476  
                 Jun. 1, 2001 
               
               
                   
                 6.  
                 91072.002 
                 09/878,974 
                 Jun. 13, 2001 
               
               
                   
                 7.  
                 91081.003 
                 10/123,222 
                 Apr. 17, 2002 
               
               
                   
               
            
           
         
       
     
     Through the seven applications listed above, the present application also claims priority under 35 USC § 119(e) of the following applications, the entire contents of which are hereby incorporated by reference: 
     1. Appln. Ser. No. 09/790,663 filed Feb. 23, 2001 claims priority under 35 USC § 119(e) of the following provisional applications: 
                                                     Appln. No.   Filing Date                          a)   60/185,140   Feb. 25, 2000           b)   60/185,398   Feb. 28, 2000           c)   60/185,750   Feb. 29, 2000                        
2. Appln. Ser. No. 09/795,359 filed Mar. 1, 2001 claims priority under 35 USC § 119(e) of the following provisional applications:
 
                                                     Appln. No.   Filing Date                          a)   60/186,277   Mar. 1, 2000           b)   60/186,670   Mar. 3, 2000           c)   60/187,379    Mar. 7, 2000           d)   60/187,985    Mar. 9, 2000           e)   60/188,174    Mar. 10, 2000           f)   60/188,687    Mar. 13, 2000           g)   60/189,460    Mar. 15, 2000           h)   60/189,958    Mar. 16, 2000           i)   60/189,965   Mar. 17, 2000           j)   60/190,090    Mar. 20, 2000           k)   60/191,549   Mar. 23, 2000           l)   60/191,826    Mar. 24, 2000           m)   60/192,420   Mar. 27, 2000           n)   60/192,855    Mar. 29, 2000           o)   60/193,243    Mar. 30, 2000           p)   60/193,469    Mar. 31, 2000                        
3. Appln. Ser. No. 09/824,790 filed Apr. 4, 2001 claims priority under 35 USC § 119(e) of the following provisional applications:
 
                                                     Appln. No.   Filing Date                          a)   60/194,385   Apr. 4, 2000           b)   60/194,682   Apr. 5, 2000           c)   60/194,698   Apr. 5, 2000           d)   60/194,884   Apr. 6, 2000           e)   60/195,258   Apr. 7, 2000           f)   60/196,168   Apr. 11, 2000           g)   60/196,483   Apr. 12, 2000           h)   60/197,397   Apr. 14, 2000           i)   60/198,268   Apr. 17, 2000           j)   60/198,400   Apr. 19, 2000           k)   60/198,629   Apr. 20, 2000           l)   60/198,765   Apr. 21, 2000           m)   60/199,123   Apr. 24, 2000                        
4. Appln. Ser. No. 09/845,311 filed May 1, 2001 claims priority under 35 USC § 119(e) of the following provisional applications:
 
                                                     Appln. No.   Filing Date                          a)   60/200,885   May 1, 2000           b)   60/201,279   May 2, 2000           c)   60/201,751    May 4, 2000           d)   60/202,178    May 5, 2000           e)   60/202,915    May 9, 2000           f)   60/202,969    May 10, 2000           g)   60/203,458    May 11, 2000           h)   60/203,911    May 12, 2000           i)   60/204,395   May 15, 2000           j)   60/205,574    May 22, 2000           k)   60/206,988    May 25, 2000           l)   60/207,242    May 26, 2000           m)   60/207,291    May 30, 2000                        
5. Appln. Ser. No. 09/870,476 filed Jun. 1, 2001 claims priority under 35 USC § 119(e) of the following provisional applications:
 
                                                     Appln. No.   Filing Date                          a)   60/208,324   Jun. 1, 2000           b)   60/208,919   Jun. 5, 2000           c)   60/208,917   Jun. 5, 2000           d)   60/210,008   Jun. 8, 2000                        
6. Appln. Ser. No. 09/878,974 filed Jun. 13, 2001 claims priority under 35 USC § 119(e) of the following provisional applications:
 
                                                     Appln. No.   Filing Date                          a)   60/211,210   Jun. 13, 2000           b)   60/211,539   Jun. 15, 2000           c)   60/212,414   Jun. 19, 2000           d)   60/212,677   Jun. 20, 2000           e)   60/212,713   Jun. 20, 2000           f)   60/213,195   Jun. 22, 2000           g)   60/213,221   Jun. 22, 2000           h)   60/214,760   Jun. 27, 2000                        
7. Appln. Ser. No. 10/123,222 filed Apr. 17, 2002 is a continuation of application Ser. No. 09/902,093 filed Jul. 11, 2001 and claims priority under 35 USC § 119(e) of the following provisional applications:
 
                                                     Appln. No.    Filing Date                          a)   60/217,385    Jul. 11, 2000           b)   60/219,021    Jul. 18, 2000           c)   60/220,814    Jul. 25, 2000           d)   60/224,516    Aug. 14, 2000           e)   60/225,302    Aug. 15, 2000           f)   60/226,725    Aug. 21, 2000           g)   60/227,026    Aug. 23, 2000           h)   60/228,897    Aug. 30, 2000                        
Number 50
 
     Application No. 50 listed above is a continuation of application Ser. No. 10/281,347, filed on Oct. 28, 2002, the entire contents of which are hereby incorporated by reference. 
     Through application Ser. No. 10/281,347, the present application also claims priority of U.S. application Ser. No. 09/935,631 filed on Aug. 24, 2001, the entire contents of which are hereby incorporated by reference: 
     Through application Ser. No. 09/935,631, the present application claims priority under 35 USC § 119(e) of the following application, the entire contents of which are hereby incorporated by reference: 
     
       
         
           
               
               
               
             
               
                   
                   
               
               
                   
                 Filed 
                 Application No. 
               
               
                   
                   
               
             
            
               
                   
                 Aug. 25, 2000 
                 60/237,363 
               
               
                   
                   
               
            
           
         
       
     
     The entire contents of the applications listed in the table above are expressly incorporated herein by reference. 
    
    
     SEQUENCE LISTING 
     The patent or application file contains Sequence Listings. A Computer Readable Format (CRF) of the Sequence Listing entitled “2015-08-28_SEQUENCE_LISTING_2750-1575PUS4.txt” is submitted in the present application. 
     FIELD OF THE INVENTION 
     The present invention relates to over 100,000 isolated polynucleotides from plants that include a complete coding sequence, or a fragment thereof, that is expressed. In addition, the present invention relates to the polypeptide or protein corresponding to the coding sequence of these polynucleotides. The present invention also relates to isolated polynucleotides that represent regulatory regions of genes. The present invention also relates to isolated polynucleotides that represent untranslated regions of genes. The present invention further relates to the use of these isolated polynucleotides and polypeptides and proteins. 
     BACKGROUND OF THE INVENTION 
     There are more than 300,000 species of plants. They show a wide diversity of forms, ranging from delicate liverworts, adapted for life in a damp habitat, to cacti, capable of surviving in the desert. The plant kingdom includes herbaceous plants, such as corn, whose life cycle is measured in months, to the giant redwood tree, which can live for thousands of years. This diversity reflects the adaptations of plants to survive in a wide range of habitats. This is seen most clearly in the flowering plants (phylum Angiospermophyta), which are the most numerous, with over 250,000 species. They are also the most widespread, being found from the tropics to the arctic. 
     The process of plant breeding involving man&#39;s intervention in natural breeding and selection is some 20,000 years old. It has produced remarkable advances in adapting existing species to serve new purposes. The world&#39;s economics was largely based on the successes of agriculture for most of these 20,000 years. 
     Plant breeding involves choosing parents, making crosses to allow recombination of gene (alleles) and searching for and selecting improved forms. Success depends on the genes/alleles available, the combinations required and the ability to create and find the correct combinations necessary to give the desired properties to the plant. Molecular genetics technologies are now capable of providing new genes, new alleles and the means of creating and selecting plants with the new, desired characteristics. 
     When the molecular and genetic basis for different plant characteristics are understood, a wide variety of polynucleotides, both endogenous polynucleotides and created variants, polypeptides, cells, and whole organisms, can be exploited to engineer old and new plant traits in a vast range of organisms including plants. These traits can range from the observable morphological characteristics, through adaptation to specific environments to biochemical composition and to molecules that the plants (organisms) exude. Such engineering can involve tailoring existing traits, such as increasing the production of taxol in yew trees, to combining traits from two different plants into a single organism, such as inserting the drought tolerance of a cactus into a corn plant. Molecular and genetic knowledge also allows the creation of new traits. For example, the production of chemicals and pharmaceuticals that are not native to particular species or the plant kingdom as a whole. 
     The application reports the inventions Applicants have discovered to build a foundation of scientific understanding of plant genomes to achieve these aims. These inventions include polynucleotide and polypeptide sequences, and data relating to where and when the genes are differentially expressed and phenotypic observations resulting from either aberrant gene activation or disruption. How these data are transformed into a scientific understanding of plant biology and the control of traits from a genetic perspective also is explained by the instant application. Applications of these discoveries to create new prototypes and products in the field of chemical, pharmaceutical, food, feed, and fiber production are described herein as well. 
     The achievements described in this application were possible because of the results from a cluster of technologies, a genomic engine, depicted below in Schematic 1, that allows information on each gene to be integrated to provide a more comprehensive understanding of gene structure and function and the deployment of genes and gene components to make new products. 
     I. The Discoveries of the Instant Application 
     Applicants have isolated and identified over one hundred thousand genes, gene components and their products and thousands of promoters. Specific genes were isolated and/or characterized from  arabidopsis , soybean, maize, wheat and rice. These species were selected because of their economic value and scientific importance and were deliberately chosen to include representatives of the evolutionary divergent dicotyledonous and monocotyledonous groups of the plant kingdom. The number of genes characterized in this application represents a large proportion of all the genes in these plant species. 
     The techniques used initially to isolate and characterize most of the genes, namely sequencing of full-length cDNAs, were deliberately chosen to provide information on complete coding sequences and on the complete sequences of their protein products. 
     Gene components and products the Applicants have identified include exons, introns, promoters, coding sequences, antisense sequences, terminators and other regulatory sequences. The exons are characterized by the proteins they encode and  arabidopsis  promoters are characterized by their position in the genomic DNA relative to where mRNA synthesis begins and in what cells and to what extent they promote mRNA synthesis. 
     Further exploitation of molecular genetics technologies has helped the Applicants to understand the functions and characteristics of each gene and their role in a plant. Three powerful molecular genetics approaches were used to this end:
         (a) Analyses of the phenotypic changes when the particular gene sequence is interrupted or activated differentially; ( arabidopsis )   (b) Analyses of in what plant organs, to what extent, and in response to what environmental signals mRNA is synthesized from the gene; ( arabidopsis  and maize) and   (c) Analysis of the gene sequence and its relatives. (all species) These were conducted using the genomics engine depicted in  FIG. 1  that allows information on each gene to be integrated to provide a more comprehensive understanding of gene structure and function and linkage to potential products.       

     The species  arabidopsis  was used extensively in these studies for several reasons: (1) the complete genomic sequence, though poorly annotated in terms of gene recognition, was being produced and published by others and (2) genetic experiments to determine the role of the genes in planta are much quicker to complete. 
     The phenotypic tables, MA tables, and reference tables and sequence tables indicate the results of these analyses and thus the specific functions and characteristics that are ascribed to the genes and gene components and products. 
     II. Integration of Discoveries to Provide Scientific Understanding 
     From the discoveries made, Applicants have deduced the biochemical activities, pathways, cellular roles, and developmental and physiological processes that can be modulated using these components. These are discussed and summarized in sections based on the gene functions characteristics from the analyses and role in determining phenotypes. These sections illustrate and emphasize that each gene, gene component or product influences biochemical activities, cells or organisms in complex ways, from which there can be many phenotypic consequences. 
     An illustration of how the discoveries on gene structure, function, expression and phenotypic observation can be integrated together to understand complex phenotypes is provided in  FIG. 2 . This sort of understanding enables conclusions to be made as to how the genes, gene components and product are useful for changing the properties of plants and other organisms. This example also illustrates how single gene changes in, for example, a metabolic pathway can cause gross phenotypic changes. 
     Furthermore, the development and properties of one part of plant can be interconnected with other parts. The dependence of shoot and leaf development on root cells is a classic example. Here, shoot growth and development require nutrients supplied from roots, so the protein complement of root cells can affect plant development, including flowers and seed production. Similarly, root development is dependent on the products of photosynthesis from leaves. Therefore, proteins in leaves can influence root developmental physiology and biochemistry. 
     Thus, the following sections describe both the functions and characteristics of the genes, gene components and products and also the multiplicity of biochemical activities, cellular functions, and the developmental and physiological processes influenced by them. The sections also describe examples of commercial products that can be realized from the inventions. 
     A. Analyses to Reveal Function and In Vivo Roles of Single Genes in One Plant Species 
     The genomics engine has focused on individual genes to reveal the multiple functions or characteristics that are associated to each gene, gene components and products of the instant invention in the living plant. For example, the biochemical activity of a protein is deduced based on its similarity to a protein of known function. In this case, the protein may be ascribed with, for example, an oxidase activity. Where and when this same protein is active can be uncovered from differential expression experiments, which show that the mRNA encoding the protein is differentially expressed in response to drought and in seeds but not roots. The gene disruption experiments reveal that absence of the same protein causes embryo lethality. 
     Thus, this protein is characterized as a seed protein and drought-responsive oxidase that is critical for embryo viability. 
     B. Analyses to Reveal Function and Roles of Single Genes in Different Species 
     The genomics engine has also been used to extrapolate knowledge from one species to many plant species. For example, proteins from different species, capable of performing identical or similar functions, preserve many features of amino acid sequence and structure during evolution. Complete protein sequences have been compared and contrasted within and between species to determine the functionally vital domains and signatures characteristic of each of the proteins that is the subject of this application. Thus, functions and characteristics of  arabidopsis  proteins have been extrapolated to proteins containing similar domains and signatures of corn, soybean, rice and wheat and by implication to all other (plant) species. 
       FIG. 3  provides an example. Two proteins with related structures, one from corn, a monocot, and one from  arabidopsis , a dicot, have been concluded to be orthologs. The known characteristics of the  arabidopsis  protein (seed protein, drought responsive oxidase) can then be attributed to the corn protein. 
     C. Analyses Over Multiple Experiments to Reveal Gene Networks and Links Across Species 
     The genomics engine can identify networks or pathways of genes concerned with the same process and hence linked to the same phenotype(s). Genes specifying functions of the same pathway or developmental environmental responses are frequently co-regulated i.e. they are regulated by mechanisms that result in coincident increases or decreases for all gene members in the group. The Applicants have divided the genes of  arabidopsis  and maize into such co-regulated groups on the basis of their expression patterns and the function of each group has been deduced. This process has provided considerable insight into the function and role of thousands of the plant genes in diverse species included in this application. 
     D. Applications of Applicant&#39;s Discoveries 
     It will be appreciated while reading the sections that the different experimental molecular genetic approaches focused on different aspects of the pathway from gene and gene product through to the properties of tissues, organs and whole organisms growing in specific environments. For each endogenous gene, these pathways are delineated within the existing biology of the species. However, Applicants&#39; inventions allow gene components or products to be mixed and matched to create new genes and placed in other cellular contexts and species, to exhibit new combinations of functions and characteristics not found in nature, or to enhance and modify existing ones. For instance, gene components can be used to achieve expression of a specific protein in a new cell type to introduce new biochemical activities, cellular attributes or developmental and physiological processes. Such cell-specific targeting can be achieved by combining polynucleotides encoding proteins with any one of a large array of promoters to facilitate synthesis of proteins in a selective set of plant cells. This emphasizes that each gene, component and protein can be used to cause multiple and different phenotypic effects depending on the biological context. The utilities are therefore not limited to the existing in vivo roles of the genes, gene components, and gene products. 
     While the genes, gene components and products disclosed herein can act alone, combinations are useful to modify or modulate different traits. Useful combinations include different polynucleotides and/or gene components or products that have (1) an effect in the same or similar developmental or biochemical pathways; (2) similar biological activities; (3) similar transcription profiles; or (4) similar physiological consequences. 
     Of particular interest are the transcription factors and key factors in regulatory transduction pathways, which are able to control entire pathways, segments of pathways or large groups of functionally related genes. Therefore, manipulation of such proteins, alone or in combination is especially useful for altering phenotypes or biochemical activities in plants. Because interactions exist between hormone, nutrition, and developmental pathways, combinations of genes and/or gene products from these pathways also are useful to produce more complex changes. In addition to using polynucleotides having similar transcription profiles and/or biological activities, useful combinations include polynucleotides that may exhibit different transcription profiles but which participate in common or overlapping pathways. Also, polynucleotides encoding selected enzymes can be combined in novel ways in a plant to create new metabolic pathways and hence new metabolic products. 
     The utilities of the various genes, gene components and products of the Application are described below in the sections entitled as follows:
     I. Organ Affecting Genes, Gene Components, Products (Including Differentiation Function)
       I.A. Root Genes, Gene Components And Products
           I.A.1. Root Genes, Gene Components And Products   I.A.2. Root Hair Genes, Gene Components And Products   
           I.B. Leaf Genes, Gene Components And Products
           I.B.1. Leaf Genes, Gene Components And Products   I.B.2. Trichome Genes And Gene Components   I.B.3. Chloroplast Genes And Gene Components   
           I.C. Reproduction Genes, Gene Components And Products
           I.C.1. Reproduction Genes, Gene Components And Products   I.C.2. Ovule Genes, Gene Components And Products   I.C.3. Seed And Fruit Development Genes, Gene Components And Products   
           I.D. Development Genes, Gene Components And Products
           I.D.1. Imbibition and Germination Responsive Genes, Gene Components And Products   I.D.2. Early Seedling Phase Genes, Gene Components And Products   I.D.3. Size and Stature Genes, Gene Components And Products   I.D.4. Shoot-Apical Meristem Genes, Gene Components And Products   I.D.5. Vegetative-Phase Specific Responsive Genes, Gene Components And Products   
           
       II. Hormones Responsive Genes, Gene Components And Products
       II.A. Abscissic Acid Responsive Genes, Gene Components And Products   II.B. Auxin Responsive Genes, Gene Components And Products   II.C. Brassinosteroid Responsive Genes, Gene Components And Products   II.D. Cytokinin Responsive Genes, Gene Components And Products   II.E. Gibberellic Acid Responsive Genes, Gene Components And Products   
       III. Metabolism Affecting Genes, Gene Components And Products
       III.A. Nitrogen Responsive Genes, Gene Components And Products   III.B. Circadian Rhythm Responsive Genes, Gene Components And Products   III.C. Blue Light (Phototropism) Responsive Genes, Gene Components And Products   III.D. Co2 Responsive Genes, Gene Components And Products   III.E. Mitochondria Electron Transport Genes, Gene Components And Products   III.F. Protein Degradation Genes, Gene Components And Products   III.G. Carotenogenesis Responsive Genes, Gene Components And Products   
       IV. Viability Genes, Gene Components And Products
       IV.A. Viability Genes, Gene Components And Products   IV.B. Histone Deacetylase (Axel) Responsive Genes, Gene Components And Products   
       V. Stress Responsive Genes, Gene Components And Products
       V.A. Cold Responsive Genes, Gene Components And Products   V.B. Heat Responsive Genes, Gene Components And Products   V.C. Drought Responsive Genes, Gene Components And Products   V.D. Wounding Responsive Genes, Gene Components And Products   V.E. Methyl Jasmonate Responsive Genes, Gene Components And Products   V.F. Reactive Oxygen Responsive Genes, Gene Components And H2O2 Products   V.G. Salicylic Acid Responsive Genes, Gene Components And Products   V.H. Nitric Oxide Responsive Genes, Gene Components And Products   V.I. Osmotic Stress Responsive Genes, Gene Components And Products   V.J. Aluminum Responsive Genes, Gene Components And Products   V.K. Cadmium Responsive Genes, Gene Components And Products   V.L. Disease Responsive Genes, Gene Components And Products   V.M. Defense Responsive Genes, Gene Components And Products   V.N. Iron Responsive Genes, Gene Components And Products   V.O. Shade Responsive Genes, Gene Components And Products   V.P. Sulfur Responsive Genes, Gene Components And Products   V.Q. Zinc Responsive Genes, Gene Components And Products   
       VI. Enhanced Foods   VII. Pharmaceutical Products   VIII. Precursors Of Industrial Scale Compounds   IX. Promoters As Sentinels   

     SUMMARY OF THE INVENTION 
     The present invention comprises polynucleotides, such as complete cDNA sequences and/or sequences of genomic DNA encompassing complete genes, fragments of genes, and/or regulatory elements of genes and/or regions with other functions and/or intergenic regions, hereinafter collectively referred to as Sequence-Determined DNA Fragments (SDFs) or sometimes collectively referred to as “genes or gene components”, or sometimes as “genes, gene components or products,” from different plant species, particularly corn, wheat, soybean, rice and  Arabidopsis thaliana , and other plants and or mutants, variants, fragments or fusions of said SDFs and polypeptides or proteins derived therefrom. In some instances, the SDFs span the entirety of a protein-coding segment. In some instances, the entirety of an mRNA is represented. Other objects of the invention that are also represented by SDFs of the invention are control sequences, such as, but not limited to, promoters. Complements of any sequence of the invention are also considered part of the invention. 
     Other objects of the invention are polynucleotides comprising exon sequences, polynucleotides comprising intron sequences, polynucleotides comprising introns together with exons, intron/exon junction sequences, 5′ untranslated sequences, and 3′ untranslated sequences of the SDFs of the present invention. Polynucleotides representing the joinder of any exons described herein, in any arrangement, for example, to produce a sequence encoding any desirable amino acid sequence are within the scope of the invention. 
     The present invention also resides in probes useful for isolating and identifying nucleic acids that hybridize to an SDF of the invention. The probes can be of any length, but more typically are 12-2000 nucleotides in length; more typically, 15 to 200 nucleotides long; even more typically, 18 to 100 nucleotides long. 
     Yet another object of the invention is a method of isolating and/or identifying nucleic acids using the following steps:
         (a) contacting a probe of the instant invention with a polynucleotide sample under conditions that permit hybridization and formation of a polynucleotide duplex; and   (b) detecting and/or isolating the duplex of step (a).       

     The conditions for hybridization can be from low to moderate to high stringency conditions. The sample can include a polynucleotide having a sequence unique in a plant genome. Probes and methods of the invention are useful, for example, without limitation, for mapping of genetic traits and/or for positional cloning of a desired fragment of genomic DNA. 
     Probes and methods of the invention can also be used for detecting alternatively spliced messages within a species. Probes and methods of the invention can further be used to detect or isolate related genes in other plant species using genomic DNA (gDNA) and/or cDNA libraries. In some instances, especially when longer probes and low to moderate stringency hybridization conditions are used, the probe will hybridize to a plurality of cDNA and/or gDNA sequences of a plant. This approach is useful for isolating representatives of gene families which are identifiable by possession of a common functional domain in the gene product or which have common cis-acting regulatory sequences. This approach is also useful for identifying orthologous genes from other organisms. 
     The present invention also resides in constructs for modulating the expression of the genes comprised of all or a fragment of an SDF. The constructs comprise all or a fragment of the expressed SDF, or of a complementary sequence. Examples of constructs include ribozymes comprising RNA encoded by an SDF or by a sequence complementary thereto, antisense constructs, constructs comprising coding regions or parts thereof, constructs comprising promoters, introns, untranslated regions, scaffold attachment regions, methylating regions, enhancing or reducing regions, DNA and chromatin conformation modifying sequences, etc. Such constructs can be constructed using viral, plasmid, bacterial artificial chromosomes (BACs), plasmid artificial chromosomes (PACs), autonomous plant plasmids, plant artificial chromosomes or other types of vectors and exist in the plant as autonomous replicating sequences or as DNA integrated into the genome. When inserted into a host cell the construct is, preferably, functionally integrated with, or operatively linked to, a heterologous polynucleotide. For instance, a coding region from an SDF might be operably linked to a promoter that is functional in a plant. 
     The present invention also resides in host cells, including bacterial or yeast cells or plant cells, and plants that harbor constructs such as described above. Another aspect of the invention relates to methods for modulating expression of specific genes in plants by expression of the coding sequence of the constructs, by regulation of expression of one or more endogenous genes in a plant or by suppression of expression of the polynucleotides of the invention in a plant. Methods of modulation of gene expression include without limitation (1) inserting into a host cell additional copies of a polynucleotide comprising a coding sequence; (2) modulating an endogenous promoter in a host cell; (3) inserting antisense or ribozyme constructs into a host cell and (4) inserting into a host cell a polynucleotide comprising a sequence encoding a variant, fragment, or fusion of the native polypeptides of the instant invention. 
    
    
     
       BRIEF DESCRIPTION OF THE DRAWINGS 
         FIG. 1  is a genomics engine with five different sorts of technologies deployed to discover functions of the genes. 
         FIG. 2  illustrates genes A, B, C and D being activated by internal stimuli and then their mRNA transcripts translated into proteins. 
         FIG. 3  is an integration of data across species to link gene products and phenotypes. 
         FIG. 4  shows the regions of the Maximum Length Sequence, including the 5′ and 3′ UTRs as well as the coding sequence of the Maximum Length Sequence. 
         FIG. 5  shows possible transcription profiles over time of mRNA from plants as exposed to drought conditions. 
         FIG. 6  shows expression pattern of a cell wall synthesis gene, cDNAID 1595707, during fruit development of  Arabidopsis.    
         FIG. 7  shows the different regions of a typical gene. 
     
    
    
     DETAILED DESCRIPTION OF THE INVENTION 
     I. Description of the Tables 
     As noted above, the Applicants have obtained and analyzed an extensive amount of information on a large number of genes by use of the Ceres Genomic Engine to determine. This information can be categorized into three basic types:
         A. Sequence Information for the Inventions   B. Transcriptional Information for the Inventions   C. Phenotypic Information for the Inventions       

     I.A. Sequence Information 
     To harness the potential of the plant genome, Applicants began by elucidating a large number gene sequences, including the sequences of gene components and products, and analyzing the data. The list of sequences and associated data are presented in the Reference and Sequence Tables of the present application (sometimes referred to as the “REF” and “SEQ” Tables). The Reference and Sequence tables include:
         cDNA sequence;   coding sequence;   5′ &amp; 3′ UTR;   transcription start sites;   exon and intron boundaries in genomic sequence; and   protein sequence.       

     The Reference and Sequence Tables also include computer-based, comparative analyses between the protein sequences of the invention and sequences with known function. Proteins with similar sequences typically exhibit similar biochemical activities. The Reference table notes:
         sequences of known function that are similar to the Applicants&#39; proteins; and   biochemical activity that is associated with Applicants&#39; proteins.       

     Also, by analyzing the protein sequences, Applicants were able to group the protein sequences into groups, wherein all the sequences in the group contain a signature sequence. The groups are presented in the Protein Group Table. The signature sequences are reported in the Protein Group Table. More detailed analyses of the signature sequences are shown in the Protein Group Matrix Table. 
     To identify gene components and products, Applicants took a cDNA/coding sequence approach. That is, Applicants initiated their studies either by isolating cDNAs and determining their sequences experimentally, or by identifying the coding sequence from genomic sequence with the aid of predictive algorithms. The cDNA sequences and coding sequences also are referred to as “Maximum Length Sequences” in the Reference tables. The cDNA and coding sequences were given this designation to indicate these were the maximum length of coding sequences identified by Applicants. 
     Due to this cDNA/coding sequence focus of the present application, the Reference and Sequence Tables were organized around cDNA and coding sequences. Each of these Maximum Length Sequences was assigned a unique identifier: Ceres Sequence ID NO, which is reported in the Tables. 
     All data that relate to these Maximum Length Sequences are grouped together, including 5′ &amp; 3′ UTRs; transcription start sites; exon and intron boundaries in genomic sequence; protein sequence, etc. 
     Below, a more detailed explanation of the organization of the Reference and Sequence Tables and how the data in the tables were generated is provided.
         a. cDNA       

     Applicants have ascertained the sequences of mRNAs from different organisms by reverse transcription of mRNA to DNA, which was cloned and then sequenced. These complementary DNA or cDNA sequences also are referred to as Maximum Length Sequences in the Reference Tables, which contain details on each of the sequences in the Sequence Tables. 
     Each sequence was assigned a Pat. Appln. Sequence ID NO: and an internal Ceres Sequence ID NO: as reported in the Reference Table, the section labeled “(Ac) cDNA Sequence.” An example is shown below:
         Max Len. Seq.:   (Ac) cDNA Sequence
           Pat. Appln. Sequence ID NO: 174538   Ceres Sequence ID NO: 5673127   
               

     Both numbers are included in the Sequence Table to aid in tracking of information, as shown below: 
     
       
         
           
               
               
            
               
                 &lt;210&gt; 174538 (Pat. Appln. Sequence ID NO:) 
                   
               
               
                 &lt;211&gt; 1846 
               
               
                 &lt;212&gt; DNA (genomic) 
               
               
                 &lt;213&gt;  Arabidopsis thaliana   
               
               
                   
               
               
                 &lt;220&gt; 
               
               
                 &lt;221&gt; misc_feature 
               
               
                 &lt;222&gt; (1) . . . (1846) 
               
               
                 &lt;223&gt; Ceres Seq. ID no. 5673127 
               
               
                   
               
               
                 &lt;220&gt; 
               
               
                 &lt;221&gt; misc_feature 
               
               
                 &lt;222&gt; () . . . () 
               
               
                 &lt;223&gt; n is a, c, t, g, unknown, or other 
               
               
                   
               
               
                 &lt;400&gt; 174538 
               
            
           
           
               
               
               
            
               
                 acaagaacaa caaaacagag gaagaagaag aagaagatga agcttctggc tctgtttcca 
                 60 
                   
               
               
                   
               
               
                 tttctagcga tcgtgatcca actcagctgt . . . etc. (SEQ ID NO: 200513) 
                   
               
            
           
         
       
     
     The Sequence and Reference Tables are divided into sections by organism:  Arabidopsis thaliana, Brassica napus, Glycine max, Zea mays, Triticum aestivum ; and  Oryza sativa.    
     b. Coding Sequence 
     The coding sequence portion of the cDNA was identified by using computer-based algorithms and comparative biology. The sequence of each coding sequence of the cDNA is reported in the “PolyP Sequence” section of the Reference Tables, which are also divided into sections by organism. An example is shown below for the peptides that relate to the cDNA sequence above. 
     PolyP Sequence 
     
         
         
           
             Pat. Appln. Sequence ID NO 174539 
             Ceres Sequence ID NO 5673128 
             Loc. Sequence ID NO 174538: @ 1 nt. 
             Loc. Sig. P. Sequence ID NO 174539: @ 37 aa.
 
The polypeptide sequence can be found in the Sequence Tables by either the Pat. Appln. Sequence ID NO or by the Ceres Sequence ID NO: as shown below:
 
           
         
       
    
     
       
         
           
               
            
               
                 &lt;210&gt; 174539 (Pat. Appln. Sequence ID NO) 
               
               
                 &lt;211&gt; 443 
               
               
                 &lt;212&gt; PRT 
               
               
                 &lt;213&gt;  Arabidopsis thaliana   
               
               
                   
               
               
                 &lt;220&gt; 
               
               
                 &lt;221&gt; peptide 
               
               
                 &lt;222&gt; (1) . . . (443) 
               
               
                 &lt;223&gt; Ceres Seq. ID no. 5673128 
               
               
                   
               
               
                 &lt;220&gt; 
               
               
                 &lt;221&gt; misc_feature 
               
               
                 &lt;222&gt; () . . . () 
               
               
                 &lt;223&gt; xaa is any aa, unknown or other 
               
               
                   
               
               
                 &lt;400&gt; 174539 
               
               
                 Thr Arg Thr Thr Lys Gln Arg Lys Lys Lys Lys Lys 
               
               
                 1        5            10      15 
               
               
                   
               
               
                 Met Lys Leu Leu Ala Leu Phe Pro Phe Leu Ala 
               
               
                                 25 
               
               
                   
               
               
                 Ile . . . etc. (SEQ ID NO: 200514) 
               
            
           
         
       
     
     The PolyP section also indicates where the coding region begins in the Maximum Length Sequence. More than one coding region may be indicated for a single polypeptide due to multiple potential translation start codons. Coding sequences were identified also by analyzing genomic sequence by predictive algorithms, without the actual cloning of a cDNA molecule from a mRNA. By default, the cDNA sequence was considered the same as the coding sequence, when Maximum Length Sequence was spliced together from a genomic annotation. 
     c. 5′ and 3′ UTR 
     The 5′ UTR can be identified as any sequence 5′ of the initiating codon of the coding sequence in the cDNA sequence. Similarly, the 3′ UTR is any sequence 3′ of the terminating codon of the coding sequence. 
     d. Transcription Start Sites 
     Applicants cloned a number of cDNAs that encompassed the same coding sequence but comprised 5′ UTRs of different lengths. These different lengths revealed the multiple transcription start sites of the gene that corresponded to the cDNA. These multiple transcription start sites are reported in the “Sequence # w. TSS” section” of the Reference Tables. 
     e. Exons &amp; Introns 
     Alignment of the cDNA sequences and coding portions to genomic sequence permitted Applicants to pinpoint the exon/intron boundaries. These boundaries are identified in the Reference Table under the “Pub gDNA” section. That section reports the gi number of the public BAC sequence that contains the introns and exons of interest. An example is shown below:
         Max Len. Seq.:   Pub gDNA:
           gi No: 1000000005   Gen. seq. in cDNA:
               115777 . . . 115448 by Method #1   115105 . . . 114911 by Method #1   114822 . . . 114700 by Method #1   114588 . . . 114386 by Method #1   114295 . . . 113851 by Method #1   115777 . . . 115448 by Method #2   115105 . . . 114911 by Method #2   114822 . . . 114700 by Method #2   114588 . . . 114386 by Method #2   114295 . . . 113851 by Method #2   115813 . . . 115448 by Method #3   115105 . . . 114911 by Method #3   114822 . . . 114700 by Method #3   114588 . . . 114386 by Method #3   114295 . . . 113337 by Method #3   
               
           (Ac) cDNA Sequence       

     All the gi numbers were assigned by Genbank to track the public genomic sequences except:
         gi 1000000001   gi 1000000002   gi 1000000003   gi 1000000004; and   gi 1000000005.       

     These gi numbers were assigned by Applicants to the five  Arabidopsis  chromosome sequences that were published by the Institute of Genome Research (TIGR). Gi 1000000001 corresponds to chromosome 1, Gi 1000000002 to chromosome 2, etc. 
     The method of annotation is indicated as well as any similar public annotations. 
     f. Promoters &amp; Terminators 
     Promoter sequences are 5′ of the translational start site in a gene; more typically, 5′ of the transcriptional start site or sites. Terminator sequences are 3′ of the translational terminator codon; more typically, 3′ of the end of the 3′ UTR. 
     For even more specifics of the Reference and Sequence Tables, see the section below titled “Brief Description of the Tables.” 
     I.B. Transcriptional (Differential Expression) Information-Introduction to Differential Expression Data &amp; Analyses 
     A major way that a cell controls its response to internal or external stimuli is by regulating the rate of transcription of specific genes. For example, the differentiation of cells during organogenensis into forms characteristic of the organ is associated with the selective activation and repression of large numbers of genes. Thus, specific organs, tissues and cells are functionally distinct due to the different populations of mRNAs and protein products they possess. Internal signals program the selective activation and repression programs. For example, internally synthesized hormones produce such signals. The level of hormone can be raised by increasing the level of transcription of genes encoding proteins concerned with hormone synthesis. 
     To measure how a cell reacts to internal and/or external stimuli, individual mRNA levels can be measured and used as an indicator for the extent of transcription of the gene. Cells can be exposed to a stimulus, and mRNA can be isolated and assayed at different time points after stimulation. The mRNA from the stimulated cells can be compared to control cells that were not stimulated. The mRNA levels of particular Maximum Length Sequences that are higher in the stimulated cell versus the control indicate a stimulus-specific response of the cell. The same is true of mRNA levels that are lower in stimulated cells versus the control condition. Similar studies can be performed with cells taken from an organism with a defined mutation in their genome as compared with cells without the mutation. Altered mRNA levels in the mutated cells indicate how the mutation causes transcriptional changes. These transcriptional changes are associated with the phenotype that the mutated cells exhibit that is different from the phenotype exhibited by the control cells. 
     Applicants have utilized microarray techniques to measure the levels of mRNAs in cells from mutant plants, stimulated plants, and/or selected from specific organs. The differential expression of various genes in the samples versus controls are listed in the MA_diff Tables. Applicants have analyzed the differential data to identify genes whose mRNA transcription levels are positively correlated. From these analyses, Applicants were able to group different genes together whose transcription patterns are correlated. The results of the analyses are reported in the MA_clust Tables. 
     a. Experimental Detail 
     A microarray is a small solid support, usually the size of a microscope slide, onto which a number of polynucleotides have been spotted onto or synthesized in distinct positions on the slide (also referred to as a chip). Typically, the polynucleotides are spotted in a grid formation. The polynucleotides can either be Maximum Length Sequences or shorter synthetic oligonucleotides, whose sequence is complementary to specific Maximum Length Sequence entities. A typical chip format is as follows: 
     
       
         
           
               
               
               
               
             
               
                   
               
             
            
               
                   
                 Oligo #1 
                 Oligo #2 
                 Oligo #3 
               
               
                   
                 Oligo #4 
                 Oligo #5 
                 Oligo #6 
               
               
                   
                 Oligo #7 
                 Oligo #8 
                 Oligo #9 
               
               
                   
               
            
           
         
       
     
     For Applicants&#39; experiments, samples were hybridized to the chips using the “two-color” microarray procedure. A fluorescent dye was used to label cDNA reverse-transcribed from mRNA isolated from cells that had been stimulated, mutated, or collected from a specific organ or developmental stage. A second fluorescent dye of another color was used to label cDNA prepared from control cells. 
     The two differentially-labeled cDNAs were mixed together. Microarray chips were incubated with this mixture. For Applicants&#39; experiments the two dyes that are used are Cy3, which fluoresces in the red color range, and Cy5, which fluoresces in the green/blue color range. Thus, if:
         cDNA#1 binds to Oligo #1;   cDNA#1 from the sample is labeled red;   cDNA#1 from the control is labeled green, and   cDNA#1 is in both the sample and control,
 
then cDNA#1 from both the sample and control will bind to Oligo#1 on the chip. If the sample has 10 times more cDNA#1 than the control, then 10 times more of the cDNA#1 would be hybridized to Oligo#1. Thus, the spot on the chip with Oligo#1 spot would look red.
       

                                                Oligo #1   Oligo #2   Oligo #3           Oligo #4   Oligo #5   Oligo #6           Oligo #7   Oligo #8   Oligo #9                    
If the situation were reversed, the spot would appear green. If the sample has approximately the same amount of cDNA#1 as the control, then the Oligo#1 spot on the chip would look yellow. These color differentials are measured quantitatively and used to deduce the relative concentration of mRNAs from individual genes in particular samples.
 
     b. MA_Diff Data Table 
     To generate data, Applicants labeled and hybridized the sample and control mRNA in duplicate experiments. One chip was exposed to a mixture of cDNAs from both a sample and control, where the sample cDNA was labeled with Cy3, and the control was labeled with Cy5 dye. For the second labeling and chip hybridization experiments, the fluorescent labels were reversed; that is, the Cy5 dye for the sample, and the Cy3 dye for the control. 
     Whether Cy5 or Cy3 was used to label the sample, the fluorescence produced by the sample was divided by the fluorescence of the control. A cDNA was determined to be differentially expressed in response to the stimulus in question if a statistically-significantly ration difference in the sample versus the control was measured by both chip hybridization experiments. 
     The MA_diff tables show which cDNA were significantly up-regulated as designated by a “+” and which were significantly down-regulated as designated by a “−” for each pair of chips using the same sample and control. 
     I.C. Phenotypic Information 
     One means of determining the phenotypic effect of a gene is either to insert extra active copies of the gene or coding sequence, or to disrupt an existing copy of the gene in a cell or organism and measure the effects of the genetic change on one or more phenotypic characters or traits. “Knock-in” is used herein to refer to insertion of additional active copies of a gene or coding sequence. “Knock-out” refers to a plant where an endogenous gene(s) is disrupted. Applicants have used both methods of addition or disruption to determine the phenotypic effects of gene or gene components or products, and have thereby discovered the function of the genes and their utilities. 
     1. Knock-In Results 
     The coding sequence of a desired protein can be functionally linked to a heterologous promoter to facilitate expression. Here, Applicants have operably linked a number of coding sequences to either one of the promoters listed below: 
     
       
         
           
               
               
               
             
               
                   
               
               
                   
                 Specific Promoter 
                 Plant Line  
               
               
                 GFP Pattern 
                 activity 
                 Descriptor 
               
               
                   
               
             
            
               
                 Root epidermis/mostly toward the lower 
                 Specific to the root basal  
                 Root basal 
               
               
                 region of root (more intense than CS9094) 
                 region. 
                   
               
               
                 Root-endodermis/cortex (initials sharp); 
                 Specific to the root 
                 Root/Petiole/ 
               
               
                 shoot-mesophyll of one leaf, sharp guard cell 
                 endodermis-cortex 
                 Flowers 
               
               
                 marking. New leaf petioles near tip of 
                 region, leaf petiole, and 
                   
               
               
                 primary inflorescence; floral stems; in 
                 flowers. 
                   
               
               
                 flowers at base of sepal, anther stems, and 
                   
                   
               
               
                 pistil 
                   
                   
               
               
                 Broad root exp. (some dermal, some cortical, 
                 Specific to root and stem. 
                 Root/Stem1 
               
               
                 some vascular); shoot apex. Faintly in 
                   
                   
               
               
                 petiole; stem 
                   
                   
               
               
                 High expression in stem, excluded from 1st 
                 Specific to stem and root. 
                 Root/Stem2 
               
               
                 true leaves/High in root. Faint expression in 
                   
                   
               
               
                 stem 
                   
                   
               
               
                 Shoot meristem/whole root region; little bit  
                 Specific to roots, shoot 
                 Root/Stem/ 
               
               
                 on cotyledons. Base of leaves(axillary 
                 meristem, base of leaves 
                 Leaves/Flowers 
               
               
                 meristem?); base of sepals; inflorescence 
                 and flowers. 
                   
               
               
                 meristem; small amount in unfertilized pistil. 
                   
                   
               
               
                 root tip vascular initials; vascular system 
                 Specific to vascular 
                 Vascular/Ovule/ 
               
               
                 throughout plant; Bud petal vasculature and 
                 systems. 
                 Young Seed/ 
               
               
                 pistil septum; Flower petal vascualture; 
                   
                 Embryo 
               
               
                 Flower pistil septum; Pre fertilization ovules; 
                   
                   
               
               
                 Post fertilization ovule at chalazal end; 
                   
                   
               
               
                 Developing seed (young, maturing siliques); 
                   
                   
               
               
                 Seed coat and young embryos. GFP not 
                   
                   
               
               
                 observed in mature embryos. 
                   
                   
               
               
                 Flower, sepal/vascular tissue of root, stem,  
                 Specific to flowers, seed  
                 Flowers/Seed/ 
               
               
                 and cotyledons. Stems of new flowers; 
                 and vasculature. 
                 Vasculature/ 
               
               
                 vasculature or petals, anthers, sepals, and 
                   
                 Embryo 
               
               
                 pistil/silique; Vasculature throughtout 
                   
                   
               
               
                 seedling: root, hypocotyl, petioles, stem, 
                   
                   
               
               
                 cotyledons, first true leaves; Rosette 
                   
                   
               
               
                 vasculature; Cauline leaf vasculature; Bud 
                   
                   
               
               
                 pedicel vasculature; Flower vasculature: 
                   
                   
               
               
                 (sepals, petals, filaments, pistil); Bud 
                   
                   
               
               
                 vasculature (sepal, petal, filament, pistil); 
                   
                   
               
               
                 Funiculus in both flower and bud; Some 
                   
                   
               
               
                 possible seed coat expression; Silique 
                   
                   
               
               
                 funiculus; Very faint fluorescence in mature 
                   
                   
               
               
                 embryo (auto fluorescence perhaps); 
                   
                   
               
               
                 Root expression-primarily in cortex (upper 
                 Specific to root. 
                 Roots2 
               
               
                 refion of the root). No shoot expression 
                   
                   
               
               
                 Root expression-less intense in whole root 
                 Specific to root and shoot 
                 Root/SAM 
               
               
                 of young seedling. Shoot apical meristem; 
                 apical meristem. 
                   
               
               
                 organ primordia in SAM region. 
                   
                   
               
               
                 Root epidermis/tip; shoot epidermis/vascular;  
                 Specific to seed and to 
                 Seed/Epidermis/ 
               
               
                 leaf epidermis; expression in developing 
                 epidermal layers of roots, 
                 Ovary/Fruit 
               
               
                 seed/ovule-mature embryo; Primary and 
                 shoots and leaves. 
                   
               
               
                 lateral root cortex; Very strong in root cap; 
                   
                   
               
               
                 Base of flower bud and epidermis of carpels; 
                   
                   
               
               
                 Base of flower, epidermis of filaments, 
                   
                   
               
               
                 epidermis of carpels; Trichomes; Weak 
                   
                   
               
               
                 (hardly detectable) gfp expression in 
                   
                   
               
               
                 vasculature throughout seedling; Strong 
                   
                   
               
               
                 expression in trichomes; POST- fertilization 
                   
                   
               
               
                 SEED only; GFP strength increases as 
                   
                   
               
               
                 silique matures; Weak at suspensor end of 
                   
                   
               
               
                 the embryo; GFP observed in seed coat; Root 
                   
                   
               
               
                 and post fertilization seed specific gfp 
                   
                   
               
               
                 expression; Expression in seed coat. 
                   
                   
               
               
                 Young root dermis; dermal/cortical?/vascular 
                 Specific to roots, shoots,  
                 Roots/Shoots/ 
               
               
                 in older root; general (epidermal?) shoot 
                 and ovules. 
                 Ovule 
               
               
                 expression; ovules. some in sepals; 
                   
                   
               
               
                 vasculature of stem 
                   
                   
               
               
                 Vascular tissue of root; Meristem tissues: 
                 Specific to root structural 
                 Vasculature/ 
               
               
                 axillary meristems, floral meristems, base of 
                 leaf vascular region and 
                 Meristem 
               
               
                 flowers/sepals; Weak expression in 
                 to floral buds and axillary 
                   
               
               
                 hypocotyl, petiole and cotyledon vasculature. 
                 meristem 
               
               
                   
               
            
           
         
       
     
     The chimeric constructs were transformed into  Arabidopsis thaliana . The resulting transformed lines were screened to determine what phenotypes were changed due to introduced transgene. The phenotype changes, relative to the control, are reported in the Knock-in tables. 
     2. Knock-Out Results 
     Knock-out plants in  Arabidopsis thaliana  were created by inserting a polynucleotide tag into the genome. The location of the tag was identified using primers to the tag sequence and isolation of the plant genomic sequence that flanks the tag using a variation of the polymerase chain reaction. The plants were generated using the procedure described in Feldmann et al., (1987) Molec. Gen. Genet. 208: 1-9; Feldmann (1991) Plant Journal, 1:71-83 and Forsthoefel et al., (1992) Aust. J. Plant Physiol. 19:353-366. On average, the population of plants that was screened had ˜1.5 to 2 tags. Generally, the number of tags ranged from 1 to greater than 5. 
     The polynucleotide tags were classified as either incorporated within a gene, or between two genes. The data in the Knock-out Table indicates which plants have a tag(s) causing a disruption in a gene, or a disruption between genes. 
     a. Disruption in a Gene 
     For the sake of this analysis, the tag was considered to be causing a disruption in a gene when the tag was located:
         1) less than 501 upstream of the transcriptional start site;   2) less than 701 upstream of the translational initiation codon;   3) between the translational initiation and termination codons of the gene,   4) less than 301 downstream of the translational stop codon; or   5) less than 151 downstream of a transcriptional termination site.       

     By this definition, a tag can be inserted in two genes. For example, if two genes have only 700 nucleotides between the translational termination codon of one gene and the translational initiation codon of the other gene, the tag can be inserted into the terminator of one gene and the promoter of the other gene according to the definition above. 
     Genomic annotations by the method OCKHAM-OCDNA identify the transcriptional start and stop site of a gene. 
     b. Disruption Between Genes 
     When a tag causes a disruption between two genes, either or both genes can be affected. Typically, a tag can affect a gene if it disrupts the genome at a location 3000 nt downstream to the start codon of a gene. More typically, insertions found 1000-2000 nt upstream (5′), or 750-1000 nt downstream (3′) could be expected to disrupt expression. 
     c. More than One Insert 
     A plant can have multiple tags. If a mutant phenotype is observed, then it can be attributed to any one or all of the tags. 
     I.D. Brief Description of the Figures and Individual Tables 
     Figures 
     
         
         
           
             1.  FIG. 1  illustrates the Genomics Engine used by Applicants and depicts how gene sequences were determined using five different types of technologies. 
             2.  FIG. 2  illustrates how genes are activated by internal stimuli and protein is produced from them. 
             3.  FIG. 3  illustrates the integration of data across species to link gene products and phenotypes. 
             4.  FIG. 4  illustrates the regions found in a typical MLS. 
             5.  FIG. 5  is a graph illustrating how the genes, gene components and products were classified as either early or late responders following a specific treatment. 
             6.  FIG. 6  shows expression pattern of a cell wall synthesis gene, cDNAID 1595707, during fruit development. 
             7.  FIG. 7  shows the different regions of a typical gene.
 
Tables
 
Reference and Sequence Tables
 
           
         
       
    
     The sequences of exemplary SDFs and polypeptides corresponding to the coding sequences of the instant invention are described in the Reference and Sequence Tables (sometimes referred to as the REF and SEQ Tables. The Reference Table refers to a number of “Maximum Length Sequences” or “MLS.” Each MLS corresponds to the longest cDNA obtained, either by cloning or by the prediction from genomic sequence. The sequence of the MLS is the cDNA sequence as described in the Av subsection of the Reference Table. 
     The Reference Table includes the following information relating to each MLS:
         I. cDNA Sequence
           A. 5′ UTR   B. Coding Sequence   C. 3′ UTR   
           II. Genomic Sequence
           A. Exons   B. Introns   C. Promoters   
           III. Link of cDNA Sequences to Clone IDs   IV. Multiple Transcription Start Sites   V. Polypeptide Sequences
           A. Signal Peptide   B. Domains   C. Related Polypeptides   
           VI. Related Polynucleotide Sequences       

     I. cDNA Sequence 
     The Reference Table indicates which sequence in the Sequence Table represents the sequence of each MLS. The MLS sequence can comprise 5′ and 3′ UTR as well as coding sequences. In addition, specific cDNA clone numbers also are included in the Reference Table when the MLS sequence relates to a specific cDNA clone. 
     A. 5′ UTR 
     The location of the 5′ UTR can be determined by comparing the most 5′ MLS sequence with the corresponding genomic sequence as indicated in the Reference Table. The sequence that matches, beginning at any of the transcriptional start sites and ending at the last nucleotide before any of the translational start sites corresponds to the 5′ UTR. 
     B. Coding Region 
     The coding region is the sequence in any open reading frame found in the MLS. Coding regions of interest are indicated in the PolyP SEQ subsection of the Reference Table. 
     C. 3′ UTR 
     The location of the 3′ UTR can be determined by comparing the most 3′ MLS sequence with the corresponding genomic sequence as indicated in the Reference Table. The sequence that matches, beginning at the translational stop site and ending at the last nucleotide of the MLS corresponds to the 3′ UTR. 
     II. Genomic Sequence 
     Further, the Reference Table indicates the specific “gi” number of the genomic sequence if the sequence resides in a public databank. For each genomic sequence, Reference tables indicate which regions are included in the MLS. These regions can include the 5′ and 3′ UTRs as well as the coding sequence of the MLS. See, for example,  FIG. 4 . 
     The Reference Table reports the first and last base of each region that are included in an MLS sequence. An example is shown below:
         gi No. 47000:   37102 . . . 37497   37593 . . . 37925       

     The numbers indicate that the MLS contains the following sequences from two regions of gi No. 47000; a first region including bases 37102-37497, and a second region including bases 37593-37925. 
     A. Exon Sequences 
     The location of the exons can be determined by comparing the sequence of the regions from the genomic sequences with the corresponding MLS sequence as indicated by the Reference Table. 
     i. Initial Exon 
     To determine the location of the initial exon, information from the 
     (1) polypeptide sequence section; 
     (2) cDNA polynucleotide section; and 
     (3) the genomic sequence section 
     of the Reference Table is used. First, the polypeptide section will indicate where the translational start site is located in the MLS sequence. The MLS sequence can be matched to the genomic sequence that corresponds to the MLS. Based on the match between the MLS and corresponding genomic sequences, the location of the translational start site can be determined in one of the regions of the genomic sequence. The location of this translational start site is the start of the first exon. 
     Generally, the last base of the exon of the corresponding genomic region, in which the translational start site was located, will represent the end of the initial exon. In some cases, the initial exon will end with a stop codon, when the initial exon is the only exon. 
     In the case when sequences representing the MLS are in the positive strand of the corresponding genomic sequence, the last base will be a larger number than the first base. When the sequences representing the MLS are in the negative strand of the corresponding genomic sequence, then the last base will be a smaller number than the first base. 
     ii. Internal Exons 
     Except for the regions that comprise the 5′ and 3′ UTRs, initial exon, and terminal exon, the remaining genomic regions that match the MLS sequence are the internal exons. Specifically, the bases defining the boundaries of the remaining regions also define the intron/exon junctions of the internal exons. 
     iii. Terminal Exon 
     As with the initial exon, the location of the terminal exon is determined with information from the 
     (1) polypeptide sequence section; 
     (2) cDNA polynucleotide section; and 
     (3) the genomic sequence section 
     of the Reference Table. The polypeptide section will indicate where the stop codon is located in the MLS sequence. The MLS sequence can be matched to the corresponding genomic sequence. Based on the match between MLS and corresponding genomic sequences, the location of the stop codon can be determined in one of the regions of the genomic sequence. The location of this stop codon is the end of the terminal exon. Generally, the first base of the exon of the corresponding genomic region that matches the cDNA sequence, in which the stop codon was located, will represent the beginning of the terminal exon. In some cases, the translational start site will represent the start of the terminal exon, which will be the only exon. 
     In the case when the MLS sequences are in the positive strand of the corresponding genomic sequence, the last base will be a larger number than the first base. When the MLS sequences are in the negative strand of the corresponding genomic sequence, then the last base will be a smaller number than the first base. 
     B. Intron Sequences 
     In addition, the introns corresponding to the MLS are defined by identifying the genomic sequence located between the regions where the genomic sequence comprises exons. Thus, introns are defined as starting one base downstream of a genomic region comprising an exon, and end one base upstream from a genomic region comprising an exon. 
     C. Promoter Sequences 
     As indicated below, promoter sequences corresponding to the MLS are defined as sequences upstream of the first exon; more usually, as sequences upstream of the first of multiple transcription start sites; even more usually as sequences about 2,000 nucleotides upstream of the first of multiple transcription start sites. 
     III. Link of cDNA Sequences to Clone IDs 
     As noted above, the Reference Table identifies the cDNA clone(s) that relate to each MLS. The MLS sequence can be longer than the sequences included in the cDNA clones. In such a case, the Reference Table indicates the region of the MLS that is included in the clone. If either the 5′ or 3′ termini of the cDNA clone sequence is the same as the MLS sequence, no mention will be made. 
     IV. Multiple Transcription Start Sites 
     Initiation of transcription can occur at a number of sites of the gene. The Reference Table indicates the possible multiple transcription sites for each gene. In the Reference Table, the location of the transcription start sites can be either a positive or negative number. 
     The positions indicated by positive numbers refer to the transcription start sites as located in the MLS sequence. The negative numbers indicate the transcription start site within the genomic sequence that corresponds to the MLS. 
     To determine the location of the transcription start sites with the negative numbers, the MLS sequence is aligned with the corresponding genomic sequence. In the instances when a public genomic sequence is referenced, the relevant corresponding genomic sequence can be found by direct reference to the nucleotide sequence indicated by the “gi” number shown in the public genomic DNA section of the Reference Table. When the position is a negative number, the transcription start site is located in the corresponding genomic sequence upstream of the base that matches the beginning of the MLS sequence in the alignment. The negative number is relative to the first base of the MLS sequence which matches the genomic sequence corresponding to the relevant “gi” number. 
     In the instances when no public genomic DNA is referenced, the relevant nucleotide sequence for alignment is the nucleotide sequence associated with the amino acid sequence designated by “gi” number of the later PolyP SEQ subsection. 
     V. Polypeptide Sequences 
     The PolyP SEQ subsection lists SEQ ID NOs and Ceres SEQ ID NO for polypeptide sequences corresponding to the coding sequence of the MLS sequence and the location of the translational start site with the coding sequence of the MLS sequence. 
     The MLS sequence can have multiple translational start sites and can be capable of producing more than one polypeptide sequence. 
     A. Signal Peptide 
     The Reference tables also indicate in subsection (B) the cleavage site of the putative signal peptide of the polypeptide corresponding to the coding sequence of the MLS sequence. Typically, signal peptide coding sequences comprise a sequence encoding the first residue of the polypeptide to the cleavage site residue. 
     B. Domains 
     Subsection (C) provides information regarding identified domains (where present) within the polypeptide and (where present) a name for the polypeptide domain. 
     C. Related Polypeptides 
     Subsection (Dp) provides (where present) information concerning amino acid sequences that are found to be related and have some percentage of sequence identity to the polypeptide sequences of the Reference and Sequence Tables. These related sequences are identified by a “gi” number. 
     VI. Related Polynucleotide Sequences 
     Subsection (Dn) provides polynucleotide sequences (where present) that are related to and have some percentage of sequence identity to the MLS or corresponding genomic sequence. 
                                 Abbreviation   Description                  Max Len. Seq.   Maximum Length Sequence       rel to   Related to       Clone Ids   Clone ID numbers       Pub gDNA   Public Genomic DNA       gi No.   gi number       Gen. Seq. in Cdna   Genomic Sequence in cDNA           (Each region for a single gene prediction            is listed on a separate line.           In the case of multiple gene predictions,            the group of regions relating to a single            prediction are separated by a blank line)       (Ac) cDNA SEQ   cDNA sequence       Pat. Appln. SEQ ID NO   Patent Application SEQ ID NO:       Ceres SEQ ID NO: 1673877   Ceres SEQ ID NO:       SEQ # w. TSS   Location within the cDNA sequence,            SEQ ID NO:, of Transcription Start Sites            which are listed below       Clone ID #: # -&gt; #   Clone ID comprises bases # to # of the            cDNA Sequence       PolyP SEQ   Polypeptide Sequence       Pat. Appln. SEQ ID NO:   Patent Application SEQ ID NO:       Ceres SEQ ID NO   Ceres SEQ ID NO:       Loc. SEQ ID NO: @ nt.   Location of translational start site in            cDNA of SEQ ID NO: at nucleotide            number       (C) Pred. PP Nom. &amp; Annot.   Nomination and Annotation of Domains            within Predicted Polypeptide(s)       (Title)   Name of Domain       Loc. SEQ ID NO #: # -&gt; # aa.   Location of the domain within the            polypeptide of SEQ ID NO: from # to #            amino acid residues.       (Dp) Rel. AA SEQ   Related Amino Acid Sequences       Align. NO   Alignment number       gi No   Gi number       Desp.   Description       % Idnt.   Percent identity       Align. Len.   Alignment Length       Loc. SEQ ID NO: # -&gt; # aa   Location within SEQ ID NO: from #            to # amino acid residue.                    
1. Protein Group Table
 
     This table indicates groups of proteins that share a signature sequence (also referred to as a consensus sequence). The Protein group also referred to as the Ortholog group is named by the peptide ID with which all members were compared. Each group contains sequences that were included at the 10 −50 , 10 −30 , and 10 −10  p-value cutoffs. For each group, the peptide ID and at which cutoff the peptide was included into the group. The same peptide ID may be included in the group three times as peptide ID 50, peptide ID 30 and peptide ID 10. The data indicates that peptide ID was included in the group when the threshold was either 10 −50 , 10 −30 °, or 10 −10 . All the peptide IDs that are followed by “50” were included in the protein group when the e-value cutoff was 10 −50 . All the peptide IDs that are followed by either “30” or “50” were included in the protein group when the threshold e-value was 10 −30 . All the peptide IDs that are followed by “10”, “30” or “50” were included in the protein group when 10 −10  was used as the e-value cutoff. At the end of each protein group is a list of the consensus sequence that proteins share at the 10 −50 , 10 −30 , or 10 −10 . The consensus sequence contains both lower-case and upper-case letters. The upper-case letters represent the standard one-letter amino acid abbreviations. The lower case letters represent classes of amino acids:
         “t” refers to tiny amino acids, which are specifically alanine, glycine, serine and threonine.   “p” refers to polar amino acids, which are specifically, asparagine and glutamine   “n” refers to negatively charged amino acids, which are specifically, aspartic acid and glutamic acid   “+” refers to positively charged residues, which are specifically, lysine, arginine, and histidine   “r” refers to aromatic residues, which are specifically, phenylalanine, tyrosine, and tryptophan,   “a” refers to aliphatic residues, which are specifically, isoleucine, valine, leucine, and methonine
 
2. Protein Group Matrix Table
       

     In addition to each consensus sequence, Applicants have generated a scoring matrix to provide further description of the consensus sequence. The first row of each matrix indicates the residue position in the consensus sequence. The matrix reports number of occurrences of all the amino acids that were found in the group members for every residue position of the signature sequence. The matrix also indicates for each residue position, how many different organisms were found to have a polypeptide in the group that included a residue at the relevant position. The last line of the matrix indicates all the amino acids that were found at each position of the consensus. 
     3. MA_Diff Table 
     The MA_diff Table presents the results of the differential expression experiments for the mRNAs, as reported by their corresponding cDNA ID number, that were differentially transcribed under a particular set of conditions as compared to a control sample. The cDNA ID numbers correspond to those utilized in the Reference and Sequence Tables. Increases in mRNA abundance levels in experimental plants versus the controls are denoted with the plus sign (+). Likewise, reductions in mRNA abundance levels in the experimental plants are denoted with the minus (−) sign. 
     The Table is organized according to each set of experimental conditions, which are denoted by the term “Expt ID:” followed by a particular number. The table below links each Expt ID with a short description of the experiment and the parameters. 
     For each experiment ID a method of the normalization is specified. “Method: 2” represents normalization by median the goal of the method is to adjust the ratios by a factor so that the median of the ratio distribution is 1. Method 3 is the normalization procedure conducted by Aglilent Technologies, Inc. Palo Alto, Calif., USA. 
     The MA_diff Table also specifies the specific parameters and the experiment number (e.g. 107871) used in compiling the data. The experiment numbers are referenced in the appropriate utility/functions sections herein. The background threshold was set to “BKG_Threshold=X” to reduce the effect of the background on the signal. 
     Finally, the Table includes reference to an “Organism_ID” number. This number refers to the cDNA spotted on the chip were similar to  Arabidopsis thaliana  (3769) sequences or whether the oligo used for the chips were similar to  Zea mays  (311987) sequences. 
     4. MA_diff (Experiment) Table 
     The following Table summarizes the experimental procedures utilized for the differential expression experiments, each experiment being identified by a unique “Expt ID” number. 
                                Exam-   Experiment                                         ple No.   short name   genome   EXPT_ID   Value   PARAMETER   UNITS               3ii   3642-1     Arabidopsis     108512   3746-1   Plant Line   Hours       3n   Arab_0.001%_MeJA_1     Arabidopsis     108568   Aerial   Tissue   Tissue                       0.001%_MeJA   Treatment   Compound                       1   Timepoint   Hours       3n   Arab_0.001%_MeJA_1     Arabidopsis     108569   Aerial   Tissue   Tissue                       6   Timepoint   Hours                       0.001%_MeJA   Treatment   Compound       3j   Arab_0.1 uM_Epi-Brass_1     Arabidopsis     108580   Aerial   Tissue   Tissue                       1   Timepoint   Hours                       0.1 uM_Brassino_Steroid   Treatment   Compound       3j   Arab_0.1 uM_Epi-Brass_1     Arabidopsis     108581   Aerial   Tissue   Tissue                       6   Timepoint   Hours                       0.1 uM_Brassino_Steroid   Treatment   Compound       3g   Arab_100 uM_ABA_1     Arabidopsis     108560   Aerial   Tissue   Tissue                       1   Timepoint   Hours                       100 uM_ABA   Treatment   Compound       3g   Arab_100 uM_ABA_1     Arabidopsis     108561   Aerial   Tissue   Tissue                       100 uM_ABA   Treatment   Compound                       6   Timepoint   Hours       3I   Arab_100 uM_BA_1     Arabidopsis     108566   Aerial   Tissue   Tissue                       1   Timepoint   Hours                       100 uM_BA   Treatment   Compound       3I   Arab_100 uM_BA_1     Arabidopsis     108567   Aerial   Tissue   Tissue                       100 uM_BA   Treatment   Compound                       6   Timepoint   Hours       3k   Arab_100 uM_GA3_1     Arabidopsis     108562   Aerial   Tissue   Tissue                       1   Timepoint   Hours                       100 uM GA3   Treatment   Compound       3k   Arab_100 uM_GA3_1     Arabidopsis     108563   Aerial   Tissue   Tissue                       100 uM GA3   Treatment   Compound                       6   Timepoint   Hours       3h   Arab_100 uM_NAA_1     Arabidopsis     108564   Aerial   Tissue   Tissue                       1   Timepoint   Hours                       100 uM_NAA   Treatment   Compound       3h   Arab_100 uM_NAA_1     Arabidopsis     108565   Aerial   Tissue   Tissue                       100 uM_NAA   Treatment   Compound                       6   Timepoint   Hours       3r   Arab_20%_PEG_1     Arabidopsis     108570   Aerial   Tissue   Tissue                       1   Timepoint   Hours                       20% PEG   Treatment   Compound       3r   Arab_20%_PEG_1     Arabidopsis     108571   Aerial   Tissue   Tissue                       20% PEG   Treatment   Compound                       6   Timepoint   Hours       3o   Arab_2 mM_SA_1     Arabidopsis     108586   Aerial   Tissue   Tissue                       2 mM_SA   Treatment   Compound                       1   Timepoint   Hours       3o   Arab_2 mM_SA_1     Arabidopsis     108587   Aerial   Tissue   Tissue                       6   Timepoint   Hours                       2 mM_SA   Treatment   Compound       3u   Arab_5 mM_H2O2_1     Arabidopsis     108582   Aerial   Tissue   Tissue                       1   Timepoint   Hours                       5 mM_H2O2   Treatment   Compound       3u   Arab_5 mM_H2O2_1     Arabidopsis     108583   Aerial   Tissue   Tissue                       5 mM_H2O2   Treatment   Compound                       6   Timepoint   Hours       3v   Arab_5 mM_NaNP_1     Arabidopsis     108584   Aerial   Tissue   Tissue                       1   Timepoint   Hours                       5 mM_NaNP   Treatment   Compound       3v   Arab_5 mM_NaNP_1     Arabidopsis     108585   Aerial   Tissue   Tissue                       5 mM_NaNP   Treatment   Compound                       6   Timepoint   Hours       3t   Arab_Cold_1     Arabidopsis     108578   Aerial   Tissue   Tissue                       Cold   Treatment   Compound                       1   Timepoint   Hours       3t   Arab_Cold_1     Arabidopsis     108579   Aerial   Tissue   Tissue                       6   Timepoint   Hours                       Cold   Treatment   Compound       3g   Arab_Drought_1     Arabidopsis     108572   Aerial   Tissue   Tissue                       1   Timepoint   Hours                       Drought   Treatment   Compound       3g   Arab_Drought_1     Arabidopsis     108573   Aerial   Tissue   Tissue                       Drought   Treatment   Compound                       6   Timepoint   Hours       3s   Arab_Heat_1     Arabidopsis     108576   Aerial   Tissue   Tissue                       1   Timepoint   Hours                       Heat (42 deg   Treatment   Compound                       C.)       3s   Arab_Heat_1     Arabidopsis     108577   Aerial   Tissue   Tissue                       Heat (42 deg   Treatment   Compound                       C.)                       6   Timepoint   Hours       3aa (ovule)   Arab_Ler-pi_ovule_1     Arabidopsis     108595   Ler_pi   Plant Line   Hours                       Ovule   Tissue   Tissue       3b   Arab_Ler-rhl_root_1     Arabidopsis     108594   Ler_rhl   Plant Line   Hours                       Root   Tissue   Tissue       3l   Arab_NO3_H-to-L_1     Arabidopsis     108592   Aerial   Tissue   Tissue                       Low Nitrogen   Treatment   Compound                       12    Timepoint   Hours       3l   Arab_NO3_H-to-L_1     Arabidopsis     108593   Aerial   Tissue   Tissue                       24    Timepoint   Hours                       Low Nitrogen   Treatment   Compound       3l   Arab_NO3_L-to-H_1     Arabidopsis     108588   Aerial   Tissue   Tissue                       2   Timepoint   Hours                       Nitrogen   Treatment   Compound       3l   Arab_NO3_L-to-H_1     Arabidopsis     108589   Aerial   Tissue   Tissue                       Nitrogen   Treatment   Compound                       6   Timepoint   Hours       3l   Arab_NO3_L-to-H_1     Arabidopsis     108590   Aerial   Tissue   Tissue                       9   Timepoint   Hours                       Nitrogen   Treatment   Compound       3l   Arab_NO3_L-to-H_1     Arabidopsis     108591   Aerial   Tissue   Tissue                       Nitrogen   Treatment   Compound                       12    Timepoint   Hours       3p   Arab_Wounding_1     Arabidopsis     108574   Aerial   Tissue   Tissue                       1   Timepoint   Hours                       Wounding   Treatment   Compound       3p   Arab_Wounding_1     Arabidopsis     108575   Aerial   Tissue   Tissue                       Wounding   Treatment   Compound                       6   Timepoint   Hours       3o   Columbia/CS3726 flower SA     Arabidopsis     108475   Columbia   species   Hours                       SA   Treatment   Compound                                     5   weeks   Timepoint   Hours                                         3o   Columbia/CS3726 flower SA     Arabidopsis     108476   CS3726   species   Hours                                     5   weeks   Timepoint   Hours                                                         SA   Treatment   Compound       3p   Corn_0.001Percent_MeJA     Zea Mays     108555   Aerial   Tissue   Tissue                       24    Timepoint   Hours                       0.001%_MeJA   Treatment   Compound       3j   Corn_0.1 uM_Brassino_Steroid     Zea Mays     108557   24    Timepoint   Hours                       Aerial   Tissue   Tissue                       0.1 uM_Brassino_Steroid   Treatment   Compound       3g   Corn_100 uM_ABA     Zea Mays     108513   Aerial   Tissue   Tissue                       ABA   Treatment   Compound                       6   Timepoint   Hours       3g   Corn_100 uM_ABA     Zea Mays     108597   Aerial   Tissue   Tissue                       24    Timepoint   Hours                       100 uM_ABA   Treatment   Compound       3i   Corn_100 uM_BA     Zea Mays     108517   Aerial   Tissue   Tissue                       6   Timepoint   Hours                       BA   Treatment   Compound       3k   Corn_100 uM_GA3     Zea Mays     108519   Aerial   Tissue   Tissue                       100 uM   Treatment   Compound                       Giberillic                       Acid                       1   Timepoint   Hours       3k   Corn_100 uM_GA3     Zea Mays     108520   Aerial   Tissue   Tissue                       6   Timepoint   Hours                       100 uM   Treatment   Compound                       Giberillic                       Acid       3k   Corn_100 uM_GA3     Zea Mays     108521   Aerial   Tissue   Tissue                       100 uM   Treatment   Compound                       Giberillic                       Acid                       12    Timepoint   Hours       3h   Corn_100 uM_NAA     Zea Mays     108516   Aerial   Tissue   Tissue                       NAA   Treatment   Compound                       6   Timepoint   Hours       3h   Corn_100 uM_NAA     Zea Mays     108554   Aerial   Tissue   Tissue                       24    Timepoint   Hours                       NAA   Treatment   Compound       3hh   Corn_1400-6/S-17     Zea Mays     108598   Shoot apices   Tissue   Tissue       3r   Corn_150 mM_NaCl     Zea Mays     108541   Aerial   Tissue   Tissue                       1   Timepoint   Hours                       150 mM_NaCl   Treatment   Compound       3r   Corn_150 mM_NaCl     Zea Mays     108542   Aerial   Tissue   Tissue                       150 mM_NaCl   Treatment   Compound                       6   Timepoint   Hours       3r   Corn_150 mM_NaCl     Zea Mays     108553   Aerial   Tissue   Tissue                       24    Timepoint   Hours                       150 mM_NaCl   Treatment   Compound       3r   Corn_20%_PEG     Zea Mays     108539   Aerial   Tissue   Tissue                       1   Timepoint   Hours                       20% PEG   Treatment   Compound       3r   Corn_20%_PEG     Zea Mays     108540   Aerial   Tissue   Tissue                       20% PEG   Treatment   Compound                       6   Timepoint   Hours       3o   Corn_2 mM_SA     Zea Mays     108515   Aerial   Tissue   Tissue                       SA   Treatment   Compound                       12    Timepoint   Hours       3o   Corn_2 mM_SA     Zea Mays     108552   Aerial   Tissue   Tissue                       SA   Treatment   Compound                       24    Timepoint   Hours       3u   Corn_5 mM_H2O2     Zea Mays     108537   Aerial   Tissue   Tissue                       H2O2   Treatment   Compound                       1   Timepoint   Hours       3u   Corn_5 mM_H2O2     Zea Mays     108538   Aerial   Tissue   Tissue                       6   Timepoint   Hours                       H2O2   Treatment   Compound       3u   Corn_5 mM_H2O2     Zea Mays     108558   Aerial   Tissue   Tissue                       24    Timepoint   Hours                       H2O2   Treatment   Compound       3v   Corn_5 mM_NO     Zea Mays     108526   Aerial   Tissue   Tissue                       NO   Treatment   Compound                       1   Timepoint   Hours       3v   Corn_5 mM_NO     Zea Mays     108527   Aerial   Tissue   Tissue                       6   Timepoint   Hours                       NO   Treatment   Compound       3v   Corn_5 mM_NO     Zea Mays     108559   Aerial   Tissue   Tissue                       12    Timepoint   Hours                       NO   Treatment   Compound       3t   Corn_Cold     Zea Mays     108533   Aerial   Tissue   Tissue                       1   Timepoint   Hours                       Cold   Treatment   Compound       3t   Corn_Cold     Zea Mays     108534   Aerial   Tissue   Tissue                       Cold   Treatment   Compound                       6   Timepoint   Hours       3q   Corn_Drought     Zea Mays     108502   Drought   Treatment   Compound                       1   Timepoint   Hours       3q   Corn_Drought     Zea Mays     108503   Drought   Treatment   Compound                       6   Timepoint   Hours       3q   Corn_Drought     Zea Mays     108504   Drought   Treatment   Compound                       12    Timepoint   Hours       3q   Corn_Drought     Zea Mays     108556   Drought   Treatment   Compound                       24    Timepoint   Hours       3s   Corn_Heat     Zea Mays     108522   Aerial   Tissue   Tissue                       1   Timepoint   Hours                       Heat (42 deg   Treatment   Compound                       C.)       3s   Corn_Heat     Zea Mays     108523   Aerial   Tissue   Tissue                       6   Timepoint   Hours                       Heat (42 deg   Treatment   Compound                       C.)       3gg   Corn_Imbibed Seeds     Zea Mays     108518   Imbibed   Treatment   Compound                       4   Age   days old                       Roots   Tissue   Tissue       3gg   Corn_Imbibed Seeds     Zea Mays     108528   Imbibed   Treatment   Compound                       Aerial   Tissue   Tissue                       5   Age   days old       3gg   Corn_Imbibed Seeds     Zea Mays     108529   Imbibed   Treatment   Compound                       5   Age   days old                       Root   Tissue   Tissue       3gg   Corn_Imbibed Seeds     Zea Mays     108530   Imbibed   Treatment   Compound                       Aerial   Tissue   Tissue                       6   Age   days old       3gg   Corn_Imbibed Seeds     Zea Mays     108531   Imbibed   Treatment   Compound                       6   Age   days old                       root   Tissue   Tissue       3gg   Corn_Imbibed Seeds     Zea Mays     108545   Imbibed   Treatment   Compound                       Aerial   Tissue   Tissue                       3   Age   days old       3gg   Corn_Imbibed Seeds     Zea Mays     108546   Imbibed   Treatment   Compound                       3   Age   days old                       Root   Tissue   Tissue       3gg   Corn_Imbibed Seeds     Zea Mays     108547   Imbibed   Treatment   Compound                       Aerial   Tissue   Tissue                       4   Age   days old       3gg   Corn_Imbibed_Embryo_Endosperm     Zea Mays     108543   2   Age   days old                       Imbibed   Treatment   Compound                       Embryo   Tissue   Tissue       3gg   Corn_Imbibed_Embryo_Endosperm     Zea Mays     108544   2   Age   days old                       Endosperm   Tissue   Tissue                       Imbibed   Treatment   Compound       3ee   Corn_Meristem     Zea Mays     108535   Root   Tissue   Tissue                       Meristem                       192    Timepoint   Hours       3ee   Corn_Meristem     Zea Mays     108536   Shoot   Tissue   Tissue                       Meristem                       192    Timepoint   Hours       3n   Corn_Nitrogen_H_to_L     Zea Mays     108532   Roots   Tissue   Tissue                       Low Nitrogen   Treatment   Compound                       16    Timepoint   Hours       3n   Corn_Nitrogen_H_to_L     Zea Mays     108548   Root   Tissue   Tissue                       Low Nitrogen   Treatment   Compound                       4   Timepoint   Hours       3m   Corn_Nitrogen_L_to_H     Zea Mays     108549   Aerial   Tissue   Tissue                          0.166   Timepoint   Hours                       Nitrogen   Treatment   Compound       3m   Corn_Nitrogen_L_to_H     Zea Mays     108550   Aerial   Tissue   Tissue                       Nitrogen   Treatment   Compound                         1.5   Timepoint   Hours       3m   Corn_Nitrogen_L_to_H     Zea Mays     108551   Aerial   Tissue   Tissue                       3   Timepoint   Hours                       Nitrogen   Treatment   Compound       3ff   Corn_RT1     Zea Mays     108599   Unknown   Plant Line   Hours                       Root   Tissue   Tissue       3p   Corn_Wounding     Zea Mays     108524   Aerial   Tissue   Tissue                       Wounding   Treatment   Compound                       1   Timepoint   Hours       3p   Corn_Wounding     Zea Mays     108525   Aerial   Tissue   Tissue                       6   Timepoint   Hours                       Wounding   Treatment   Compound       3g   Drought_Flowers     Arabidopsis     108473   Flowers   Tissue   Tissue                                     7   d   Timepoint   Hours                                                         Drought   Treatment   Compound       3g   Drought_Flowers     Arabidopsis     108474   Flowers   Tissue   Tissue                       Drought   Treatment   Compound                       8 d (1 d-post_re-   Timepoint   Hours                       watering)       3k   GA Treated     Arabidopsis     108484   1   Timepoint   Hours                       1   Timepoint   Hours       3k   GA Treated     Arabidopsis     108485   6   Timepoint   Hours                       6   Timepoint   Hours       3k   GA Treated     Arabidopsis     108486   12    Timepoint   Hours                       12    Timepoint   Hours                                             3e   Germinating Seeds     Arabidopsis     108461   Day   1   Timepoint   Hours       3e   Germinating Seeds     Arabidopsis     108462   Day   2   Timepoint   Hours       3e   Germinating Seeds     Arabidopsis     108463   Day   3   Timepoint   Hours       3e   Germinating Seeds     Arabidopsis     108464   Day   4   Timepoint   Hours                                         3bb   Herbicide V3.1     Arabidopsis     108465   Round up   Treatment   Compound                       12    Timepoint   Hours       3bb   Herbicide V3.1     Arabidopsis     108466   Trimec   Treatment   Compound                       12    Timepoint   Hours       3bb   Herbicide V3.1     Arabidopsis     108467   Finale   Treatment   Compound                       12    Timepoint   Hours       3bb   Herbicide V3.1     Arabidopsis     108468   GLEAN ®   Treatment   Compound                       12    Timepoint   Hours       3bb   Herbicide_v2     Arabidopsis     107871   Finale   Treatment   Compound                       4   Timepoint   Hours       3bb   Herbicide_v2     Arabidopsis     107876   Finale   Treatment   Compound                       12    Timepoint   Hours       3bb   Herbicide_v2     Arabidopsis     107881   GLEAN ®   Treatment   Compound                       4   Timepoint   Hours       3bb   Herbicide_v2     Arabidopsis     107886   Trimec   Treatment   Compound                       4   Timepoint   Hours       3bb   Herbicide_v2     Arabidopsis     107891   Trimec   Treatment   Compound                       12    Timepoint   Hours       3bb   Herbicide_v2     Arabidopsis     107896   ROUNDUP   Treatment   Compound                       4   Timepoint   Hours       3d   Trichome Inflorescences expt     Arabidopsis     108452   Hairy   Tissue   Tissue                       Influorescence                       #1       3o   SA treatment_1 hour     Arabidopsis     108471   Columbia   Species   Hours                       1   Timepoint   Hours                       SA   Treatment   Compound       3o   SA treatment_1 hour     Arabidopsis     108472   CS3726   Species   Hours                       1   Timepoint   Hours                       SA   Treatment   Compound       3o   SA treatment_4 hour     Arabidopsis     108469   columbia   Species   Hours                       4   Timepoint   Hours                       SA   Treatment   Compound       3o   SA treatment_4 hour     Arabidopsis     108470   CS3726   Species   Hours                       SA   Treatment   Compound                       4   Timepoint   Hours       3o   SA treatment_AJ     Arabidopsis     107953   50    Probe   % of                             Amount   Standard               Amount                                 SA   Treatment   Compound           24    Timepoint   Hours           Clontech   Probe Type   Probe                         method                                         3o   SA treatment_AJ     Arabidopsis     107960   50    Probe   % of                             Amount   Standard               Amount                                 SA   Treatment   Compound           24    Timepoint   Hours           Operon   Probe Type   Probe                         method                                         3o   SA_treatment 24 hour     Arabidopsis     108443   SA   Treatment   Compound                       24    Timepoint   Hours       3o   SA_treatment 6 hour     Arabidopsis     108440   SA treatment   Treatment   Compound                                     6   hour                                                                 CS3726   species   Hours       3o   SA_treatment 6 hour     Arabidopsis     108441   SA treatment   Treatment   Compound                                     6   hour                                         Columbia   species   Hours                                             3l   Nitrogen High transition to Low     Arabidopsis     108454   10   min   Timepoint   Hours       3l   Nitrogen High transition to Low     Arabidopsis     108455   1   hr   Timepoint   Hours                                         3j   BR_Shoot Apices Expt     Arabidopsis     108478   dwf4-1   Plant Line   Hours       3j   BR_Shoot Apices Expt     Arabidopsis     108479   AOD4-4   Plant Line   Hours       3j   BR_Shoot Apices Expt     Arabidopsis     108480   Ws-2   Plant Line   Hours                       BL   Treatment   Compound       3j   BR_Shoot Apices Expt     Arabidopsis     108481   Ws-2   Plant Line   Hours                       BRZ   Treatment   Compound       3jj   Tissue Specific Expression     Arabidopsis     108429   green flower   Tissue   Tissue                       operon   Probe Type   Probe                         method                                 50    Probe   % of                             Amount   Standard               Amount                                         3jj   Tissue Specific Expression     Arabidopsis     108430   white flower   Tissue   Tissue                       50    Probe   % of                             Amount   Standard               Amount                                 operon   Probe Type   Probe                         method                                         3jj   Tissue Specific Expression     Arabidopsis     108431   flowers (bud)   Tissue   Tissue                       operon   Probe Type   Probe                         method                                 50    Probe   % of                             Amount   Standard               Amount                                         3c   Tissue Specific Expression     Arabidopsis     108436   5-10 mm   Tissue   Tissue                       siliques                       33    Probe   % of                             Amount   Standard               Amount                                 operon   Probe Type   Probe                         method                                         3c   Tissue Specific Expression     Arabidopsis     108437   &lt;5 mm   Tissue   Tissue                       siliques                       operon   Probe Type   Probe                         method                                 33    Probe   % of                             Amount   Standard               Amount                                         3c   Tissue Specific Expression     Arabidopsis     108438   5 wk siliques   Tissue   Tissue                       33    Probe   % of                             Amount   Standard               Amount                                 operon   Probe Type   Probe                         method                                         3a   Tissue Specific Expression     Arabidopsis     108439   Roots (2 wk)   Tissue   Tissue                       operon   Probe Type   Probe                         method                                 33    Probe   % of                             Amount   Standard               Amount                                         3c   Tissue Specific Expression     Arabidopsis     108497   3 week   Tissue   Tissue                       Rossette                       leaves                       100    Probe   % of                             Amount   Standard               Amount                                 operon   Probe Type   Probe                         method                                         3c   Tissue Specific Expression     Arabidopsis     108498   3-week stems   Tissue   Tissue                       operon   Probe Type   Probe                         method                                 100    Probe   % of                             Amount   Standard               Amount                                         3dd   U.A.E. Knockout     Arabidopsis     108451   13B12   Plant Line   Hours       3q   Ws  Arabidopsis  Drought 2 days     Arabidopsis     108477   stems and   Tissue   Tissue                       leaves                                                             2   days   Timepoint   Hours       3q   Ws  Arabidopsis  Drought 4 days     Arabidopsis     108482   4   days   Timepoint   Hours       3q   Ws  Arabidopsis  Drought 6 days     Arabidopsis     108483   6   days   Timepoint   Hours                                         3cc   ap2-floral buds     Arabidopsis     108501   ap2 (Ler.)   Plant Line   Hours                       floral buds   Tissue   Tissue       3m   nitrogen-seed set     Arabidopsis     108487     0.5   Timepoint   Hours       3m   nitrogen-seed set     Arabidopsis     108488   2   Timepoint   Hours       3m   nitrogen-seed set     Arabidopsis     108489   4   Timepoint   Hours       3b   rhl mutant2     Arabidopsis     108433   mutant   Tissue   Tissue       3ee   root tips     Arabidopsis     108434   root tips   Tissue   Tissue       3f   stm mutants     Arabidopsis     108435   stem   Tissue   Tissue                                                 Aluminum       SMD 7304,                                   SMD 7305           Axel       SMD 6654,                   SMD 6655           Cadium       SMD 7427,                   SMD 7428           Cauliflower       SMD 5329,                   SMD 5330           Chloroplast       SMD 8093,                   SMD 8094           Circadian       SMD 2344,                   SMD 2359,                   SMD 2361,                   SMD 2362,                   SMD 2363,                   SMD 2364,                   SMD 2365,                   SMD 2366,                   SMD 2367,                   SMD 2368,                   SMD 3242           CO2       SMD7561,                   SMD 7562,                   SMD 7261,                   SMD 7263,                   SMD 3710,                   SMD 4649,                   SMD 4650           Disease       SMD 7342,                   SMD 7343           reactive oxygen       SMD 7523           Iron       SMD 7114,                   SMD 7115,                   SMD 7125           defense       SMD 8031,                   SMD 8032           Mitchondria-Electron       SMD 8061,           Transport       SMD 8063           NAA       SMD 3743,                   SMD 3749,                   SMD 6338,                   SMD 6339           Nitrogen       SMD 3787,                   SMD 3789           Phototropism       SMD 4188,                   SMD 6617,                   SMD 6619           Shade       SMD 8130,                   SMD 7230           Sqn       SMD 7133,                   SMD 7137           Sulfur       SMD 8034,                   SMD 8035           Wounding       SMD 3714,                   SMD 3715           Zinc       SMD 7310,                   SMD 7311                        
5. MA_Clusters Table
 
     Microarray data was clustered using one of two methods: “complete linkage” or “nearest neighbor” analysis. These clustering methods are described in more detail elsewhere herein. The results of the clustering analysis are presented in the MA_clust table. The table is organized as follows: 
     “METHOD” refers to a method number which clustering method used. 
     “CL_METHOD_TYPE=TRUE” refers to complete linkage method. 
     “NN_METHOD_TYPE=TRUE” refers to the nearest neighbor method. 
     “FULL_NN_METHOD_TYPE=TRUE” refers to the nearest neighbor method, where no size limitation was placed on the cluster. 
     “PARAMETERS” refers to the parameters utilized for the analysis. The nature of these is also described in more detail elsewhere herein. 
     “ORGANISM” refers to the cDNA spotted on the chip were similar to  Arabidopsis thaliana  (3769) sequences or whether the oligo used for the chips were similar to  Zea mays  (311987) sequences. 
     Each cluster or group of cDNA is identified by a “Group #”, following which are the individual cDNA_Ids that are a member of that Group 
     6. Knock-In Table 
     The Knock-In Table presents the results of knock-in experiments wherein plants are grown from tissues transformed with a marker gene-containing insert and phenotypes are ascertained from the transformed plants. Each section of the Table relating to information on a new transformant begins with a heading “Knock-in phenotype in gene (cDNA_id):” followed by a number which represents the Ceres internal code for a proprietary cDNA sequence. The described transformant was prepared by procedures described herein, wherein the identified Ceres proprietary cDNA_id (corresponding to the cDNA_id in the Reference and Sequence Tables) was interrupted by the marker gene-containing insert. The following information is presented for each section.
         Parent plants used in cross—presents the id numbers of the parent plants which were crossed to produce the F1 generation plant for which a phenotype is described. The parent plant with the promoter is described by a plant line descriptor.   Clone ID—presents the clone number of the Ceres proprietary clone which was the source of the cDNA_id.   Phenotype ID—represents an internal identification code.   Unique FI plant ID—represents the internal code for the F1 plant for which a phenotype is described.   Assay—presents the type of growth analyzed (e.g. soil gross morphology), followed by the assay name which corresponds to the type/location of the tissue that was observed, the name of the assay conducted for which the result provided the identified phenotype.   Phenotype—describes the phenotype noted for the F1 generation transformant.   Notes—may provide additional information on the described phenotype for the transformant.       

     Each knock-in representing a transformant with an interruption in the identified cDNA_id may be correlated with more than one identified phenotype. 
     7. Knock-Out Table 
     The Knock-Out Table presents the results of knock-out experiments wherein plants are grown from tissues transformed with a marker gene-containing insert wherein phenotypes are ascertained from the transformed plants. Each section of the Table relating to information on a new transformant begins with a heading “tail id:” representing an internal code. The following information is presented for each section.
         br—provides another internal code for the experiment.   Phenotype_id—provides an identification number for the particular phenotype identified for the transformant.   assay—identifies the assay procedure utilized in the experiment to identify a phenotype for the transformant.   phenotype—represents an internal identification code.   ratio—represents a segregation ratio.   notes—lists any notes relevant to the identified phenotype.   Knock-out in-genes—Identifies the genes in which the tag has inserted
           6) the less than 501 upstream of the transcriptional start site;   7) less than 701 upstream of the translational initiation codon;   8) between the translational initiation and termination codons of the gene,   9) less than 301 downstream of the translational stop codon; or   10) less than 151 downstream of a transcriptional termination site or a gene.   
           In this table the gene is identified by its cDNA ID number, the Ceres SEQ ID that is indicated in the (Ac) portion of the Reference tables. For each cDNA_id, the following information is provided:
           the cDNA_id number.   in parenthesis, the cluster number of which the identified cDNA is a member.   the “gDNA_Insert pos” representing the position of the insert in the corresponding gDNA sequence   the gi number refers to the TIGR chromosome sequences for  Arabidopsis.      
           Knock-out out of-genes: Identifies the Ceres cDNA proprietary sequences (noted by cDNA_id which are the same as those identified in the Reference and Sequence Tables) which are closest in position to the insert, both upstream and downstream from the insert. For each cDNA_id, the following information is provided:
           In the first parentheses, R indicates that the gene is to the right of the tag, L indicates that the gene is to right of the tag as the sequences is read left to right   the cDNA_id number   in next parentheses, the cluster number of which the identified cDNA is a member.   the distance (in number of nucleotides) of the insert is upstream of the start of the gene annotation as described in the Reference Tables or downstream at the end the gene annotation.   the “gDNA_Insert pos” representing the position of the insert in the corresponding gDNA sequence   the gi number refers to the TIGR chromosome sequences for  Arabidopsis.  
 
8. Protein Domain Table
   
               

     The Protein Domain table provides details concerning the protein domains noted in the Reference Table. The majority of the protein domain descriptions given in the Protein Domain Table are obtained from Prosite (available on the internet) and Pfam (also available on the internet). Each description in The Table begins with the pfam and Prosite identifying numbers, the full name of the domain, and a detailed description, including biological and in vivo implications/functions for the domain, references which further describe such implications/functions, and references that describe tests/assays to measure the implications/functions. 
     9. Single Gene Functions &amp; Utilities Table 
     The Single Gene Functions &amp; Utilities Table describes particular utilities/functions of interest for individual genes. The Table identifies the cDNA_ID of interest, correlates to that cDNA the relevant phenotype, protein domain and microarray/differential expression data. The final column of the Table identifies the utilities/functions of particular interest for the identified cDNA. 
     10. Cluster Functions &amp; Utilities Table 
     The Cluster Functions &amp; Utilities Table describes particular utilities/functions of interest for identified clusters of genes. The Table provides the following information: 
     Record #—an internal identifier. 
     Group—identifies the group of clusters of interest, wherein each group is identified with the same utilities/functions as set forth in the right-hand most column. 
     CDNA—identifies the cDNA of interest with the noted utility/function. 
     CDNA_Cluster—identifies the cDNA Cluster ID of interest. 
     Gi No—refers to the public genomic sequence that matches to the cDNA 
     NR Hit—refers to the most relevant protein domain for the cDNA of interest. 
     Pfam and Pfam Desc—provide the protein domain name. 
     Notes/Annotations—provides some notes relevant to the data/information analysis. 
     Utilities/Functions—this rightmost column identifies utilities/functions of particular interest for the group of cDNAs and clusters. 
     11. cDNA Clusters Table 
     The cDNA_Clusters Table correlates the Ceres cDNA_ID nos. (in numerical order) with the relevant cDNA cluster which contains each cDNA_ID. 
     12. Stanford Old New cDNA Map Table 
     During the course of the experiments reported herein, some of the cDNA sequences were assigned new Ceres internal cDNA_id numbers. The cDNA_map Table provides a list of the original “old” cDNA_ids and correlates those id numbers with any new cDNA_id which may have been assigned. Thus, any “old” and “new” cDNA ids which are on the same line in the Table are, in fact, the same sequence. 
     13. gb Only Peptides Table 
     In the Protein Group table, a number of proteins encoded by Genbank predictions are included. These proteins were referenced with a peptide ID number. The peptide ID number is linked to the amino acid sequence of the Genbank prediction in this table. 
     14. Stanford Old New cDNA Table 
     During the course of the experiments reported herein, some of the cDNA sequences utilized in the Stanford Microarray differential expression analysis experiments were assigned new Ceres internal cDNA_id numbers. The Stanford_old_new_cDNA Table provides a list of the original “old” cDNA_ids and correlates those id numbers with any new cDNA_id which may have been assigned. Thus, any “old” and “new” cDNA ids which are on the same line in the Table are, in fact, the same sequence. 
     15. Enhanced Amino Table 
     This table lists the peptide IDs of polypeptides with enhanced amino acid content. The table list the peptide ID following with the single letter code of the amino acid that is enhanced. The table also includes a frequency that the amino acid occurred. The frequency was calculated by dividing the total number of the desired amino acid indicated in the column by the number of residues in the peptide. For example, if amino acid A, occurred 50 times in a polypeptide that is 100 amino acid long, the frequency would be 50 divided by 100 or 0.5. 
     16. Stanford old new cDNA map Table 
     During the course of the experiments reported herein, some of the cDNA sequences were assigned new Ceres internal cDNA_id numbers. The docket_80090_101_cDNA_map provides a list of the original “old” cDNA_ids in the Reference and Sequence tables and correlates those id numbers with any new cDNA_id which may have been assigned and utilized in the remaining tables. Thus, any “old” and “new” cDNA ids which are on the same line in the Table are, in fact, the same sequence. 
     II. How the Inventions Reveal how Genes, Gene Components and Products Function 
     The different experimental molecular genetic approaches focused on different aspects of genes, gene components, and gene products of the inventions. The variety of the data demonstrates the multiple functions and characteristics of single genes, gene components, and products. The data also explain the pathways and networks in which individual genes and products participate and interact. As a result, the circumstances or conditions are now known when these genes and networks are active. These new understandings of biology are relevant for many plant species. The following section describes the process by which Applicants analyzed the inventions generated by the Ceres Genomic Engine: 
     II.A. Experimental Results Reveal Many Facets of a Single Gene 
     The experimental results are used to dissect the function of individual components and products of the genes. For example, the biochemical activity of the encoded protein could be surmised from sequence analyses, and promoter specificity could be identified through transcriptional analyses. Generally, the data presented herein can be used to functionally annotate either the protein sequence and/or the regulatory sequence that control transcription and translation. 
     II.A.1. Functions of Coding Sequences Revealed by the Ceres Genomic Engine 
     II.A.1.a. Sequence Similarity to Proteins of Known Function can be Used to Associate Biochemical Activities and Molecular Interaction to the Proteins of the Invention 
     The protein sequences of the invention were analyzed to determine if they shared any sequence characteristics with proteins of known activity. Proteins can be grouped together based on sequence similarity, either localized or throughout the length of the proteins. Typically, such groups of proteins exhibit common biochemical activities or interact with similar molecules. 
     II.A.1.a.1. Presence of Amino Acid Motifs Indicates Biological Function 
     Localized protein sequence similarity, also referred to as amino acid motifs, have been attributed to enzyme or protein functions. A library of motifs, important for function, have been documented in PROSITE, a public database available on the internet. This library includes descriptions of the motifs and their functions. The zinc finger motif is one such entry in PROSITE, which reports that the zinc finger domain of DNA-binding proteins is typically defined by a 25-30 amino acid motif containing specific cysteine or histidine residues that are involved in the tetrahedral coordination of a zinc ion. Any protein comprising a sequence similar to the zinc finger amino acid motif will have similar functional activity (specific binding of DNA). 
     Protein sequences of the invention have been compared to a library of amino acid motifs in the pFAM database, which is linked to the PROSITE database. If any of Applicants&#39; protein sequences exhibit similarity to these amino acid motifs or domains, the Reference Table notes the name and location of the motif in the “Pred. PP Nom. &amp; Annot” section of the Reference tables. A description of any biochemical activities that are associated to these domains, and therefore associated with Applicants&#39; proteins, is included in the Protein Domain table. 
     For example, polypeptide, CERES Sequence ID NO: 1545823 is associated with zinc finger motif as follows in the Reference Table:
         (C) Pred. PP Nom. &amp; Annot.
           Zinc finger, C3HC4 type (RING finger)   Loc. Sequence ID NO 133059: 58→106 aa.   
               

     II.A.1.a.2. Related Amino Acid Sequences Share Similar Biological Functions 
     It is apparent, when studying protein sequence families, that some regions have been better conserved than others during evolution. These regions are generally important for the function of a protein and/or for the maintenance of its three-dimensional structure. 
     The Reference Table reports in section “(Dp) Rel. AA Sequence” when a protein shares amino acid similarity with a protein of known activity. The section reports the gi number of the protein of known activity, a brief description of the activity, and the location where it shares sequence similarity to Applicants&#39; polypeptide sequence. 
     Using this analysis, biochemical activity of the known protein is associated with Applicants&#39; proteins. An example for the polypeptide described above is as follows:
         (Dp) Rel. AA Sequence
           Align. NO 524716   gi No 2502079   Desp.: (AF022391) immediate early protein; ICP0 [Feline herpesvirus 1]   % Idnt.: 33.7   Align. Len.: 87   Loc. Sequence ID NO 133059: 52→137 aa.   
               

     II.A.1.b. Differential Expression Results Explain in which Cellular Responses the Proteins of the Invention are Involved 
     Differential expression results show when the coding sequence is transcribed, and therefore when the activity of the protein is deployed by the cell. Similar coding sequences can have very different physiological consequences because the sequences are expressed at different times or places, rather than because of any differences in protein activity. Therefore, modified levels (increased or decreased) of expression as compared to a control provide an indication of the function of a corresponding gene, gene components, and gene products. 
     These experiments can determine which are genes “over-expressed” under a given stimulus. Such over-expressed genes give rise to higher transcript levels in a plant or cell that is stimulated as compared to the transcript levels of the same genes in a control organism or cell. Similarly, differential expression experiments can reveal “under-expressed” genes. 
     To increase the cellular response to a stimulus, additional copies of the coding sequences of a gene that is over-expressed are inserted into a cell. Increasing transcript levels of an over-expressed gene can either heighten or prolong the particular cellular response. A similar enhancement can occur when transcription of an under-expressed gene is inhibited. In contrast, the cellular response will be shortened or less severe when the over-expressed genes are inhibited or when expression of the under-expressed genes are increased. 
     In addition to analyzing the levels of transcription, the data were also analyzed to gain insight into the changes in transcription over time. That is, while the plants in the experiments were reacting to either an external or internal stimulus, a differential experiment takes a snapshot of the transcription levels in the cells at one specific time. However, a number of snap-shots can be taken at different time points during an external stimulus regime, or at different stages of development during an internal stimulus. These results show how the plant changes transcription levels over time, and therefore protein levels in response to specific stimuli to produce phenotypic changes. These results show that a protein can be implicated in a single, but more likely, in a number of cellular responses. 
     II.A.1.b.1. The Transcript Levels of a Protein Over Time in Response to a Stimuli are Revealed by Transcriptional Analyses Over Many Experiments 
     Applicants produced data from plants at different times after a specific stimulus. These results show whether the expression level of a gene spikes at a key moment during the cellular response, or whether the transcript level remains constant. Thus, coding sequences not only can be determined to be over- or under-expressed, but also can be classified by the initial timing and duration of differential expression. This understanding of timing can be used to increase or decrease any desired cellular response. 
     Generally, Applicants have assayed plants at 2 to 4 different time points after exposing the plants to the desired stimuli. From these experiments, “early” and “late” responders were identified. These labels are applied to either the regulatory sequences driving transcription of the gene as well as to the protein encoded by the gene. 
     The example in  FIG. 5  illustrates how the genes, gene components and products were classified as either early or late responders following a specific. The mRNAs from plants exposed to drought conditions were isolated 1 hour and 6 hours after exposure to drought conditions. These mRNAs were tested utilizing microarray techniques.  FIG. 5  illuminates possible transcription profiles over the time course, plotting all the (+) data points as +1 and all the (−) data points as −1 (the value for each time point was determined using a pair of microarray chips as described above). 
     Data acquired from this type of time course experiment are useful to understand how one may increase or decrease the speed of the cellular response. Inserting into a cell extra copies of the coding sequence of early responders in order to over-express the specific gene can trigger a faster cellular response. Alternatively, coding sequences of late responders that are over-expressed can be placed under the control of promoters of early responders as another means to increase the cellular response. 
     Inserting anti-sense or sense mRNA suppression constructs of the early responders that are over-expressed can retard action of the late responders, thereby delaying the desired cellular response. In another embodiment, extra copies of the promoters of both early and late responders can be added to inhibit expression of both types of over-expressed genes. 
     The experiments described herein can be grouped together to determine the time course of the transcript levels of different coding sequences in response to different stimuli. Examples of different groups are as follows (the examples include the IDs for both corn and  Arabidopsis  experiments):
         NAA (EXPT IDs 108564, 108565, 108516, 108554)   BA (EXPT IDs 108566, 108567, 108517)   GA (EXPT IDs 108562, 108563, 108519, 108520, 108521, 108484, 108485, 108486)   BR (EXPT IDs 108580, 108581, 108557, 108478, 108479, 108480, 108481)   ABA (EXPT IDs 108560, 108561, 108513, 108597)   Drought (EXPT IDs 108572, 108573, 108502, 108503, 108504, 108556, 108482, 108483, 108473, 108474, 108477)   Cold (EXPT IDs 108578, 108579, 108533, 108534)   Heat (EXPT IDs 108576, 108577, 108522, 108523)   Osmotic stress (EXPT IDs108570, 108571, 108541, 108542, 108553, 108539, 108540)   Reactive Oxygen (EXPT IDs 108582, 108583, 108537, 108538, 108558)   NO (EXPT IDs 108584, 108585, 108526, 108527, 108559)   Wounding (EXPT IDs 108574, 108575, 108524, 108525)   SA (EXPT IDs 108586, 108587, 108515, 108552, 108471, 108472, 108469, 108470, 107953, 107960, 108443, 108440, 108441, 108475, 108476)   MeJA (EXPT IDs 108568, 108569)   Finale (EXPT IDs 108467, 107871, 107876)   Trimec (EXPT IDs 108466, 107886, 107891)   ROUNDUP (EXPT IDs 108465, 107896)   GLEAN® (EXPT IDs 108468, 107881)       

     II.A.1.b.2. The Transcript Levels of a Protein Over Different Developmental Stages can be Identified by Transcriptional Analyses Over Many Experiments 
     Differential expression data were produced for different development stages of various organs and tissues. Measurement of transcript levels can divulge whether specific genes give rise to spikes of transcription at specific times during development, or whether transcription levels remain constant. This understanding can be used to increase speed of development, or to arrest development at a specific stage. 
     Like the time-course experiments, the developmental stage data can classify genes as being transcribed at early or late stages of development. Generally, Applicants assayed different organs or tissues at 2-4 different stages. 
     Inhibiting under-expressed genes at either early or late stages can trigger faster development times. The overall development time also can be increased by this means to allow organs and tissue to grow to a larger size or to allow more organs or tissues to be produced. Alternatively, coding sequences of late stage genes that are under-expressed can be placed under the control of promoters of early stage genes to increase heighten development. 
     Inserting extra copies of the coding sequence early stage genes that are under-expressed can retard action of the late-stage genes and delay the desired development. 
     Fruit development of  Arabidopsis  is one example that can be studied. Siliques of varying sizes, which are representative of different stages, were assayed by microarray techniques. Specifically, mRNA was isolated from siliques between 0-5 mm, between 5-10 mm and &gt;10 mm in length.  FIG. 6  shows expression pattern of a cell wall synthesis gene, cDNAID 1595707, during fruit development. 
     The developmental course shows that the gene encoding a cell wall synthesis protein is up-regulated when the fruit is 0-5 mm but returns to normal levels at 5-10 mm and &gt;10 mm. Increase of cell wall synthesis can lead to larger cells and/or greater number of cells. This type of increase can boost fruit yield. The coding sequence of the cell wall synthesis protein under the control of a strong early stage promoter would increase fruit size or number. 
     A pectinesterase gene was also differentially expressed during fruit development, cDNA ID 1396123. Pectinesterase catalyzes the hydrolysis of pectin into pectate and methanol. This biochemical activity plays an important role in cell wall metabolism during fruit ripening. To shorten the time for fruit ripening, extra copies of this gene with its endogenous promoter can be inserted into a desired plant. With its native promoter, the extra copies of the gene will be expressed at the normal time, to promote extra pectinesterase at the optimal stage of fruit development thereby shortening ripening time. 
     A number of Applicant&#39;s experiments can be grouped together to study changes of transcript levels over a number development stages. Below are examples of groups of experiments:
         Root, Root Tip, and rhl mutant (EXPT IDs 108594, 108433, 108599, 108434, 108439)   Flowers Drought Exposed Flowers, SA Treated Flowers (EXPT IDs 108473, 108474, 108429, 108430, 108431, 108475, 108476, 108501)   BR Shoot Apices, Leaves, Stm (EXPT IDs 108478, 108479, 108480, 108481, 108598, 108535, 108536, 108435)   Leaf and Stm (EXPT IDs 108477, 108512, 108497, 108498, 108598108478, 108479, 108480, 108481, 108598, 108535, 108536, 108435)   Imbibded &amp; Germinating Seeds 1, 2, 3, And 4 Days (EXPT IDs 108461, 108462, 108463, 108464, 108528, 108529, 108530, 108531, 108545, 108546, 108547, 108518, 108529, 108543, 108544)   Tissue Specific Expression (3 week rosette leaves, Tissue Specific Expression (3 week stems), Tissue Specific Expression (2 week roots) (EXPT IDs 108497, 108498, 108439)   Tissue Specific Expression (3 week rosette leaves), Germinating Seeds (EXPT IDs 108497, 108461)   Tissue Specific Expression (3 week rosette leaves, stm mutants, BR_Shoot Apices Expt, root tips, Tissue Specific Expression (2 week roots) (EXPT IDs 108497, 108435, 108480, 108434, 108439)   BR_Shoot Apices Expt, root tips, Tissue Specific Expression (flower buds) (EXPT IDs 108480, 108434, 108431)   Arab_Ler-pi_ovule_1, ap2-floral buds, Tissue Specific Expression (flower buds), Tissue Specific Expression (&lt;5 mm siliques) (EXPT IDs 108595, 108501, 108431, 108437)   Tissue Specific Expression (2 week roots), rhl mutant2, BR_Shoot Apices Expt, Trichome Inflorescences (EXPT IDs 108439, 108433, 108480, 108452)       

     II.A.1.b.3. Proteins that are Common in a Number of Similar Responses can be Identified by Transcriptional Analyses Over a Number of Experiments 
     The differential expression experiments also reveal the genes, and therefore the coding sequence, that are common to a number of cellular responses. By identifying the genes that are differentially expressed in a number of similar responses, the genes at the nexus of a range of responses are discovered. For example, genes that are differentially expressed in all the stress responses are at the hub of many of the stress response pathways. 
     These types of nexus genes, proteins, and pathways are differentially expressed in many or majority of the responses or developmental conditions of interest. Typically, a nexus gene, protein, or pathway is differentially expressed in generally the same direction in many or majority of all the desired experiments. By doing so, the nexus gene can be responsible for triggering the same or similar set of pathways or networks for various cellular responses. This type of gene is useful in modulating pleiotropic effects or triggering or inhibiting a general class of responses. 
     When nexus genes are differentially expressed in a set of responses, but in different directions, these data indicate that a nexus gene is responsible for creating the specificity in a response by triggering the same pathway but to a different degree. Placing such nexus genes under a constitutive promoter to express the proteins at a more constant level can remove the fluctuations. For example, a plant that is better drought adapted, but not cold adapted can be modified to be tolerant to both conditions by placing under the control of a constitutive promoter a nexus gene that is up-regulated in drought but down regulated in cold. 
     Applicants&#39; experiments can be grouped together to identify such nexus genes. Examples of these groups are as follows: 
     Herbicide Response
         Trimec, Finale, GLEAN®, ROUNDUP (EXPT IDs 108467, 107871, 107876, 108468, 107881, 108465, 107896, 108466, 107886, 107891)       

     Stress Response
         Drought, Cold, Heat, Osmotic Stress (EXPT IDs 108578, 108579, 108533, 108534, 108572, 108573, 108502, 108503, 108504, 108556, 108482, 108483, 108473, 108474, 108477, 108576, 108577, 108522, 108523, 108570, 108571, 108541, 108542, 108553, 108539, 108540)   Drought, Cold, Heat, PEG, Trimec, Finale, GLEAN®, ROUNDUP (EXPT IDs 108578, 108579, 108533, 108534, 108572, 108573, 108502, 108503, 108504, 108556, 108482, 108483, 108473, 108474, 108477, 108576, 108577, 108522, 108523, 108570, 108571, 108541, 108542, 108553, 108539, 108540)   Wounding, SA, MeJA, Reactive Oxygen, NO (EXPT IDs 108568, 108569, 108555, 108584, 108585, 108526, 108527, 108559, 108582, 108583, 108537, 108538, 108558, 108586, 108587, 108515, 108552, 108471, 108472, 108469, 108470, 107953, 107960, 108443, 108440, 108441, 108475, 108476, 108574, 108575, 108524, 108525)       

     Hormone Responses
         NAA, BA, BR, GA, TRIMEC (EXPT IDs 108566, 108567, 108517, 108580, 108581, 108557, 108478, 108479, 108480, 108481, 108562, 108563, 108519, 108520, 108521, 108484, 108485, 108486, 108564, 108565, 108516, 108554, 108466, 107886, 107891)   NAA, Trimec (EXPT IDs 108566, 108567, 108517, 108580, 108581, 108557, 108478, 108479, 108480, 108481, 108562, 108563, 108519, 108520, 108521, 108484, 108485, 108486, 108564, 108565, 108516, 108554, 108466, 107886, 107891)       

     II.A.1.b.4. Proteins that are Common to Disparate Responses can be Identified by Transcriptional Analyses Over a Number of Experiments 
     Phenotypes and traits result from complex interactions between cellular pathways and networks. Which pathways are linked by expression of common genes to specify particular traits can be discerned by identifying the genes that show differential expression of seemingly disparate responses or developmental stages. For example, hormone fluxes in a plant can direct cell patterning and organ development. Genes that are differentially expressed both in the hormone experiments and organ development experiments would be of particular interest to control plant development. 
     Examples Of Such Pathway Interactions Include:
         (i) The Interaction Between Stress Tolerance Pathways And Metabolism Pathways;   (ii) Interaction Between Hormone Responses And Developmental Changes In The Plant;   (iii) Interactions Between Nutrient Uptake And Developmental Changes;   (iv) Mediation Of Stress Response By Hormone Responses; And   (v) Interactions Between Stress Response And Development.
 
Applicant&#39;s experiments can be grouped together to identify proteins that participate in interacting pathways or networks. Specific groups of experiments include, for example:
       

     (i) Stress &amp; Metabolism
         Germinating Seeds (Day 1), Arab_0.1 uM_Epi-Brass_1, Arab_NO3_H-to-L_1, Arab_100 uM_GA3_1 (EXPT IDs 108461, 108580, 108592, 108562)       

     (ii) Hormones &amp; Development
         NAA, BA &amp; Root Tips (EXPT IDs 108566, 108567, 108517, 108564, 108565, 108516, 108554, 108434, 108466, 107886, 107891)   NAA, Roots &amp; Root Tips (EXPT IDs 108564, 108565, 108516, 108554, 108599, 108434, 108439, 108466, 107886, 107891)   NAA, BA, Roots And/Or Root Tips (EXPT IDs 108564, 108565, 108516, 108554, 108599, 108434, 108439, 108466, 107886, 107891, 108566, 108567, 108517)   NAA, BA And Leaf (EXPT IDs 108566, 108567, 108517, 108518, 108529, 108512, 108497, 108498, 108598, 108564, 108565, 108516, 108554, 108466, 107886, 107891)   NAA, BA, Leaves, Roots And/Or Root Tips (EXPT IDs 108566, 108567, 108517, 108518, 108529, 108512, 108497, 108498, 108598, 108564, 108565, 108516, 108554, 108466, 107886, 107891, 108599, 108434, 108439)   ABA &amp; Siliques (Of Any Size) (EXPT IDs 108560, 108561, 108513, 108597, 108436, 108437, 108438)   GA, Imbibed &amp; Germinating Seeds, ABA &amp; Siliques (Of Any Size) (EXPT IDs 108560, 108561, 108513, 108597, 108562, 108563, 108519, 108520, 108521, 108484, 108485, 108486, 108461, 108462, 108463, 108464, 108528, 108529, 108530, 108531, 108545, 108546, 108547, 108518, 108529, 108543, 108544, 108436, 108437, 108438)   Tissue Specific Expression (3 week rosette leaves), Arab_0.1 uM_Epi-Brass_1, Arab_100 uM_GA3_1, Germinating Seeds (Day 1), (EXPT IDs 108461, 108497, 108580, 108562, 108461)       

     (iii) Nutrient Uptake And Development
         Any Or All Nitrogen Experiments With Siliques (Of Any Size) (EXPT IDs 108592, 108593, 108588, 108589, 108590, 108591, 108532, 108548, 108549, 108550, 108551, 108454, 108455, 108487, 108488, 108489, 108436, 108437, 108438)   Any Or All Nitrogen Experiments With Roots Or Root Tips (EXPT IDs 108518, 108529, 108592, 108593, 108588, 108589, 108590, 108591, 108532, 108548, 108549, 108550, 108551, 108454, 108455, 108487, 108488, 108489, 108594, 108433, 108599, 108434, 108439)       

     (iv) Stress &amp; Hormones
         ABA, Drought (EXPT IDs 108560, 108561, 108513, 108597, 108572, 108573, 108502, 108503, 108504, 108556, 108482, 108483, 108473, 108474, 108477)   ABA, Drought, Cold, Heat, &amp; Wounding (EXPT IDs 108560, 108561, 108513, 108597, 108578, 108579, 108533, 108534, 108572, 108573, 108502, 108503, 108504, 108556, 108482, 108483, 108473, 108474, 108477, 108576, 108577, 108522, 108523, 108574, 108575, 108524, 108525)   Tissue Specific Expression (3 week rosette leaves), Arab_100 uM_ABA_1, Ws  Arabidopsis  Drought 2 days, Ws  Arabidopsis  Drought 4 days (EXPT IDs 108497, 108560, 108477, 108482)       

     (v) Stress &amp; Hormones Stress &amp; Hormones
         Nitrogen High transition to Low, Arab_NO3_H-to-L_1, Tissue Specific Expression (&lt;5 mm siliques), Tissue Specific Expression (5-10 mm siliques) (EXPT IDs 108455, 108592, 108437, 108436)       

     II.A.1.c. Observations of Phenotypic Changes Show What Physiological Consequences Applicants&#39; Proteins can Produce 
     Another direct means of determining the physiological consequences of a protein is to make aberrant decreases or increases of its expression level in a cell. To this end, Applicants have produced plants where specific genes have been disrupted, or produced plants that include an extra expressed copy of the gene. The plants were then planted under various conditions to determine if any visible physiological changes are caused. These changes then are attributed to the changes in protein levels. 
     II.A.2. Differential Expression Results Explain which External or Internal Stimuli Trigger the Regulatory Sequences 
     Transcriptional studies can reveal the time and place that genes are expressed. Typically, regulatory sequences, such as promoters, introns, UTRs, etc., control when and in which cells transcription occurs. Differential studies can explain the temporal- and location-specific regulatory sequences that control transcription. 
     Using the experiments that are provided herein, one skilled in the art can choose a promoter or any other regulatory sequence that is capable of facilitating the desired pattern of transcription. For example, if a promoter is needed to give rise to increased levels of transcription in response to Auxin, but little expression in response to cytokinin, then the promoters of cDNAs that were up-regulated in the Auxin experiments, but down-regulated the cytokinin experiments would be of interest. 
     Time Course Experiments—Time Sensitive 
     Evaluation of time-course data as described above is also useful to identify time-specific promoters. Promoters or regulatory sequences, like the coding sequences, can be classified as early or late responding according to the microarray data. Promoters that facilitate expression of early or late genes are useful to direct expression of heterologous coding sequences to modulate the cellular response. In the drought data, promoters from “early” responding genes can be selected to activate expression of any desired coding sequence. Thus, a coding sequence for a salt-tolerance protein that is not typically expressed early in response to drought could be linked to an “early” responding promoter to increase salt tolerance within one hour after exposure to drought conditions. 
     Developmental Experiments—Time Sensitive 
     Another class of time-sensitive promoters and other regulatory sequence can be identified from the experiments examining different developmental stages. These regulatory sequences can drive transcription of heterologous sequence at particular times during development. For example, expression of stress-responsive genes during fruit development can protect any gain in fruit yield. 
     Common To Many Pathways—Cause General Effects 
     Promoters and other regulatory sequence associated with cDNAs that are differentially expressed in a number of similar responses can be used to cause general effects. These types of regulatory sequences can be used to inhibit or increase expression of a desired coding sequence in a number circumstances. For example, protein that is capable of acting as an insecticide can be placed under the control a general “stress” promoter to increase expression, not only when the plant is wounded, but under other stress attack. 
     II.B. Experimental Results Also Reveal Pathways or Networks of Genes 
     II.B.1. Genes Whose Transcription are Well Coordinated Generally Act Together to Produce Proteins that Participate in the Same Pathway or Network 
     Patrick Brown, one of the pioneers of microarray chip technology, demonstrated that differential expression experiments can identify groups of genes that encode proteins that participate the same pathway or network. The work focused on phosphate accumulation and metabolism genes in yeast and was published in the paper Ogawa et al.,  Mol Biol Cell  (2000) December; 11(12):4309-21. The authors identified by microarray analysis 22 genes whose transcription was regulated by phosphate concentration. Promoter analysis of these genes showed that 21 of them contained a sequence in their promoters that is recognized by a transcriptional activator that is regulated by phosphate. Further, phenotypic studies were completed by mutational analysis of many of these 22 genes in yeast. The mutants were shown to be either severely deficient in accumulation of inorganic polyphosphate (polyP) and P(i), or associated with normal catabolism of polyP in the yeast vacuole. This publication proves that genes with correlated transcriptional profiles do indeed participate in the same pathway or network. 
     II.B.1.a. Calculating the Correlation Coefficient Between Pairs of Genes Based on the Differential Expression Data 
     The differential expression data obtained over many experiments reveal the global pattern of transcription of a gene. Transcription patterns, also referred to as profiles, of two different genes can be compared. From this comparison, a correlation coefficient can be calculated as a measure of the strength of the relationship between the two profiles. 
     Transcription profiles can be compared by plotting as a point, the differential expression of genel on the x-axis and gene 2 on the y-axis on one experiment. If all the pairs lie on a regression line the relationship and correlation between the two genes are strong. The correlation coefficient can be calculated using a number of methods. In the present case, the Spearman method was utilized. 
     The correlation coefficient can vary from −1 to 1. The coefficient indicates the strength of the relationship between two mRNA transcripts of any set of data that is examined. A zero coefficient indicates that no correlation exists between the transcription profiles of two genes in the samples examined. 
     Biologically, a high correlation coefficient indicates that a gene(s) triggers the activation or repression of the correlated genes, or have related functional roles. Thus, illumination of the activity of one gene can indicate the activities of the genes with highly correlated transcription profiles. This implication is true whether the activity is a biochemical activity, molecular interaction, cellular response, or physiological consequence. 
     II.B.1.b. The Complete Linkage Analyses of Differential Identity Genes with Similar Pattern of Transcription 
     The complete linkage analysis can build groups (or “clusters”) of genes whose transcription patterns are highly correlated or co-regulated. 
     Because genes with related functions are frequently expressed in similar patterns, utilities or roles can be ascribed for genes (without observation of transformed plants) based on their temporal association with other genes of known function (a “guilt-by-association” analysis). Ogawa et al. has used correlated mRNA transcription profiles to identify the function of proteins of unknown function. 
     The complete linkage analysis utilizes the correlation coefficients that are calculated for each pair of genes tested in the microarray experiments. A cluster is first seeded with any arbitrary transcript tested on the chip. The seed transcript, for this illustration, is designated mRNA#0. Next, a minimum threshold is chosen for all acceptable correlation coefficients. In this case, the threshold used was 0.75. A list of potential cluster members is compiled by choosing mRNA transcripts that have a correlation coefficient with mRNA#0 that is greater than the threshold. No limit is placed on the number of mRNAs that can be added to a cluster so long as the correlation coefficient meets the threshold limit criterion. 
     For this example, assume that four mRNAs were added to the cluster, mRNA_1 to mRNA_4. Once the potential cluster members are identified, the cDNA IDs of each member is added to the potential list in order its correlation coefficient to mRNA#1, the largest correlation coefficient first. For this example, let&#39;s suppose four mRNAs 1-4 are potential members, they would be ordered as follows: 
     
       
         
           
               
               
               
             
               
                   
               
               
                   
                   
                 Correlation Coefficient 
               
               
                   
                 MRNA# 
                 with mRNA#0 
               
               
                   
               
             
            
               
                   
               
            
           
           
               
               
               
            
               
                   
                 MRNA#1 
                 0.9 
               
               
                   
                 MRNA#2 
                 0.8 
               
               
                   
                 MRNA#3 
                 0.78 
               
               
                   
                 MRNA#4 
                 0.75 
               
               
                   
               
            
           
         
       
     
     A potential member is accepted into the group, if its correlation coefficients with all other potential members are all greater than the threshold. Thus, for mRNA#1 to remain in the group the correlation coefficient between mRNA#1 and mRNA#2 must be greater than 0.75; and mRNA#1 and #3&gt;0.75; and mRNA#1 and mRNA#4&gt;0.75. Potential cluster members are removed only after reviewing the correlation coefficients in a specific order where mRNAs are reviewed in the order that they appear on the list. 
     Consequently, review of the correlation coefficients does not begin with any random pair, such as mRNA#3 and mRNA#4. The review begins between mRNA#1 and mRNA#2, which are the top two on the list. 
     If correlation coefficient between mRNA#1 and mRNA#2 is less than the threshold, then mRNA#2 is removed from the cluster. mRNA#2 is removed because its correlation coefficient with mRNA#0 is 0.8 which is less than 0.9, the correlation coefficient of mRNA#1 and mRNA#0. 
     This illustrates the rule that if the correlation coefficient is less than the threshold, then only one of the pair not accepted as a cluster member, specifically, the one with the lower coefficient to the seed mRNA#0. 
     This process of iterative reviewing of correlation coefficients between potential members continues until all pairs are reviewed. In this case, the coefficient between mRNA#1 and mRNA#3 would be reviewed because these are the two highest ones on the list besides mRNA#1 and #2. The next pair to be reviewed would be mRNA#1 and #4, etc. 
     Applicants have analyzed the data using several sets of parameters for the complete linkage analysis as shown in the table below: 
     
       
         
           
               
               
               
               
             
               
                   
               
               
                   
                 Correlation 
                 Max number of 
                   
               
               
                   
                 Coefficient 
                 members in a 
               
               
                 Method 
                 Threshold 
                 cluster 
                 Organism 
               
               
                   
               
             
            
               
                   
               
            
           
           
               
               
               
               
            
               
                 CL_METHOD_TYPE=TRUE 
                 0.9 
                 MAX_SIZE=15 
                 
                   Arabidopsis 
                 
               
               
                 CL_METHOD_TYPE=TRUE 
                 0.75 
                 MAX_SIZE=30000 
                 
                   Arabidopsis 
                 
               
               
                 CL_METHOD_TYPE=TRUE 
                 0.70 
                 MAX_SIZE=30000 
                 
                   Arabidopsis 
                 
               
               
                 CL_METHOD_TYPE=TRUE 
                 0.9 
                 MAX_SIZE=15 
                 
                   Zea 
                 
               
               
                 CL_METHOD_TYPE=TRUE 
                 0.75 
                 MAX_SIZE=30000 
                 
                   Zea 
                 
               
               
                 CL_METHOD_TYPE=TRUE 
                 0.70 
                 MAX_SIZE=30000 
                 
                   Zea 
                 
               
               
                 CL_METHOD_TYPE=TRUE 
                 0.9 
                 MAX_SIZE=15 
                 
                   Arabidopsis 
                 
               
               
                 CL_METHOD_TYPE=TRUE 
                 0.75 
                 MAX_SIZE=30000 
                 
                   Arabidopsis 
                 
               
               
                 CL_METHOD_TYPE=TRUE 
                 0.70 
                 MAX_SIZE=30000 
                 
                   Arabidopsis 
                 
               
               
                 CL_METHOD_TYPE=TRUE 
                 0.9 
                 MAX_SIZE=15 
                 
                   Zea 
                 
               
               
                 CL_METHOD_TYPE=TRUE 
                 0.75 
                 MAX_SIZE=30000 
                 
                   Zea 
                 
               
               
                 CL_METHOD_TYPE=TRUE 
                 0.70 
                 MAX_SIZE=30000 
                 
                   Zea 
                 
               
               
                   
               
            
           
         
       
     
     The results of these cluster analyses are reported in the MA_clust table. 
     II.B.1.c. The Nearest Neighbor Analyses of Differential Group Genes with Correlated but Dissimilar Transcription Profiles 
     The nearest neighbor analysis differs from the complete linkage algorithm by not requiring all members to meet the correlation threshold with each other. Thus, a member of a nearest neighbor cluster need only be closely correlated to one other member of the cluster. It is not even required that all members be closely correlated to the seed mRNA transcript. 
     In a complete linkage cluster all the transcription profile of all members are correlated to a greater or lesser extent. In contrast, a cluster deduced by the nearest neighbor analysis may include members with differing transcription profiles. However, nearest neighbor brings to light clusters of interacting genes. In the nearest neighbor analysis, the seed mRNA may not have a very high correlation coefficient with the last mRNA added to the cluster. 
     The nearest neighbor analysis, like the complete linkage analysis, is initiated by seeding each cluster with a mRNA_0. The cluster size is determined by setting a threshold coefficient and setting a limit on the number of members that can be added to the cluster. 
     The cluster is expanded in an iterative fashion determining which mRNA has the highest correlation coefficient with mRNA_0. The additional member is labeled mRNA_1. Next, a list of potential candidates is generated by finding the mRNA that has the highest correlation to mRNA_0 (besides mRNA_1) and finding the mRNA that has the highest coefficient with mRNA_1. Whichever of the candidates has the highest correlation coefficient is added to the cluster. Then, a list of three potential candidates is generated similarly. 
     Addition of members continues until either (1) all the correlation coefficients of potential members is lower than the threshold or (2) number of members in the cluster meets the size limitation. 
     Applicants have analyzed the data using several sets of parameters for the nearest neighbor analysis as shown in the table below: 
     
       
         
           
               
               
               
               
             
               
                   
               
               
                   
                 Correlation 
                 Max number of 
                   
               
               
                   
                 Coefficient 
                 members in a 
               
               
                 Method 
                 Threshold 
                 cluster 
                 Organism 
               
               
                   
               
             
            
               
                   
               
            
           
           
               
               
               
               
            
               
                 NN_METHOD_TYPE=TRUE 
                 0.5 
                 MAX_HITS=15 
                 
                   Arabidopsis 
                 
               
               
                 FULL_NN_METHOD_TYPE=TRUE 
                 0.8 
                 NONE 
                 
                   Arabidopsis 
                 
               
               
                 FULL_NN_METHOD_TYPE=TRUE 
                 0.6 
                 NONE 
                 
                   Arabidopsis 
                 
               
               
                 NN_METHOD_TYPE=TRUE 
                 0.5 
                 MAX_HITS=15 
                 
                   Zea 
                 
               
               
                 FULL_NN_METHOD_TYPE=TRUE 
                 0.8 
                 NONE 
                 
                   Zea 
                 
               
               
                 FULL_NN_METHOD_TYPE=TRUE 
                 0.6 
                 NONE 
                 
                   Zea 
                 
               
               
                 NN_METHOD_TYPE=TRUE 
                 0.5 
                 MAX_HITS=15 
                 
                   Arabidopsis 
                 
               
               
                 FULL_NN_METHOD_TYPE=TRUE 
                 0.8 
                 NONE 
                 
                   Arabidopsis 
                 
               
               
                 FULL_NN_METHOD_TYPE=TRUE 
                 0.6 
                 NONE 
                 
                   Arabidopsis 
                 
               
               
                 NN_METHOD_TYPE=TRUE 
                 0.5 
                 MAX_HITS=15 
                 
                   Zea 
                 
               
               
                 FULL_NN_METHOD_TYPE=TRUE 
                 0.8 
                 NONE 
                 
                   Zea 
                 
               
               
                 FULL_NN_METHOD_TYPE=TRUE 
                 0.6 
                 NONE 
                 
                   Zea 
                 
               
               
                   
               
            
           
         
       
     
     The results of these cluster analyses are reported in the MA_clust table. 
     II.C. Experimental Results Reveal the Functions and Characteristics of Genes, Pathways and Networks 
     II.C.1. Linking Biochemical or Metabolic Activities of One Protein in a Cluster to the Other Proteins in the Same Microarray Cluster 
     As shown in the Ogawa et al.,  Mol Biol Cell  (2000), genes whose transcription profiles cluster together as being strongly correlated typically take part in the same pathway or network. Thus, the activity of one gene in the cluster can be associated to the other genes in the cluster with highly correlated transcription profiles. This association is true whether the activity is a biochemical activity, molecular interaction, cellular response or physiological consequence. 
     One example of this is cluster 420 of the report (shown below). In this cluster, a protein encoded by cDNA ID 1025791 did not match to any pFAM domain. However, through the microarray data, the gene that encodes that protein had a transcription profile that was correlated with other genes that encode ribosomal proteins. Thus, the activity of the ribosomal genes can be associated with the protein with no pFAM match. All the proteins in the same cluster would be associated with mRNA translation and protein synthesis. 
     
       
         
           
               
               
               
               
               
               
               
             
               
                   
               
             
            
               
                 405 
                 4/72428 
                 49012 
                 4741952 
                 (AF134126) Lhcb3 
                 chloroa_b-bind 
                 Chlorophyll 
               
               
                   
                 | 
                   
                   
                 protein 
                   
                 A-B binding 
               
               
                   
                 pheno 
                   
                   
                 [ Arabidopsis  th 
                   
                 proteins 
               
               
                 405 
                 4901465 
                 49012 
                 4741952 
                 (AF134126) Lhcb3 
                 chloroa_b-bind 
                 Chlorophyll 
               
               
                   
                 | 
                   
                   
                 protein 
                   
                 A-B binding 
               
               
                   
                 pheno 
                   
                   
                 [ Arabidopsis  th 
                   
                 proteins 
               
               
                 405 
                 4913083 
                   
                 1345698 
                 CHLOROPHYLL A-B 
                 chloroa_b-bind 
                 Chlorophyll 
               
               
                   
                 | 
                   
                   
                 BINDING 
                   
                 A-B binding 
               
               
                   
                 pheno 
                   
                   
                 PROTEIN 
                   
                 proteins 
               
               
                   
                   
                   
                   
                 151 PREC 
               
               
                 405 
                 5754134 
                 833168 
                 1345698 
                 CHLOROPHYLL A-B 
                 chloroa_b-bind 
                 Chlorophyll 
               
               
                   
                 | 
                   
                   
                 BINDING 
                   
                 A-B binding 
               
               
                   
                 pheno 
                   
                   
                 PROTEIN 
                   
                 proteins 
               
               
                   
                   
                   
                   
                 151 PREC 
               
               
                 406 
                 1018755 
                 806154 
                 1710549 
                 60S 
                 Ribosomal_L39 
                 Ribosomal 
               
               
                   
                 | 
                   
                   
                 RIBOSOMAL 
                   
                 L39 protein 
               
               
                   
                 pheno 
                   
                   
                 PROTEIN 
               
               
                   
                   
                   
                   
                 L39 
               
               
                 406 
                 1032316 
                 811467 
                 11276649 
                 RIBOSOMAL 
                 Ribosomal_S28e 
                 Ribosomal 
               
               
                   
                 | 
                   
                   
                 PROTEIN 
                   
                 protein S28e 
               
               
                   
                 pheno 
                   
                   
                 S28-like- 
               
               
                   
                   
                   
                   
                 
                   Arabidopsis 
                 
               
               
                 406 
                 3433904 
                 819486 
                 11762182 
                 (AF325017) 
                 Ribosomal_S10 
                 Ribosomal 
               
               
                   
                 | 
                   
                   
                 T21L8.120 
                   
                 protein 
               
               
                   
                 pheno 
                   
                   
                 [ Arabidopsis   
                   
                 S10p/S20e 
               
               
                   
                   
                   
                   
                 thalia 
               
               
                 405 
                 4772428 
                 49012 
                 4741952 
                 (AF134126) Lhcb3 
                 chloroa_b-bind 
                 Chlorophyll 
               
               
                   
                 | 
                   
                   
                 protein [ Arabidopsis  th 
                   
                 A-B binding 
               
               
                   
                 pheno 
                   
                   
                   
                   
                 proteins 
               
               
                 405 
                 4901465 
                 49012 
                 4741952 
                 (AF134126) Lhcb3 
                 chloroa_b-bind 
                 Chlorophyll 
               
               
                   
                 | 
                   
                   
                 protein [ Arabidopsis  th 
                   
                 A-B binding 
               
               
                   
                 pheno 
                   
                   
                   
                   
                 proteins 
               
               
                 405 
                 4913083 
                   
                 1345698 
                 CHLOROPHYLL A-B 
                 chloroa_b-bind 
                 Chlorophyll 
               
               
                   
                 | 
                   
                   
                 BINDING PROTEIN 151 
                   
                 A-B binding 
               
               
                   
                 pheno 
                   
                   
                 PREC 
                   
                 proteins 
               
               
                 405 
                 5754134 
                 833168 
                 1345698 
                 CHLOROPHYLL A-B 
                 chloroa_b-bind 
                 Chlorophyll 
               
               
                   
                 | 
                   
                   
                 BINDING PROTEIN 151 
                   
                 A-B binding 
               
               
                   
                 pheno 
                   
                   
                 PREC 
                   
                 proteins 
               
               
                 406 
                 1018755 
                 806154 
                 1710549 
                 60S RIBOSOMAL 
                 Ribosomal_L39 
                 Ribosomal L39 
               
               
                   
                 | 
                   
                   
                 PROTEIN L39 
                   
                 protein 
               
               
                   
                 pheno 
               
               
                 406 
                 1032316 
                 811467 
                 11276649 
                 RIBOSOMAL PROTEIN 
                 Ribosomal_S28e 
                 Ribosomal protein 
               
               
                   
                 | 
                   
                   
                 S28-like -  Arabidopsis   
                   
                 S28e 
               
               
                   
                 pheno 
               
               
                 406 
                 3433904 
                 819486 
                 11762182 
                 (AF325017) T21L8.120 
                 Ribosomal_S10 
                 Ribosomal protein 
               
               
                   
                 | 
                   
                   
                 [ Arabidopsis  thalia 
                   
                 S10p/S20e 
               
               
                   
                 pheno 
               
               
                 406 
                 4772776 
                 512850 
                 6521012 
                 (AB031739) cytoplasmic 
                 Ribosomal_S15 
                 Ribosomal protein 
               
               
                   
                 | 
                   
                   
                 ribosomal protein 
                   
                 S15 
               
               
                   
                 pheno 
               
               
                 407 
                 4283441 
                 822607 
                 7670036 
                 (AB026636) 
               
               
                   
                 | 
                   
                   
                 gb|AAD22658.1~gene_id: 
               
               
                   
                 pheno 
                   
                   
                 K14A17. 
               
               
                 407 
                 4773015 
                 47667 
                 7670036 
                 (AB026636) 
               
               
                   
                 | 
                   
                   
                 gb|AAD22658.1~gene_id: 
               
               
                   
                 pheno 
                   
                   
                 K14A17. 
               
               
                 407 
                 5776387 
                 834698 
                 6006279 
                 (AB015859) photosystem 
               
               
                   
                 | 
                   
                   
                 || 22 kDa protein 
               
               
                   
                 pheno 
               
               
                 408 
                 1023210 
                 306382 
                 3882081 
                 (AJ012552) polyubiquitin 
                 ubiquitin 
                 Ubiquitin family 
               
               
                   
                 | 
                   
                   
                 [ Vicia faba ] gi 
               
               
                   
                 pheno 
               
               
                 408 
                 5670300 
                   
                 7439572 
                 ubiquitin homolog 
                 ubiquitin 
                 Ubiquitin family 
               
               
                   
                 | 
                   
                   
                 T8F5.13 -  Arabidopsis   
               
               
                   
                 pheno 
               
               
                 408 
                 5671852 
                 824621 
                 7439572 
                 ubiquitin homolog 
                 ubiquitin 
                 Ubiquitin family 
               
               
                   
                 | 
                   
                   
                 T8F5.13 -  Arabidopsis   
               
               
                   
                 pheno 
               
               
                 409 
                 1021923 
                 773758 
                 7488279 
                 protein phosphatase 2C 
                 PP2C 
                 Protein 
               
               
                   
                 | 
                   
                   
                 homolog FIIC18.60 
                   
                 phosphatase 2C 
               
               
                   
                 pheno 
               
               
                 409 
                 2992261 
                   
                 7435459 
                 alpha-galactosidase (EC 
                 Melibiase 
                 Melibiase 
               
               
                   
                 | 
                   
                   
                 3.2.1.22) - soyb 
               
               
                   
                 pheno 
               
               
                 409 
                 4801635 
                 833808 
                 2462761 
                 (AC002292) Highly 
                 aldo_ket_red 
                 Aldo/keto 
               
               
                   
                 | 
                   
                   
                 similar to auxin-induc 
                   
                 reductase family 
               
               
                   
                 pheno 
               
               
                 41 
                 1012078 
                 824731 
                 8096347 
                 (AB042810) NAD- 
                 adh_zinc 
                 Zinc-binding 
               
               
                   
                 | 
                   
                   
                 dependent sorbitol 
                   
                 dehydrogenases 
               
               
                   
                 pheno 
                   
                   
                 dehydr 
               
               
                 41 
                 1377714 
                 790347 
                 8096347 
                 (AB042810) NAD- 
                 adh_zinc 
                 Zinc-binding 
               
               
                   
                 | 
                   
                   
                 dependent sorbitol 
                   
                 dehydrogenases 
               
               
                   
                 pheno 
                   
                   
                 dehydr 
               
               
                 41 
                 1441460 
                 824732 
                 8096347 
                 (AB042810) NAD- 
                 adh_zinc 
                 Zinc-binding 
               
               
                   
                 | 
                   
                   
                 dependent sorbitol 
                   
                 dehydrogenases 
               
               
                   
                 pheno 
                   
                   
                 dehydr 
               
               
                 410 
                 1008443 
                 736633 
                 9758519 
                 (AB024025) ribosomal 
                 Ribosomal_S27e 
                 Ribosomal protein 
               
               
                   
                 | 
                   
                   
                 protein S27 [Arabid 
                   
                 S27 
               
               
                   
                 pheno 
               
               
                 410 
                 1010094 
                 804644 
                 6174956 
                 60S RIBOSOMAL 
                 Ribosomal_L7Ae 
                 Ribosomal protein 
               
               
                   
                 | 
                   
                   
                 PROTEIN 
                   
                 L7Ae/L30e/S12e/ 
               
               
                   
                 pheno 
                   
                   
                 L7A gi|7440707|pir 
                   
                 Gadd45 
               
               
                 410 
                 1024837 
                 576803 
                 7441024 
                 ribosomal protein L23a, 
                 Ribosomal_L23 
                 Ribosomal protein 
               
               
                   
                 | 
                   
                   
                 cytosolic - Arab 
                   
                 L23 
               
               
                   
                 pheno 
               
               
                 410 
                 1031267 
                 824697 
                 9802763 
                 (AC008046) Putative 
                 Ribosomal_L35Ae 
                 Ribosomal protein 
               
               
                   
                 | 
                   
                   
                 ribosomal protein [A 
                   
                 L35Ae 
               
               
                   
                 pheno 
               
               
                 410 
                 1032498 
                   
                 730526 
                 60S RIBOSOMAL 
                 Ribosomal_L13e 
                 Ribosomal protein 
               
               
                   
                 | 
                   
                   
                 PROTEIN L13 (BBC1 
                   
                 L13e 
               
               
                   
                 pheno 
                   
                   
                 PROTEIN 
               
               
                 410 
                 1383552 
                 50902 
                 7442279 
                 probable acyl carrier 
                 pp-binding 
                 Phosphopantetheine 
               
               
                   
                 | 
                   
                   
                 protein T8F5.6 - A 
                   
                 attachment site 
               
               
                   
                 pheno 
               
               
                 410 
                 4899830 
                 720622 
                 11276861 
                 60S RIBOSOMAL 
                 Ribosomal_L24 
                 KOW motif 
               
               
                   
                 | 
                   
                   
                 PROTEIN-like -  Arabidopsis   
               
               
                   
                 pheno 
               
               
                 411 
                 1008443 
                 736633 
                 9758519 
                 (AB024025) ribosomal 
                 Ribosomal_S27e 
                 Ribosomal protein 
               
               
                   
                 | 
                   
                   
                 protein S27 [Arabid 
                   
                 S27 
               
               
                   
                 pheno 
               
               
                 411 
                 4899873 
                   
                 10176963 
                 (AB008266) 
                 Ribosomal_S28e 
                 Ribosomal protein 
               
               
                   
                 | 
                   
                   
                 gene_id: 
                   
                 S28e 
               
               
                   
                 pheno 
                   
                   
                 MHJ24.13~similar to u 
               
               
                 411 
                 5776417 
                 834706 
                 7715609 
                 (AC010793) F20B17.4 
                 Na_H_Exchanger 
                 Sodium/hydrogen 
               
               
                   
                 | 
                   
                   
                 [ Arabidopsis thalian   
                   
                 exchanger family 
               
               
                   
                 pheno 
               
               
                 412 
                 1014406 
                   
                 6714454 
                 (AC011620) putative 60S 
                 Ribsomal_L22e 
                 Ribosomal L22e 
               
               
                   
                 | 
                   
                   
                 ribosomal protei 
                   
                 protein family 
               
               
                   
                 pheno 
               
               
                 412 
                 4900035 
                 763830 
                 4678226 
                 (AC007135) 40S 
                 Ribosomal_S11 
                 Ribosomal protein 
               
               
                   
                 | 
                   
                   
                 ribosomal protein S14 
                   
                 S11 
               
               
                   
                 pheno 
                   
                   
                 [Ar 
               
               
                 412 
                 5773772 
                 747111 
                 12325151 
                 (AC016662) putative 60S 
                 Ribosomal_L6e 
                 Ribosomal protein 
               
               
                   
                 | 
                   
                   
                 ribosomal protei 
                   
                 L6e 
               
               
                   
                 pheno 
               
               
                 413 
                 1809157 
                 490070 
                 7440305 
                 ribosomal protein S20, 
                 Ribosomal_S10 
                 Ribosomal protein 
               
               
                   
                 | 
                   
                   
                 cytosilic - Arabi 
                   
                 S10p/S20e 
               
               
                   
                 pheno 
               
               
                 413 
                 4900353 
                 729532 
                 4263826 
                 (AC006067) unknown 
               
               
                   
                 | 
                   
                   
                 protein [ Arabidopsis   
               
               
                   
                 pheno 
               
               
                 413 
                 5756166 
                 732086 
                 11358793 
                 RNA binding protein- 
                 rrm 
                 RNA recognition 
               
               
                   
                 | 
                   
                   
                 like -  Arabidopsis  t 
                   
                 motif (a.k.a. RRM, 
               
               
                   
                 pheno 
                   
                   
                   
                   
                 RBD, 
               
               
                 414 
                 3433862 
                   
                 6225833 
                 PROLIFERATING CELL 
                 PCNA 
                 Proliferating cell 
               
               
                   
                 | 
                   
                   
                 NUCLEAR ANTIGEN 
                   
                 nuclear antigen 
               
               
                   
                 pheno 
                   
                   
                 (PCNA 
               
               
                 414 
                 4901133 
                 714959 
                 7440568 
                 ribosomal protein S27, 
                 Ribosomal_S27e 
                 Ribosomal protein 
               
               
                   
                 | 
                   
                   
                 cytosilic - Arabi 
                   
                 S27 
               
               
                   
                 pheno 
               
               
                 414 
                 4978201 
                 802742 
                 3122753 
                 60S RIBOSOMAL 
                 Ribosomal_L44 
                 Ribosomal protein 
               
               
                   
                 | 
                   
                   
                 PROTEIN 
                   
                 L44 
               
               
                   
                 pheno 
                   
                   
                 L44 gi|7440769|pir 
               
               
                 415 
                 1008443 
                 736633 
                 9758519 
                 (AB024025) ribosomal 
                 Ribosomal_S27e 
                 Ribosomal protein 
               
               
                   
                 | 
                   
                   
                 protein S27 [Arabid 
                   
                 S27 
               
               
                   
                 pheno 
               
               
                 415 
                 1031291 
                 379314 
                 12229933 
                 40S RIBOSOMAL 
                 Ribosomal_L7Ae 
                 Ribosomal protein 
               
               
                   
                 | 
                   
                   
                 PROTEIN S12- 
                   
                 L7Ae/L30e/S12e/ 
               
               
                   
                 pheno 
                   
                   
                 B gi|4263712|g 
                   
                 Gadd45 
               
               
                 415 
                 1386998 
                 47924 
                 11066135 
                 (AF195545) putative 
                 zf-C2H2 
                 Zinc finger, C2H2 
               
               
                   
                 | 
                   
                   
                 histone deacetylase 
                   
                 type 
               
               
                   
                 pheno 
               
               
                 415 
                 4772398 
                 769390 
                 9759463 
                 (AB006696) 40S 
                 Ribosomal_S19e 
                 Ribosomal protein 
               
               
                   
                 | 
                   
                   
                 ribosomal protein S19 
                   
                 S19e 
               
               
                   
                 pheno 
                   
                   
                 [Ar 
               
               
                 415 
                 4901736 
                 111892 
                 9758556 
                 (AB006703) 
               
               
                   
                 | 
                   
                   
                 gene_id: 
               
               
                   
                 pheno 
                   
                   
                 MRH10.8~pir∥T00965~s 
               
               
                 416 
                 1008148 
                 761370 
                 8953720 
                 (AB025606) contains 
               
               
                   
                 | 
                   
                   
                 similarity to 40S ri 
               
               
                   
                 pheno 
               
               
                 416 
                 1024236 
                 57022 
                 3122673 
                 60S RIBOSOMAL 
                 Ribosomal_L15e 
                 Ribosomal L15 
               
               
                   
                 | 
                   
                   
                 PROTEIN 
               
               
                   
                 pheno 
                   
                   
                 L15 gi|7441105|pir 
               
               
                 416 
                 1387671 
                 822158 
                 1350664 
                 60S RIBOSOMAL 
                 Ribosomal_L13e 
                 Ribosomal protein 
               
               
                   
                 | 
                   
                   
                 PROTEIN L13 (CLONE 
                   
                 L13e 
               
               
                   
                 pheno 
                   
                   
                 6.2.1) 
               
               
                 416 
                 1442476 
                 706502 
                 3123264 
                 60S RIBOSOMAL 
                 Ribosomal_L27e 
                 Ribosomal L27e 
               
               
                   
                 | 
                   
                   
                 PROTEIN 
                   
                 protein family 
               
               
                   
                 pheno 
                   
                   
                 L27 gi|7441032|pir 
               
               
                 416 
                 4282667 
                 822768 
                 7549643 
                 (AC023912) ribosomal 
                 Ribosomal_L29e 
                 Ribosomal L29e 
               
               
                   
                 | 
                   
                   
                 protein L29, putati 
                   
                 protein family 
               
               
                   
                 pheno 
               
               
                 416 
                 4909449 
                 833360 
                 1173045 
                 60S RIBOSOMAL 
                 Ribosomal_L37ae 
                 Ribosomal L37ae 
               
               
                   
                 | 
                   
                   
                 PROTEIN 
                   
                 protein family 
               
               
                   
                 pheno 
                   
                   
                 L37A gi|421866|pir 
               
               
                 416 
                 5773091 
                 834732 
                 7262674 
                 (AC012188) Strong 
                 Ribosomal_L10e 
                 Ribosomal L10 
               
               
                   
                 | 
                   
                   
                 similarity, practicall 
               
               
                   
                 pheno 
               
               
                 417 
                 1017282 
                 666913 
                 464707 
                 40S RIBOSOMAL 
                 Ribosomal_S13 
                 Ribosomal protein 
               
               
                   
                 | 
                   
                   
                 PROTEIN 
                   
                 S13/S18 
               
               
                   
                 pheno 
                   
                   
                 S18 gi|480908|pir 
               
               
                 417 
                 1022748 
                 706504 
                 3123264 
                 60S RIBOSOMAL 
                 Ribosomal_L27e 
                 Ribosomal L27e 
               
               
                   
                 | 
                   
                   
                 PROTEIN 
                   
                 protein family 
               
               
                   
                 pheno 
                   
                   
                 L27 gi|7441032|pir 
               
               
                 417 
                 1023297 
                 781025 
                 11276884 
                 60S RIBOSOMAL 
                 Ribosomal_L36e 
                 Ribosomal protein 
               
               
                   
                 | 
                   
                   
                 PROTEIN L36 homolog- 
                   
                 L36e 
               
               
                   
                 pheno 
                   
                   
                 Arab 
               
               
                 417 
                 1031799 
                 706181 
                 6714451 
                 (AC011620) putative 60S 
                 Ribosomal_L18e 
                 Eukaryotic 
               
               
                   
                 | 
                   
                   
                 ribosomal protei 
                   
                 ribosomal protein 
               
               
                   
                 pheno 
                   
                   
                   
                   
                 L18 
               
               
                 417 
                 3439213 
                 437454 
                 1173045 
                 60S RIBOSOMAL 
                 Ribosomal_L37ae 
                 Ribosomal L37ae 
               
               
                   
                 | 
                   
                   
                 PROTEIN 
                   
                 protein family 
               
               
                   
                 pheno 
                   
                   
                 L37A gi|421866|pir 
               
               
                 417 
                 4771334 
                 802750 
                 11762182 
                 (AF325017) T21L8.120 
                 Ribosomal_S10 
                 Ribosomal protein 
               
               
                   
                 | 
                   
                   
                 [ Arabidopsis thalia   
                   
                 S10p/S20e 
               
               
                   
                 pheno 
               
               
                 417 
                 4911380 
                 576635 
                 7488307 
                 ribosomal protein L14 
                 Ribosomal_L14e 
                 Ribosomal protein 
               
               
                   
                 | 
                   
                   
                 homolog T24A18.40 
                   
                 L14 
               
               
                   
                 pheno 
               
               
                 417 
                 5668292 
                 820676 
                 3122753 
                 60S RIBOSOMAL 
                 Ribosomal_L44 
                 Ribosomal protein 
               
               
                   
                 | 
                   
                   
                 PROTEIN 
                   
                 L44 
               
               
                   
                 pheno 
                   
                   
                 L44 gi|7440769|pir 
               
               
                 418 
                 1021968 
                 576661 
                 2651314 
                 (AC002336) 40S 
                 Ribosomal_S26e 
                 Ribosomal protein 
               
               
                   
                 | 
                   
                   
                 ribosomal protein S26 
                   
                 S26e 
               
               
                   
                 pheno 
                   
                   
                 [Ar 
               
               
                 418 
                 3438734 
                   
                 7549643 
                 (AC023912) ribosomal 
                 Ribosomal_L29e 
                 Ribosomal L29e 
               
               
                   
                 | 
                   
                   
                 protein L29, putati 
                   
                 protein family 
               
               
                   
                 pheno 
               
               
                 418 
                 4914438 
                 822558 
                 7549645 
                 (AC023912) ribosomal 
                 Ribosomal_L29e 
                 Ribosomal L29e 
               
               
                   
                 | 
                   
                   
                 protein L29, putati 
                   
                 protein family 
               
               
                   
                 pheno 
               
               
                 419 
                 5662893 
                 818613 
                 7269839 
                 (AL161574) putative 
                 Ribosomal_L28e 
                 Ribosomal L28e 
               
               
                   
                 | 
                   
                   
                 protein [ Arabidopsis   
                   
                 protein family 
               
               
                   
                 pheno 
               
               
                 419 
                 5664311 
                 818503 
                 3122724 
                 60S RIBOSOMAL 
                 Ribosomal_L38e 
                 Ribosomal L38e 
               
               
                   
                 | 
                   
                   
                 PROTEIN 
                   
                 protein family 
               
               
                   
                 pheno 
                   
                   
                 L38 gi|11276909|pi 
               
               
                 419 
                 5758021 
                 833994 
                 6714451 
                 (AC011620) putative 60S 
                 Ribosomal_L18e 
                 Eukaryotic 
               
               
                   
                 | 
                   
                   
                 ribosomal protei 
                   
                 ribosomal protein 
               
               
                   
                 pheno 
                   
                   
                   
                   
                 L18 
               
               
                 42 
                 1012110 
                 778738 
                 6503304 
                 (AC011713) Strong 
                 DnaJ 
                 DnaJ domain 
               
               
                   
                 | 
                   
                   
                 similarity to gb|AF099 
               
               
                   
                 pheno 
               
               
                 42 
                 1383485 
                 379673 
                 2129729 
                 senescence-associated 
                 Rhodanese 
                 Rhodanese-like 
               
               
                   
                 | 
                   
                   
                 protein sen1 - Ara 
                   
                 domain 
               
               
                   
                 pheno 
               
               
                 42 
                 2187156 
                 796738 
                 2129729 
                 senescence-associated 
                 Rhodanese 
                 Rhodanese-like 
               
               
                   
                 | 
                   
                   
                 protein sen1 - Ara 
                   
                 domain 
               
               
                   
                 pheno 
               
               
                 42 
                 4577400 
                 576861 
               
               
                   
                 | 
               
               
                   
                 pheno 
               
               
                 420 
                 1025791 
                 803433 
                 4585878 
                 (AC005850) Unknown 
               
               
                   
                 | 
                   
                   
                 protein [ Arabidopsis   
               
               
                 420 
                 4608965 
                 671877 
                 8567795 
                 (AC013428) 40S 
                 Ribosomal_S17e 
                 Ribosomal S17 
               
               
                   
                 | 
                   
                   
                 ribosomal protein S17, pu 
               
               
                 420 
                 5663116 
                 818554 
                 7486478 
                 hypothetical protein 
                 DapB 
                 Dihydrodipicolinate 
               
               
                   
                 | 
                   
                   
                 F6E13.17 - Arabidop 
                   
                 reductase 
               
               
                 421 
                 1030821 
                   
                 9757825 
                 (AB007651) 60S 
                 Ribosomal_L1 
                 L1P family of 
               
               
                   
                 | 
                   
                   
                 ribosomal protein L10A [A 
                   
                 ribosomal proteins 
               
               
                   
                 pheno 
               
               
                 421 
                 1976457 
                 145369 
                 166867 
                 (J05216) ribosomal 
                 Ribosomal_S17 
                 Ribosomal protein 
               
               
                   
                 | 
                   
                   
                 protein S11 (probable 
                   
                 S17 
               
               
                   
                 pheno 
               
               
                 421 
                 5663301 
                 822232 
                 9757825 
                 (AB007651) 60S 
                 Ribosomal_L1 
                 L1P family of 
               
               
                   
                 | 
                   
                   
                 ribosomal protein L10A [A 
                   
                 ribosomal proteins 
               
               
                   
                 pheno 
               
               
                 421 
                 5664362 
                 215197 
                 9757825 
                 (AB007651) 60S 
                 Ribosomal_L1 
                 L1P family of 
               
               
                   
                 | 
                   
                   
                 ribosomal protein L10A [A 
                   
                 ribosomal proteins 
               
               
                   
                 pheno 
               
               
                 422 
                 1007370 
                 358288 
                 7440340 
                 ribosomal protein S14, 
                 Ribosomal_S11 
                 Ribosomal protein 
               
               
                   
                 | 
                   
                   
                 cytosolic - Arabi 
                   
                 S11 
               
               
                   
                 pheno 
               
               
                 422 
                 1012349 
                   
                 7440636 
                 ribosomal protein L8, 
                 Ribosomal_L2 
                 Ribosomal 
               
               
                   
                 | 
                   
                   
                 cytosolic - Arabid 
                   
                 Proteins L2 
               
               
                   
                 pheno 
               
               
                 422 
                 4767515 
                 803201 
                 5912424 
                 (AJ242970) BTF3b-like 
                 NAC 
                 NAC domain 
               
               
                   
                 | 
                   
                   
                 factor [Arabidopsi 
               
               
                   
                 pheno 
               
               
                 422 
                 4978201 
                 802742 
                 3122753 
                 60S RIBOSOMAL 
                 Ribosomal_L44 
                 Ribosomal protein 
               
               
                   
                 | 
                   
                   
                 PROTEIN 
                   
                 L44 
               
               
                   
                 pheno 
                   
                   
                 L44 gi|7440769|pir 
               
               
                 422 
                 5663862 
                 56862 
                 7440560 
                 ribosomal protein S25, 
               
               
                   
                 | 
                   
                   
                 cytosolic - Arabi 
               
               
                   
                 pheno 
               
               
                 422 
                 5677309 
                 804632 
                 464707 
                 40S RIBOSOMAL 
                 Ribosomal_S13 
                 Ribosomal protein 
               
               
                   
                 | 
                   
                   
                 PROTEIN 
                   
                 S13/S18 
               
               
                   
                 pheno 
                   
                   
                 S18 gi|480908|pir| 
               
               
                 423 
                 1569568 
                 57302 
                 12323985 
                 (AC015450) unknown 
               
               
                   
                 | 
                   
                   
                 protein; 83277-83927 
               
               
                   
                 pheno 
               
               
                 423 
                 5667720 
                 436439 
                 4314401 
                 (AC006232) putative 
                 Glyco_hydro_17 
                 Glycosyl 
               
               
                   
                 | 
                   
                   
                 beta-1,3-glucanase [ 
                   
                 hydrolases family 
               
               
                   
                 pheno 
                   
                   
                   
                   
                 17 
               
               
                 423 
                 5677344 
                 735070 
                 9758647 
                 (AB011485) 
               
               
                   
                 | 
                   
                   
                 gene_id: 
               
               
                   
                 pheno 
                   
                   
                 MXH1.11~pir∥T10200~s 
               
               
                 424 
                 1442476 
                 706502 
                 3123264 
                 60S RIBOSOMAL 
                 Ribosomal_L27e 
                 Ribosomal L27e 
               
               
                   
                 | 
                   
                   
                 PROTEIN 
                   
                 protein family 
               
               
                   
                 pheno 
                   
                   
                 L27 gi|7441032|pir 
               
               
                 424 
                 2991489 
                 674871 
                 11276881 
                 ribosomal protein L35a, 
                 Ribosomal_L35Ae 
                 Ribosomal protein 
               
               
                   
                 | 
                   
                   
                 cytosolic [simil 
                   
                 L35Ae 
               
               
                   
                 pheno 
               
               
                 424 
                 3438734 
                   
                 7549643 
                 (AC023912) ribosomal 
                 Ribosomal_L29e 
                 Ribosomal L29e 
               
               
                   
                 | 
                   
                   
                 protein L29, putati 
                   
                 protein family 
               
               
                   
                 pheno 
               
               
                 424 
                 3439472 
                 803062 
                 10176775 
                 (AB013392) 60S 
                 Ribosomal_L31e 
                 Ribosomal protein 
               
               
                   
                 | 
                   
                   
                 ribosomal protein L31 
                   
                 L31e 
               
               
                   
                 pheno 
                   
                   
                 [Ar 
               
               
                 424 
                 4282667 
                 822768 
                 7549643 
                 (AC023912) ribosomal 
                 Ribosomal_L29e 
                 Ribosomal L29e 
               
               
                   
                 | 
                   
                   
                 protein L29, putati 
                   
                 protein family 
               
               
                   
                 pheno 
               
               
                 424 
                 5665234 
                 819865 
                 7441176 
                 ribosomal protein L35, 
                 Ribosomal_L29 
                 Ribosomal L29 
               
               
                   
                 | 
                   
                   
                 cytosolic - Arabi 
                   
                 protein 
               
               
                   
                 pheno 
               
               
                 424 
                 5667812 
                 786382 
                 464638 
                 60S RIBOSOMAL 
               
               
                   
                 | 
                   
                   
                 PROTEIN 
               
               
                   
                 pheno 
                   
                   
                 L41 gi|481238|pir| 
               
               
                 424 
                 5668292 
                 820676 
                 3122753 
                 60S RIBOSOMAL 
                 Ribosomal_L44 
                 Ribosomal protein 
               
               
                   
                 | 
                   
                   
                 PROTEIN 
                   
                 L44 
               
               
                   
                 pheno 
                   
                   
                 L44 gi|7440769|pir 
               
               
                 424 
                 5669508 
                   
                 6714451 
                 (AC011620) putative 60S 
                 Ribosomal_L18e 
                 Eukaryotic 
               
               
                   
                 | 
                   
                   
                 ribosomal protei 
                   
                 ribosomal protein 
               
               
                   
                 pheno 
                   
                   
                   
                   
                 L18 
               
               
                 425 
                 1379607 
                 53378 
                 7486241 
                 hypothetical protein 
               
               
                   
                 | 
                   
                   
                 F27F23.18 - Arabido 
               
               
                   
                 pheno 
               
               
                 425 
                 1396354 
                 52394 
                 4895185 
                 (AC007661) unknown 
               
               
                   
                 | 
                   
                   
                 protein [ Arabidopsis   
               
               
                   
                 pheno 
               
               
                 425 
                 5668427 
                 490908 
                 7440779 
                 ribosomal protein L24 
                 Ribosomal_L24e 
                 Ribosomal protein 
               
               
                   
                 | 
                   
                   
                 homolog T13E15.13 
                   
                 L24e 
               
               
                   
                 pheno 
               
               
                 426 
                 1022748 
                 706504 
                 3123264 
                 60S RIBOSOMAL 
                 Ribosomal_L27e 
                 Ribosomal L27e 
               
               
                   
                 | 
                   
                   
                 PROTEIN 
                   
                 protein family 
               
               
                   
                 pheno 
                   
                   
                 L27 gi|7441032|pir 
               
               
                 426 
                 1032313 
                 48511 
                 99771 
                 ubiquitin/ribosomal 
                 ubiquitin 
                 Ubiquitin family 
               
               
                   
                 | 
                   
                   
                 protein S27a.1 - A 
               
               
                   
                 pheno 
               
               
                 426 
                 5668720 
                 498038 
                 10176841 
                 (AB005244) 40S 
                 Ribosomal_S17 
                 Ribosomal protein 
               
               
                   
                 | 
                   
                   
                 ribosomal protien S11 
                   
                 S17 
               
               
                   
                 pheno 
                   
                   
                 [Ar 
               
               
                 426 
                 5754280 
                 835386 
                 3860277 
                 (AC005824) 60S 
                 Ribosomal_L1 
                 L1P family of 
               
               
                   
                 | 
                   
                   
                 ribosomal protien L10A 
                   
                 ribosomal proteins 
               
               
                   
                 pheno 
                   
                   
                 [Ar 
               
               
                 426 
                 5754419 
                 47796 
                 11134742 
                 40S RIBOSOMAL 
                 Ribosomal_S24e 
                 Ribosomal protein 
               
               
                   
                 | 
                   
                   
                 PROTEIN 
                   
                 S24e 
               
               
                   
                 pheno 
                   
                   
                 S24 gi|12322851|gb 
               
               
                 427 
                 1010385 
                 512919 
                 11276730 
                 acidic ribosomal protein 
                 60s_ribosomal 
                 60s Acidic 
               
               
                   
                 | 
                   
                   
                 P2-like - Arabi 
                   
                 ribosomal protein 
               
               
                   
                 pheno 
               
               
                 427 
                 1384016 
                 51641 
                 12322852 
                 (AC009465) putative 40S 
                 Ribosomal_S3Ae 
                 Ribosomal S3Ae 
               
               
                   
                 | 
                   
                   
                 ribosomal protei 
                   
                 family 
               
               
                   
                 pheno 
               
               
                 427 
                 4772398 
                 769390 
                 9759463 
                 (AB006696) 40S 
                 Ribosomal_S19e 
                 Ribosomal protein 
               
               
                   
                 | 
                   
                   
                 ribosomal protein S19 
                   
                 S19e 
               
               
                   
                 pheno 
                   
                   
                 [Ar 
               
               
                 427 
                 5669025 
                 513703 
                 7484789 
                 acidic ribosomal protein 
                 60s_ribosomal 
                 60s Acidic 
               
               
                   
                 | 
                   
                   
                 P3a homolog F14 
                   
                 ribosomal protein 
               
               
                   
                 pheno 
               
               
                 428 
                 3435646 
                   
                 4206765 
                 (AF104329) putative type 
                 PsbP 
                 PsbP 
               
               
                   
                 | 
                   
                   
                 1 membrane prot 
               
               
                   
                 pheno 
               
               
                 428 
                 3437710 
                 48667 
                 1644289 
                 (X95727) chlorophyll 
                 chloroa_b-bind 
                 Chlorophyll A-B 
               
               
                   
                 | 
                   
                   
                 a/b-binding protein 
                   
                 binding proteins 
               
               
                   
                 pheno 
               
               
                 428 
                 5669724 
                   
                 7443149 
                 photosystem I chain IV 
                 PSI_PsaE 
                 Photosystem I 
               
               
                   
                 | 
                   
                   
                 homolog F16A16.14 
                   
                 reaction centre 
               
               
                   
                 pheno 
                   
                   
                   
                   
                 subunit IV 
               
               
                 429 
                 1010094 
                 804644 
                 6174956 
                 60S RIBOSOMAL 
                 Ribosomal_L7Ae 
                 Ribosomal protein 
               
               
                   
                 | 
                   
                   
                 PROTEIN 
                   
                 L7Ae/L30e/S12e/ 
               
               
                   
                 pheno 
                   
                   
                 L7A gi|7440707|pir 
                   
                 Gadd45 
               
               
                 429 
                 1024015 
                 820185 
                 11276721 
                 60S RIBOSOMAL 
                 Ribosomal_L7Ae 
                 Ribosomal protein 
               
               
                   
                 | 
                   
                   
                 PROTEIN L7A protein- 
                   
                 L7Ae/L30e/S12e/ 
               
               
                   
                 pheno 
                   
                   
                 Arab 
                   
                 Gadd45 
               
               
                 429 
                 1024236 
                 57022 
                 3122673 
                 60S RIBOSOMAL 
                 Ribosomal_L15e 
                 Ribosomal L15 
               
               
                   
                 | 
                   
                   
                 PROTEIN 
               
               
                   
                 pheno 
                   
                   
                 L15 gi|7441105|pir 
               
               
                 429 
                 1024993 
                 824724 
                 12229932 
                 40S RIBOSOMAL 
                 Ribosomal_L7Ae 
                 Ribosomal protein 
               
               
                   
                 | 
                   
                   
                 PROTEIN S12- 
                   
                 L7Ae/L30e/S12e/ 
               
               
                   
                 pheno 
                   
                   
                 A gi|6587799|g 
                   
                 Gadd45 
               
               
                 429 
                 3439213 
                 437454 
                 1173045 
                 60S RIBOSOMAL 
                 Ribosomal_L37ae 
                 Ribosomal L37ae 
               
               
                   
                 | 
                   
                   
                 PROTEIN 
                   
                 protein family 
               
               
                   
                 pheno 
                   
                   
                 L37A gi|421866|pir 
               
               
                 429 
                 4901171 
                 824724 
                 12229932 
                 40S RIBOSOMAL 
                 Ribosomal_L7Ae 
                 Ribosomal protein 
               
               
                   
                 | 
                   
                   
                 PROTEIN S12- 
                   
                 L7Ae/L30e/S12e/ 
               
               
                   
                 pheno 
                   
                   
                 A gi|6587799|g 
                   
                 Gadd45 
               
               
                 429 
                 5671204 
                 808980 
                 1710587 
                 60S ACIDIC 
                 Ribosomal_L10 
                 Ribosomal protein 
               
               
                   
                 | 
                   
                   
                 RIBOSOMAL PROTEIN 
                   
                 L10 
               
               
                   
                 pheno 
                   
                   
                 P0 gi|74407 
               
               
                 429 
                 5773091 
                 834732 
                 7262674 
                 (AC012188) Strong 
                 Ribosomal_L10e 
                 Ribosomal L10 
               
               
                   
                 | 
                   
                   
                 similarity, practicall 
               
               
                   
                 pheno 
               
               
                 43 
                 1012128 
                 796000 
                 4678226 
                 (AC007135) 40S 
                 Ribosomal_S11 
                 Ribosomal protein 
               
               
                   
                 | 
                   
                   
                 ribosomal protein S14 
                   
                 S11 
               
               
                   
                 pheno 
                   
                   
                 [Ar 
               
               
                 43 
                 1024126 
                 56624 
                 464707 
                 40S RIBOSOMAL 
                 Ribosomal_S13 
                 Ribosomal protein 
               
               
                   
                 | 
                   
                   
                 PROTEIN 
                   
                 S13/S18 
               
               
                   
                 pheno 
                   
                   
                 S18 gi|480908|pir| 
               
               
                 43 
                 1024993 
                 824724 
                 12229932 
                 40S RIBOSOMAL 
                 Ribosomal_L7Ae 
                 Ribosomal protein 
               
               
                   
                 | 
                   
                   
                 PROTEIN S12- 
                   
                 L7Ae/L30e/S12e/ 
               
               
                   
                 pheno 
                   
                   
                 A gi|6587799|g 
                   
                 Gadd45 
               
               
                 43 
                 1714831 
                 306741 
                 11994560 
                 (AP002038) 60S 
                 Ribosomal_L30 
                 Ribosomal protein 
               
               
                   
                 | 
                   
                   
                 ribosomal protein L7 
                   
                 L30p/L7e 
               
               
                   
                 pheno 
                   
                   
                 [Ara 
               
               
                 43 
                 4901171 
                 824724 
                 12229932 
                 40S RIBOSOMAL 
                 Ribosomal_L7Ae 
                 Ribosomal protein 
               
               
                   
                 | 
                   
                   
                 PROTEIN S12- 
                   
                 L7Ae/L30e/S12e/ 
               
               
                   
                 pheno 
                   
                   
                 A gi|6587799|g 
                   
                 Gadd45 
               
               
                 43 
                 5671204 
                 808980 
                 1710587 
                 60S ACIDIC 
                 Ribosomal_L10 
                 Ribosomal protein 
               
               
                   
                 | 
                   
                   
                 RIBOSOMAL PROTEIN 
                   
                 L10 
               
               
                   
                 pheno 
                   
                   
                 P0 gi|74407 
               
               
                 43 
                 5753942 
                 157527 
                 3860277 
                 (AC005824) 60S 
                 Ribosomal_L1 
                 L1P family of 
               
               
                   
                 | 
                   
                   
                 ribosomal protein L10A 
                   
                 ribosomal proteins 
               
               
                   
                 pheno 
                   
                   
                 [A 
               
               
                 43 
                 5754280 
                 835386 
                 3860277 
                 (AC005824) 60S 
                 Ribosomal_L1 
                 L1P family of 
               
               
                   
                 | 
                   
                   
                 ribosomal protein L10A 
                   
                 ribosomal proteins 
               
               
                   
                 pheno 
                   
                   
                 [A 
               
               
                 43 
                 5758021 
                 833994 
                 6714451 
                 (AC011620) putative 60S 
                 Ribosomal_L18e 
                 Eukaryotic 
               
               
                   
                 | 
                   
                   
                 ribosomal protei 
                   
                 ribosomal protein 
               
               
                   
                 pheno 
                   
                   
                   
                   
                 L18 
               
               
                 43 
                 5773091 
                 834732 
                 7262674 
                 (AC012188) Strong 
                 Ribosomal_L10e 
                 Ribosomal L10 
               
               
                   
                 | 
                   
                   
                 similarity, practicall 
               
               
                   
                 pheno 
               
               
                 430 
                 1030231 
                 721378 
                 11276860 
                 ribosomal L23a-like 
                 Ribosomal_L23 
                 Ribosomal protein 
               
               
                   
                 | 
                   
                   
                 protein -  Arabidopsi   
                   
                 L23 
               
               
                   
                 pheno 
               
               
                 430 
                 5663934 
                 819000 
                 12322482 
                 (AC025781) 60S 
                 Ribosomal_L7Ae 
                 Ribosomal protein 
               
               
                   
                 | 
                   
                   
                 ribosomal protein L30, pu 
                   
                 L7Ae/L30e/S12e/ 
               
               
                   
                 pheno 
                   
                   
                   
                   
                 Gadd45 
               
               
                 430 
                 5671318 
                 823529 
                 9294455 
                 (AB012247) 
                 Ribosomal_L37e 
                 Ribosomal protein 
               
               
                   
                 | 
                   
                   
                 gene_id: 
                   
                 L37e 
               
               
                   
                 pheno 
                   
                   
                 MSL1.12~unknown prote 
               
               
                 431 
                 1027590 
                   
                 6714285 
                 (AC017118) F6N18.2 
               
               
                   
                 | 
                   
                   
                 [ Arabidopsis thaliana   
               
               
                   
                 pheno 
               
               
                 431 
                 5671710 
                 721322 
                 282865 
                 chlorophyll a/b-binding 
                 chloroa_b-bind 
                 Chlorophyll 
               
               
                   
                 | 
                   
                   
                 protein F28P10.1 
                   
                 A-B binding 
               
               
                   
                 pheno 
                   
                   
                   
                   
                 proteins 
               
               
                 431 
                 5759467 
                 835747 
                 12324161 
                 (AC022455) chlorophyll 
                 chloroa_b-bind 
                 Chlorophyll 
               
               
                   
                 | 
                   
                   
                 A-B-binding prote 
                   
                 A-B binding 
               
               
                   
                 pheno 
                   
                   
                   
                   
                 proteins 
               
               
                 431 
                 5773759 
                 460944 
                 4741950 
                 (AF134125) Lhcb2 
                 chloroa_b-bind 
                 Chlorophyll 
               
               
                   
                 | 
                   
                   
                 protein [ Arabidopsis  th 
                   
                 A-B binding 
               
               
                   
                 pheno 
                   
                   
                   
                   
                 proteins 
               
               
                 432 
                 2106017 
                 490151 
                 10177906 
                 (AB016886) 60S acidic 
                 60s_ribosomal 
                 60s Acidic 
               
               
                   
                 | 
                   
                   
                 ribosomal protein 
                   
                 ribosomal protein 
               
               
                   
                 pheno 
               
               
                 432 
                 5672842 
                 821491 
                 10177906 
                 (AB016886) 60S acidic 
                 60s_ribosomal 
                 60s Acidic 
               
               
                   
                 | 
                   
                   
                 ribosomal protein 
                   
                 ribosomal protein 
               
               
                   
                 pheno 
               
               
                 432 
                 5773091 
                 834732 
                 7262674 
                 (AC012188) Strong 
                 Ribosomal_L10e 
                 Ribosomal L10 
               
               
                   
                 | 
                   
                   
                 similarity, practicall 
               
               
                   
                 pheno 
               
               
                 433 
                 1023278 
                 706501 
                 11994741 
                 (AP001306) 60S 
                 Ribosomal_L27e 
                 Ribosomal L27e 
               
               
                   
                 | 
                   
                   
                 ribosomal protein L27 
                   
                 protein family 
               
               
                   
                 pheno 
                   
                   
                 [Ar 
               
               
                 433 
                 1024236 
                 57022 
                 3122673 
                 60S RIBOSOMAL 
                 Ribosomal_L15e 
                 Ribosomal L15 
               
               
                   
                 | 
                   
                   
                 PROTEIN 
               
               
                   
                 pheno 
                   
                   
                 L15 gi|7441105|pir 
               
               
                 433 
                 1027760 
                 818470 
                 11276653 
                 ribosomal protein S26, 
                 Ribosomal_S26e 
                 Ribosomal protein 
               
               
                   
                 | 
                   
                   
                 cytosolic [simila 
                   
                 S26e 
               
               
                   
                 pheno 
               
               
                 433 
                 1029485 
                 54167 
                 10092293 
                 (AC021046) 60S 
                 Ribosomal_L34e 
                 Ribosomal protein 
               
               
                   
                 | 
                   
                   
                 ribosomal protein L34, pu 
                   
                 L34e 
               
               
                   
                 pheno 
               
               
                 433 
                 1387671 
                 822158 
                 1350664 
                 60S RIBOSOMAL 
                 Ribosomal_L13e 
                 Ribosomal protein 
               
               
                   
                 | 
                   
                   
                 PROTEIN L13 (CLONE 
                   
                 L13e 
               
               
                   
                 pheno 
                   
                   
                 6.2.1) 
               
               
                 433 
                 1442476 
                 706502 
                 3123264 
                 60S RIBOSOMAL 
                 Ribosomal_L27e 
                 Ribosomal L27e 
               
               
                   
                 | 
                   
                   
                 PROTEIN 
                   
                 protein family 
               
               
                   
                 pheno 
                   
                   
                 L27 gi|7441032|pir 
               
               
                 433 
                 2781341 
                   
                 3860277 
                 (AC005824) 60S 
                 Ribosomal_L1 
                 L1P family of 
               
               
                   
                 | 
                   
                   
                 ribosomal protein L10A 
                   
                 ribosomal proteins 
               
               
                   
                 pheno 
                   
                   
                 [A 
               
               
                 433 
                 3445482 
                   
                 1173045 
                 60S RIBOSOMAL 
                 Ribosomal_L37ae 
                 Ribosomal L37ae 
               
               
                   
                 | 
                   
                   
                 PROTEIN 
                   
                 protein family 
               
               
                   
                 pheno 
                   
                   
                 L37A gi|421866|pir 
               
               
                 433 
                 5668065 
                 884827 
                 11276646 
                 40S ribosomal protein 
                 Ribosomal_S21e 
                 Ribosomal protein 
               
               
                   
                 | 
                   
                   
                 S21 homolog - Arab 
                   
                 S21e 
               
               
                   
                 pheno 
               
               
                 433 
                 5674194 
                 818470 
                 11276653 
                 ribosomal protein S26, 
                 Ribosomal_S26e 
                 Ribosomal protein 
               
               
                   
                 | 
                   
                   
                 cytosolic [simila 
                   
                 S26e 
               
               
                   
                 pheno 
               
               
                 434 
                 4771334 
                 802750 
                 11762182 
                 (AF325017) T21L8.120 
                 Ribosomal_S10 
                 Ribosomal protein 
               
               
                   
                 | 
                   
                   
                 [ Arabidopsis thalia   
                   
                 S10p/S20e 
               
               
                   
                 pheno 
               
               
                 434 
                 5674666 
                 780378 
                 2459420 
                 (AC002332) 60S 
                 Ribosomal_L14 
                 Ribosomal protein 
               
               
                   
                 | 
                   
                   
                 ribosomal protein L23 
                   
                 L14p/L23e 
               
               
                   
                 pheno 
                   
                   
                 [Ar 
               
               
                 434 
                 5754419 
                 47796 
                 11134742 
                 40S RIBOSOMAL 
                 Ribosomal_S24e 
                 Ribosomal protein 
               
               
                   
                 | 
                   
                   
                 PROTEIN 
                   
                 S2 
               
               
                   
                 pheno 
                   
                   
                 S24 gi|12322851|gb 
               
               
                   
               
            
           
         
       
     
     II.C.2 Using Differential Expression Data to Determine when the Genes and Pathways are Active 
     The differential expression data can be used to associate the cellular response that results when the clusters of genes are transcribed. For the complete linkage clusters, the genes in the cluster will produce similar transcription profiles. The experiments where the genes in the cluster are differentially expressed as compared to the control define the cellular responses that all the genes of the cluster are capable of modulating. 
     For example, for the cluster shown above, the mRNA levels for the genes were significantly different in the nitrogen response experiments. Thus, the data shows that this cluster of genes is associated with protein synthesis in response to nutrient uptake. 
     II.C.3. Using Phenotype Data to Determine when Genes and Pathways are Active 
     The phenotypic data can be used to demonstrate the physiological consequences of that result when a cluster of genes is active. Whether the clusters were generated by the complete linkage or the nearest neighbor analyses, if a single gene in the cluster has been implicated in phenotypic changes, then any one or combination of the other genes in the cluster can also modulate the same or similar phenotypic changes. 
     Utilities of Particular Interest 
     The following sections describe utilities/functions for the genes, gene components and products of the invention. The sequences of the invention, as discussed above, can be recognized as a particular type of gene (e.g. root gene, leaf gene, etc.) by means of particular terms utilized in the Knock-in and Knock-out Tables and by the results of the differential expression experiments. Combined analysis of those data also identify genes with utilities/functions of particular interest. The Single Gene Functions and Utilities Table correlates that data and specific genes with those utilities/functions of particular interest. 
     Utilities of Particular Interest for Clustered Sequences 
     As discussed further herein, the genes, gene components and products of the invention have been clustered together into groups. This enables one to understand the function/utility of one member of the cluster based upon knowledge about one or more other members of the cluster. In addition, this enables an understanding of some utilities/functions of a cluster that would be of particular interest. The Cluster Fucntions and Utilities Table lists some of the clusters of the invention and notes the functions/utilities that are of particular interest for each of the clusters. Of course, these functions/utilities are of particular interest for each member of each particular cluster. 
     II.D. Experimental Results Provide an Understanding of Genes, Pathways and Networks in Many Plant Species 
     By analyzing the constant and variable properties of groups of similar sequences, it is possible to derive a structural and functional signature for a protein family, which distinguishes its members from all other proteins. This approach has allowed the Applicants to assign proteins into functional groups and identify orthologous proteins both within and between species. A pertinent analogy to be considered is the use of fingerprints by the police for identification purposes. A fingerprint is generally sufficient to identify a given individual. Similarly, a protein signature can be used to assign a newly sequenced protein to a specific family of proteins and thus to formulate hypotheses about its function. 
     Proteins can be grouped together because they share a single motif or many motifs. Typically, proteins that share a series of motifs share greater functional equivalence. Usually, signature sequences comprise more than one motif in a particular order from N-terminus to C-terminus. 
     A list of these groups can be found in the Protein Group Table. The sequences were grouped together using the iterative protein sequence local alignment software, PSI-BLAST. This software begins by aligning a number sequences where the probability that the alignment occurred by chance is set by a threshold e-value. In the Applicants&#39; case, the threshold e-value was set at 10 −50 , 10 −30 , and 10 −10 . The algorithm generates a consensus sequence from the sequences that were aligned together. The consensus sequence was then used to find sequences that matched to it with a probability that was less than the set threshold. The algorithm performs the iterative tasks of aligning and generating a consensus sequence any number of times. Generally, Applicants performed one iteration for the 10 −10  e-value threshold, two iterations for the 10 −30  threshold, and three iterations for the 10 −50  threshold. 
     Each group can contain sequences from one of more organisms. The groups included both Ceres polypeptides and public polypeptide sequences. The Ceres polypeptides are identified by their Ceres Sequence ID NO as listed in the Reference Table. 
     Each group contains sequences that were included at the 10 −50 , 10 −30 , and 10 −10  e-value cutoffs. For each group, the peptide ID and at which cutoff the peptide was included into the group. The same peptide ID may be included in the group three times as peptide ID 50, peptide ID 30 and peptide ID 10. The data indicates that peptide ID was included in the group when the threshold was either 10 −50 , 10 −30 , or 10 −10 . All the peptide IDs that are followed by “50” were included in the protein group when the e-value cutoff was 10 −50 . All the peptide IDs that are followed by either “30” or “50” were included in the protein group when the threshold e-value was 10 −10 . All the peptide IDs that are followed by “10”, “30” or “50” were included in the protein group when 10 −10  was used as the e-value cutoff. 
     II.D.1. Conserved Sequences Between Proteins of Different Species Give Rise to a Signature Sequence 
     The signature sequence for each group of proteins, also referred to as the consensus sequence. The signature sequence comprises the amino acids that are conserved throughout all the proteins in a particular protein group. The data are shown in the Protein Group table. 
     Not all the polypeptides in a group are the same length. Thus, some members of the group may not contain the entire signature sequence. However, throughout the length of any member protein, its sequence will match the signature sequence. 
     The consensus sequence contains both lower-case and upper-case letters. The upper-case letters represent the standard one-letter amino acid abbreviations. The lower case letters represent classes of amino acids:
         “t” refers to tiny amino acids, which are specifically alanine, glycine, serine and threonine.   “p” refers to polar amino acids, which are specifically, asparagine and glutamine   “n” refers to negatively charged amino acids, which are specifically, aspartic acid and glutamic acid   “+” refers to positively charged residues, which are specifically, lysine, arginine, and histidine   “r” refers to aromatic residues, which are specifically, phenylalanine, tyrosine, and tryptophan,   “a” refers to aliphatic residues, which are specifically, isoleucine, valine, leucine, and methonine       

     In addition to each consensus sequence, Applicants have generated a scoring matrix to provide further description of the consensus sequence. The matrix reports the identity and number of occurrences of all the amino acids that were found in the group members for every residue position of the signature sequence. The matrix also indicates for each residue position, how many different organisms were found to have a polypeptide in the group that included a residue at the relevant position. These results are reported in the Protein Group Matrix table. 
     Functional equivalents share similar (1) structural characteristics; (2) biochemical activities and molecular interactions; (3) cellular responses or activities; or (4) phenotypic effects. 
     II.D.2. Linking Signature Sequences to Conservation of Structural Characteristics 
     Proteins with related functions show similar three-dimensional structures but may not show extensive amino acid sequence similarity. Typically, proteins need only share a single motif or low similarity in multiple domains to exhibit similar structural features, such as alpha helix, beta sheet, charge residues, stretches of hydrophobicity, etc. Conserved structural features have been implicated in ligand binding by receptor proteins, binding to a class of substrates, polynucleotide binding, or protein-protein interactions. 
     Based on the signature sequences and the Matrix Tables described herein, a number of motifs can be discerned. Motifs are identified as regions in the signature sequence which are constant in a majority of the members of the group. Example motifs can be found among Applicant&#39;s data which are shared in the range of 75% to 95% of group members 
     Typically, a region of the consensus sequence is constant if, at each position of the region, the preferred amino acid is chosen from a single class of amino acids; even more typically, the preferred amino acid is a single amino acid. The region can contain a number of positions where an amino acid can be chosen. However, these variable positions are usually less than 15% of the total number of residues in the region; more usually, less than 10%; even more usually, less than 5%. 
     Generally, a domain is considered to be well defined if the consensus sequence is constructed from sequences from at least 2 organisms; more preferably, at least 3 organisms; even more preferably four organisms or greater. 
     Primary domains are best identified from the data presented for the 10 −10  probability criteria. Using this parameter, the largest number of proteins is associated into a group. Consequently, the signature sequence exhibits the greatest amount of variability. The conserved regions, the domains or motifs of the signature contrast against the variable regions. These variable regions become obvious when sequences from more proteins are compared. 
     Signature sequences revealed in the 10 −30  and 10 −50  e-value classes show more conservation in the domains, and can even display a degree of conservation in what is considered the variable regions in the 10 −10  analyses. These more extensively-conserved domains can reflect higher similarity in function—completely orthologous functions. Proteins that share a number of conserved domains, in the same relative order from N terminus to C terminus, are even more likely to be completely orthologous. Nevertheless, because of the natural divergence that occurs in non-conserved regions during evolution and species differentiation, orthologs can be proteins with only the domains conserved and therefore be present in the 10 −30  and 10 −10  p value classes of the Ortholog Table. 
     II.D.3. Linking Signature Sequences to Conservation of Biochemical Activities and Molecular Interactions 
     Proteins that possess the same defined domains or motifs are likely to carry out the same biochemical activity or interact with a similar class of target molecule, e.g., DNA, RNA, proteins, etc. Thus, the pFAM domains listed in the Reference Tables are routinely used as predictors of these properties. Substrates and products for the specific reactions can vary from protein to protein. Where the substrates, ligands, or other molecules bound are identical the affinities may differ between the proteins. Typically, the affinities exhibited by different functional equivalents varies no more than 50%; more typically, no more than 25%; even more typically, no more than 10%; or even less. 
     Proteins with very similar biochemical activities or molecular interactions will share similar structural properties, such as substrate grooves, as well as sequence similarity in more than one motif. Usually, the proteins will share at least two motifs of the signature sequence; more usually, three motifs; even more usually four motifs or greater. Typically, the proteins exhibit 70% sequence identity in the shared motifs; more typically, 80% sequence identity; even more typically, 90% sequence identity or greater. These proteins also often share sequence similarity in the variable regions between the constant motif regions. Further, the shared motifs will be in the same order from amino- to carboxyl-termini. The length of the variable regions between the motifs in these proteins, generally, is similar. Specifically, the number of residues between the shared motifs in these proteins varies by less than 25%; more usually, does not vary by less than 20%; even more usually, less than 15%; even more usually less than 10% or even less. 
     II.D.4. Linking Signature Sequences to Conservation of Cellular Responses or Activities 
     Proteins that exhibit similar cellular response or activities will possess the structural and conserved domain/motifs as described in the Biochemical Activities and Molecular Interactions above. 
     Proteins can play a larger role in cellular response than just their biochemical activities or molecular interactions suggest. A protein can initiate gene transcription, which is specific to the drought response of a cell. Other cellular responses and activities include: stress responses, hormonal responses, growth and differential of a cell, cell to cell interactions, etc. 
     The cellular role or activities of protein can be deduced by transcriptional analyses or phenotypic analyses as well as by determining the biochemical activities and molecular interactions of the protein. For example, transcriptional analyses can indicate that transcription of gene A is greatly increased during flower development. Such data would implicate protein A encoded by gene A, in the process of flower development. Proteins that shared sequence similarity in more than one motif would also act as functional equivalents for protein A during flower development. 
     II.D.5. Linking Signature Sequences to Conservation of Phenotypic Effects 
     Typically, proteins that are grouped together under the most stringent parameters, e-value ≤10 −50 , are likely orthologs and therefore, when present in the same or equivalent cells can cause similar phenotypic consequences. These proteins have very high sequence similarity. Typically, if one of the members of a group is an  Arabidopsis  protein, then the corn ortholog can rescue an  Arabidopsis  mutant plant that does not produce the  Arabidopsis  protein. The mutant plant would be rescued as the parental “wild-type” phenotype by expression of a coding sequence of the corn protein of the same orthologous group when present in the appropriate cell types of the plant. 
     Preferably, these functional equivalents have sequence motif identity throughout much of the length of the protein. However, proteins that share very high similarity between a number, usually more than two; even more usually, more than three motifs can act as functional equivalents to produce similar phenotypic effects. 
     A gene can have coding sequence similarity, i.e., is a homologous. The coding sequence can be sufficient to act as a functional equivalent, although the gene as a whole is not an ortholog. For example, two similar dwf4 coding sequences were found in the  Arabidopsis  genome. However, this pair of coding sequences had different promoters and hence different roles in Plantae. But when one of the pair was placed under the control of its mates&#39; promoter, the phenotypic effects were similar to the effects produced by its mate coding sequence. Therefore, the coding sequence, but not the genes are orthologous. 
     III. Description of the Genes, Gene Components and Products, Together with their Use and Application 
     As described herein, the results of Applicant&#39;s experiments provide an understanding of the function and phenotypic implications of the genes, gene components and products of the present invention. Bioinformatic analysis provides such information. The sections of the present application containing the bioinformatic analysis, together with the Sequence and Reference Tables, teach those skilled in the art how to use the genes, gene components and products of the present invention to provide plants with novel characteristics. Similarly, differential expression analysis provides additional such information and the sections of the present application on that analysis; together with the MA_Diff Tables and MA_Cluster Tables, describe the functions of the genes, gene components and products of the present invention which are understood from the results of the differential expression experiments. The same is true with respect to the phenotype data, wherein the results of the Knock-in and Knock-out experiments and the sections of the present application on those experiments provide the skilled artisan with further description of the functions of the genes, gene components and products of the present invention. 
     As a result, one reading each of these sections of the present application as an independent report will understand the function of the genes, gene components and products of the present invention. But those sections and descriptions can also be read in combination, in an integrated manner, to gain further insight into the functions and uses for the genes, gene components and products of the present invention. Such an integrated analysis does not require extending beyond the teachings of the present application, but rather combining and integrating the teachings depending upon the particular purpose of the reader. 
     Some sections of the present application describe the function of genes, gene components and products of the present invention with reference to the type of plant tissue (e.g. root genes, leaf genes, etc.), while other sections describe the function of the genes, gene components and products with respect to responses under certain conditions (e.g. Auxin-responsive genes, heat-responsive genes, etc.). Thus, if one desires to utilize a gene understood from the application to be a particular tissue-type of gene, then the condition-specific responsiveness of that gene can be understood from the differential expression tables, and very specific characteristics of actions of that gene in a transformed plant will be understood by recognizing the overlap or intersection of the gene functions as understood from the two different types of information. Thus, for example, if one desires to transform a plant with a root gene for enhancing root growth and performance, one can know the useful root genes from the results reported in the knock-in and knock-out tables. A review of the differential expression data may then show that a specific root gene is also over-expressed in response to heat and osmotic stress. The function of that gene is then described in (1) the section of the present application that discusses root genes, (2) the section of the present application that discusses heat-responsive genes, and (3) the section of the application that discusses osmotic stress-responsive genes. The function(s) which are commonly described in those three sections will then be particularly characteristic of a plant transformed with that gene. This type of integrated analysis of data can be viewed from the following schematic that summarizes, for one particular gene, the function of that gene as understood from the phenotype and differential expression experiments. 
     
       
         
           
               
               
               
             
               
                   
               
               
                 Gene function known 
                 Gene function known 
                 Gene function known 
               
               
                 from phenotype 
                 from first differential 
                 from second differential 
               
               
                 experiments 
                 expression experiment 
                 expression experiment 
               
               
                   
               
             
            
               
                 Function A 
                 Function A 
                 Function A 
               
               
                 Function B 
               
               
                   
                 Function C 
                 Function C 
               
               
                   
                 Function D 
               
               
                   
                   
                 Function E 
               
               
                 Function F 
                 Function F 
                 Function F 
               
               
                 Function G 
                 Function G 
               
               
                   
                   
                 Function H 
               
               
                 Function I 
                   
                 Function I 
               
               
                   
                 Function J 
               
               
                   
               
            
           
         
       
     
     In the above example, one skilled in the art will understand that a plant transformed with this particular gene will particularly exhibit functions A and F because those are the functions which are understood in common from the three different experiments. 
     Similar analyses can be conducted on various genes of the present invention, by which one skilled in the art can effectively modulate plant functions depending upon the particular use or conditions envisioned for the plant. 
     III.A. Organ-Affecting Genes, Gene Components, Products (Including Differentiation and Function) 
     III.A.1. Root Genes, Gene Components and Products 
     The economic values of roots arise not only from harvested adventitious roots or tubers, but also from the ability of roots to funnel nutrients to support growth of all plants and increase their vegetative material, seeds, fruits, etc. Roots have four main functions. First, they anchor the plant in the soil. Second, they facilitate and regulate the molecular signals and molecular traffic between the plant, soil, and soil fauna. Third, the root provides a plant with nutrients gained from the soil or growth medium. Fourth, they condition local soil chemical and physical properties. 
     III.A.1.a. Identification of Root Genes 
     Root genes identified herein are defined as genes, gene components and products capable of modulating one or more processes in or functions of the root as described below. They are active or potentially active to a greater extent in roots than in most other organs of the plant. These genes and gene products can regulate many plant traits from yield to stress tolerance. That single genes usually affect the development and function of roots and whole plants is a consequence of biological cellular complexity and the role roots play in supporting the growth of whole plants. Examples of such root genes and gene products are shown in the Reference and Sequence Reference and Sequence Tables and sequences encoding polypeptides of the Protein Group and Protein Group Matrix tables or fragments thereof, the Knock-In and Knock-Out Tables, and the MA-diff Tables. The function of many of the protein products gained from comparisons with proteins of known functions, are also given in the REF Tables. 
     Root Genes Identified by Phenotypic Observations 
     Root genes are active or potentially active to a greater extent in roots than in some other organs/tissue of the plant. Some of the root genes herein were discovered and characterized from a much larger set of genes in experiments designed to find genes that cause phenotypic changes in root morphology. Such morphological changes include primary and lateral root number, size and length, as well as phenotypic changes of other parts of that plant associated with changes in root morphology. 
     In these experiments, root genes were identified by either (1) ectopic expression of a cDNA in a plant or (2) mutagenesis of the plant genome. The plants were then cultivated under standardized conditions and any phenotypic differences recorded between the modified plants as compared with the parent plant. The gene(s) causing the changes were deduced from the cDNA inserted or disrupted gene. Phenotypic differences were observed in: 
     Primary Roots And Root System
         Size, Including Length And Girth   Number   Branching   Root Waving/Curling Characteristics   Gravitropism Changes   Agravitropic       

     Lateral Roots
         Size, Including Length And Girth   Number   Branching       

     Results from screening for these phenotypic changes are reported in the Knock-in and Knock-out Tables. Therefore, any sequence reported in those Tables with one of the above-noted observations is considered a “root gene”. A “root gene” is also a sequence which, in the Ortholog Tables or in the MA-clust Tables, is grouped/clustered together with at least one sequence that is identified as such by means of the Knock-in and Knock-out Tables. 
     Root Genes Identified by Differential Expression 
     Root genes were also identified by measuring the relative levels of mRNA products in the root versus the aerial portion of a plant. Specifically, mRNA was isolated from roots and root tips of  Arabidopsis  plants and compared to mRNA isolated from the aerial portion of the plants utilizing microarray procedures. The MA_diff Table(s) reports the transcript levels of the experiment (see EXPT ID: 108594, 108433, 108599, 108434, 108439). For transcripts that had higher levels in the samples than the control, a “+” is shown. A “−” is shown for when transcript levels were reduced in root tips as compared to the control. For more experimental detail see the Example section below. 
     Roots genes are those sequences that showed differential expression as compared to controls, namely those sequences identified in the MA_diff tables with a “+” or “−” indication. 
     Roots Genes Identified by Cluster Analyses of Differential Expression 
     Roots Genes Identified by Correlation to Genes that are Differentially Expressed 
     As described above, the transcription profiles of genes that act together are well correlated. Applicants not only have identified the genes that are differentially expressed in the microarray experiments, but also have identified the genes that act in concert with them. The MA_clust table indicates groups of genes that have well correlated transcription profiles and therefore participate in the same pathway or network. 
     A pathway or network of Roots genes is any group in the MA_clust that comprises a cDNA ID that also appears in Expt ID 108594, 108433, 108599, 108434, 108439 of the MA_diff table(s). 
     Roots Genes Identified by Correlation to Genes that Cause Physiological Consequences 
     Additionally, the differential expression data and the phenotypic observations can be merged to identify pathways or networks of Roots genes. A group in the MA_clust is considered a Roots pathway or network if the group comprises a cDNA ID that also appears in Knock-in or Knock-out tables that causes one or more of the phenotypes described in section above. 
     Roots Genes Identified by Amino Acid Sequence Similarity 
     Roots genes from other plant species typically encode polypeptides that share amino acid similarity to the sequences encoded by corn and  Arabidopsis  Roots genes. Groups of Roots genes are identified in the Protein Group table. In this table, any protein group that comprises a peptide ID that corresponds to a cDNA ID member of a Roots pathway or network is a group of proteins that also exhibits Roots functions/utilities. 
     Examples of phenotypes, biochemical activities, and transcription profiles that can be modulated by these genes and gene products are described above and below. 
     III.A.1.b. Use of Root Genes to Modulate Phenotypes 
     The root genes of the instant invention are capable of modulating one or more processes of root structure and/or function including (1) development; (2) interaction with the soil and soil contents; and (3) transport in the plant. 
     Root genes and gene products can be used to alter or modulate one or more of the following phenotypes.1.) 
     1.) Development 
     Roots arise from meristem cells that are protected by a root cap during root elongation, but as the root grows out, the cap cells abscise and the remaining cells differentiate to the tip. Depending on the plant species, some surface cells of roots can develop into root hairs. Some roots persist for the life of the plant; others gradually shorten as the ends slowly die back; some may cease to function due to external influences. The root genes and gene products of this invention are useful to modulate any one or all of these growth and development processes generally, as in root density and root growth; including rate, timing, direction and size. 
     Root genes and gene products are useful to modulate either the growth and development or other processes in one or more of the following types of roots, including primary, lateral, and adventitious. 
     Root genes and gene products are useful to modulate cellular changes in cell size, cell division, rate direction and/or number, cell elongation, cell differentiation, lignified cell walls, epidermal cells, such as trichoblasts, and root apical meristem cells (growth and initiation). 
     Parts of roots (i.e. root architecture) can be modulated by these genes root and gene products to affect root architecture in, for example, the epidermis cortex (including the epidermis, hypodermis, endodermis, casparian strips, suberized secondary walls, parenchyma, and aerenchyma), stele (including vaculature, xylem, phloem, and pericycle), vasculature, xylem, phloem, root cap, root apical meristem, elongating region, and symmetry. 
     The polynucleotides and polypeptides of this invention can be used to control the responses to internal plant and root programs as well as to environmental stimuli in the seminal system, nodal system, hormone systems (including Auxin and cytokinin), root cap abscission, root senescence, gravitropism, coordination of root growth and development with that of other organs (including leaves, flowers, seeds, fruits, stems, and changes in soil environment (including water, minerals, ph, and microfauna and flora). 
     2.) Interaction with Soil and Soil Contents 
     Roots are sites of intense chemical and biological activities and as a result can strongly modify the soil they contact. Roots coat themselves with surfactants and mucilage to facilitate these activities. Specifically, roots are responsible for nutrient uptake by mobilizing and assimilating water, organic and inorganic compounds, ions and attracting and interacting with beneficial microfauna and flora. Roots also help to mitigate the effects of toxic chemicals, pathogens and stress. Examples of root properties and activities that the genes and gene products of this invention are useful to modulate are root surfactants and mucilage (including mucilage composition, secretion rate and time, surfactant); nutrient uptake of water, nitrate and other sources of nitrogen, phosphate, potassium, and micronutrients (e.g. iron, copper, etc.); microbes and nematodes associations (such as bacteria including nitrogen-fixing bacteria, mycorrhizae, and nodule-forming and other nematodes); oxygen (including transpiration); detoxification of iron, aluminum, cadium, mercury, salt, and other heavy metals and toxins); pathogen interactions/control (including chemical repellents (includes glucosinolates (GSL), which release pathogen-controlling isothiocyanates); and changes in soil properties, (such as Ph, mineral depletion, and rhizosheath). 
     3) Transport of Materials in Plants 
     Uptake of nutrients by roots produces a “source-sink” effect in a plant. The greater the source of nutrients, the larger “sinks,” such as stems, leaves, flowers, seeds, fruits, etc. can grow. Thus, root genes and gene products are useful to modulate the vigor and yield of the plant overall as well as distinct cells, organs, or tissues. The root genes and gene products are, therefore, useful to modulate vigor (including plant nutrition, growth rate (such as whole plant, including height, flowering time, etc.), seedling, coleoptile elongation, young leaves, stems, flowers, seeds, fruit, and yield (including biomass (such as fresh and dry weight during any time in plant life, including maturation and senescence), root/tuber yield (such as number, size, weight, harvest index, content and composition, (i.e. amino acid, jasmonate, oil, protein and starch), number of flowers, seed yield, number, size, weight, harvest index, content and composition (e.g. amino acid, jasmonate, oil, protein and starch), and fruit yield (such as number, size, weight, harvest index, post harvest quality, content and composition, (e.g. amino acid, jasmonate, oil, protein and starch). 
     Additional Uses of Plants with Modified Roots 
     Plants with roots modified in one or more of the properties described above are used to provide:
         A. Higher vigor and yield of plants and harvested products due to pathogen resistance from conditioning the soil with plant-derived chemicals and/or more tolerance to stresses such as drought, flooding and anoxia.   B. Better Animal (Including Human) Nutrition   C. Improved Dietary Mineral Nutrition   D. Better Plant Survival
           (a) Decreased Lodging   (b) More Efficient Transport   (c) More Efficient Physiology   (d) More Efficient Metabolism   
           E. Better Resistance To Plant Density Effects   F. Increased Yield Of Valuable Molecules   G. More Efficient Root Nodulation   H. Better Access To  Rhizobia  Spray Application, For Anaerobic Soils   I. Easier Crop Harvesting And Ground Tillage   J. Decreased Soil Erosion       

     To regulate any of the phenotype(s) above, activities of one or more of the root genes or gene products is modulated and tested by screening for the desired trait. Specifically, the gene, mRNA levels, or protein levels can be altered in a plant utilizing the procedures described herein and the phenotypes can be assayed. As an example, a plant can be transformed according to Bechtold and Pelletier (1998, Methods. Mol. Biol. 82:259-266) and/or screened for variants as in Winkler et al. (1998) Plant Physiol 118: 743-50 and visually inspected for the desired phenotype or metabolically and/or functionally assayed according to Dolan et al. (1993, Development 119: 71-84), Dolan et al. (1997, Development 124: 1789-98), Crawford and Glass (1998, Trends Plant Science 3: 389-95), Wang et al. (1998, PNAS USA 95: 15134-39), Gaxiola et al. (1998, PNAS USA 95: 4046-50), Apse et al. (1999, Science 285: 1256-58), Fisher and Long (1992, Nature 357: 655-60), Schneider et al. (1998, Genes Devel 12: 2013-21) and Hirsch (1999, Curr Opin Plant Biol. 2: 320-326). 
     III.A.1.c. Use of Root Genes to Modulate Biochemical Activities 
     The activities of one or more of the root genes can be modulated to change biochemical or metabolic activities and/or pathways such as those noted below. Such biological activities can be measured according to the citations included in the Table below: 
     
       
         
           
               
               
               
             
               
                   
               
               
                   
                 BIOCHEMICAL OR 
                   
               
               
                   
                 METABOLIC 
               
               
                   
                 ACTIVITIES 
                 CITATIONS INCLUDING 
               
               
                 PROCESS 
                 AND/OR PATHWAYS 
                 ASSAYS 
               
               
                   
               
             
            
               
                 Association Of Root 
                 Cell-Cell Recognition 
                 Gage et al. (1996) J Bacteriol 
               
               
                 Morphology With Nitrogen 
                 Cell Wall Degradation 
                 178: 7159-66 
               
               
                 Fixing Bacteria 
               
               
                 Primary Root, Lateral 
                 Cell Division/Elongation 
                 Schneider et al. (1998) Genes 
               
               
                 Root, And Root Hair 
                 Cell Differentiation 
                 Devel 12: 2013-21 
               
               
                 Initiation 
                 Cell Expansion 
                 Casimiro et al. (2001). Plant 
               
               
                 Spacing 
                 Auxin Mediated Response 
                 Cell 13: 843-852. 
               
               
                 Elongation 
                 Pathways 
                 Rogg et al. (2001). Plant 
               
               
                 Branching 
                   
                 Cell 13: 465-480. 
               
               
                   
                   
                 Gaedeke et al. (2001). 
               
               
                   
                   
                 EMBO J. 20: 1875-1887. 
               
               
                   
                   
                 Neuteboom et al. (1999). 
               
               
                   
                   
                 Plant Mol. Biol. 39: 273-287. 
               
               
                   
                   
                 Schindelman et al. (2001). 
               
               
                   
                   
                 Genes and Dev. 15: 1115-1127. 
               
               
                   
                   
                 Rashotte et al. (2001) Plant 
               
               
                   
                   
                 Cell 13: 1683-1697. 
               
               
                   
                   
                 Zhang et al. (2000). J Exp 
               
               
                   
                   
                 Bot 51: 51-59. 
               
               
                   
                   
                 Zhang et al. (1998) Science 
               
               
                   
                   
                 279: 407-409. 
               
               
                 Metabolism 
                 Organic Molecule Export 
                 Moody et al. (1988) 
               
               
                   
                   
                 Phytochemistry 27: 2857-61. 
               
               
                   
                 Ion Export 
                 Uozumi et al. (2000) Plant 
               
               
                   
                   
                 Physiol 122: 1249-59 
               
               
                   
                   
                 Frachisse et al. (2000) Plant J 
               
               
                   
                   
                 21: 361-71 
               
               
                   
                 Nutrient Uptake 
                 Frachisse et al. (2000) Plant J 
               
               
                   
                   
                 21: 361-71 
               
               
                   
                   
                 Uozumio et al. (2000) Plant 
               
               
                   
                   
                 Physiol 122: 1249-59 
               
               
                   
                   
                 Williamson et al. (2001). 
               
               
                   
                   
                 Plant Physiol. 126: 875-882. 
               
               
                   
                   
                 Zhang et al. (2000). J Exp 
               
               
                   
                   
                 Bot 51: 51-59. 
               
               
                   
                   
                 Zhang et al. (1998). Science 
               
               
                   
                   
                 279: 407-409. 
               
               
                   
                   
                 Coruzzi et al. (2001). Plant 
               
               
                   
                   
                 Physiol. 125: 61-64. 
               
               
                 Root Gravitropism And 
                 Reactive Oxygen Species 
                 Joo et al. (2001) Plant 
               
               
                 Waving 
                 (ROS) Such As Superoxide 
                 Physiol. 126: 1055-60. 
               
               
                   
                 Anions And H2O2 
                 Vitha et al. (2000). Plant 
               
               
                   
                 Production 
                 Physiol. 122: 453-461. 
               
               
                   
                 Auxin Transport Pathways 
                 Tasaka et al. (2001) Int Rev 
               
               
                   
                 Flavonoid Inhibition Of 
                 Cytol 206: 135-54. 
               
               
                   
                 Auxin Transport Function 
                 Brown et al. (2001) Plant 
               
               
                   
                 Changes In Root Cap Ph 
                 Physiol 126: 524-35. 
               
               
                   
                 Starch Synthesis And 
                 Fasano et al. (2001) Plant 
               
               
                   
                 Storage 
                 Cell 13: 907-22. 
               
               
                   
                 Cell Differentiation 
                 MacCleery et al. (1999). 
               
               
                   
                 Cell Elongation 
                 Plant Physiol 120: 183-92 
               
               
                   
                   
                 Blancaflor et al. (1998). 
               
               
                   
                   
                 Plant Physiol 116: 213-22 
               
               
                   
                   
                 Schneider et al. (1998) Genes 
               
               
                   
                   
                 Devel 12: 2013-21 
               
               
                   
               
            
           
         
       
     
     Other biological activities that can be modulated by the root genes and gene products are listed in the Reference tables. Assays for detecting such biological activities are described in the Protein Domain table. 
     III.A.1.d. Use of Root Genes to Modulate Transcription Levels of Plant Genes 
     Many genes are “up regulated” or “down regulated” because they belong to networks or cascades of genes. Thus some root genes are capable of regulating many other gene activities via these networks and hence complex phenotypes. Examples of transcription profiles of root genes are described in the Table below with associated biological activities. “Up-regulated” profiles are those where the concentrations of the mRNA in total mRNA are higher in roots as compared to aerial parts of a plant; and vice-versa for “down-regulated” profiles. 
     
       
         
           
               
               
               
               
             
               
                   
               
               
                   
                   
                   
                 EXAMPLES OF 
               
               
                 TRANSCRIPT 
                   
                 PHYSIOLOGICAL 
                 BIOCHEMICAL 
               
               
                 LEVELS 
                 TYPE OF GENES 
                 CONSEQUENCES 
                 ACTIVITY 
               
               
                   
               
             
            
               
                 Up Regulated 
                 Genes Expressed In 
                 Primary Root, 
                 Transporters 
               
               
                 Transcripts 
                 Root Development 
                 Lateral Root, and/or 
                 Metabolic Enzymes 
               
               
                   
                 Responders To 
                 Root Hair Growth 
                 Change In Cell 
               
               
                   
                 Micro-Organismal 
                 and Differentiation 
                 Membrane Structure 
               
               
                   
                 Symbionts And 
                 Microorganism 
                 And Potential 
               
               
                   
                 Parasites 
                 Perception 
                 Kinases, 
               
               
                   
                 Genes involved in 
                 Entrapment Of 
                 Phosphatases, G- 
               
               
                   
                 polar Auxin transport 
                 Microorganismal 
                 Proteins 
               
               
                   
                 Genes involved in 
                 Symbionts 
                 Transcription 
               
               
                   
                 starch deposition in 
                 Nutrient Uptake 
                 Activators 
               
               
                   
                 the roots 
                 Synthesis Of 
                 Change In 
               
               
                   
                 Genes involved in 
                 Metabolites And/Or 
                 Chromatin Structure 
               
               
                   
                 production of reactive 
                 Proteins 
                 And/Or Localized 
               
               
                   
                 oxygen species 
                 Modulation Of 
                 DNA Topology 
               
               
                   
                 Genes involved in 
                 Transduction 
                 Cell Wall Proteins 
               
               
                   
                 flavonoid synthesis 
                 Pathways 
                 Ca ++  Fluctuation 
               
               
                   
                   
                 Specific Gene 
                 Reactive Oxygen 
               
               
                   
                   
                 Transcription 
                 Species (ROS) 
               
               
                   
                   
                 Initiation 
                 production 
               
               
                   
                   
                 Nutrient Uptake 
               
               
                   
                   
                 Enhancement 
               
               
                   
                   
                 Gravitropic growth 
               
               
                   
                   
                 of roots 
               
               
                   
                   
                 Associations with 
               
               
                   
                   
                 rhizobia are 
               
               
                   
                   
                 stimulated 
               
               
                 Down-Regulated 
                 Genes Repressed In 
                 Negative 
                 Transcription 
               
               
                 Transcripts 
                 Root Development 
                 Regulation Of 
                 Factors 
               
               
                   
                 Responders To 
                 Primary Root, 
                 Kinases, 
               
               
                   
                 Micro-Organismal 
                 Lateral Root, and/or 
                 Phosphatases, G- 
               
               
                   
                 Symbionts And 
                 Root Hair 
                 Proteins 
               
               
                   
                 Parasites 
                 Production 
                 Change In 
               
               
                   
                 Genes With 
                 Released 
                 Chromatin Structure 
               
               
                   
                 Discontinued 
                 Changes In 
                 And/Or DNA 
               
               
                   
                 Expression Or 
                 Pathways And 
                 Topology 
               
               
                   
                 UnsTable mRNA In 
                 Processes 
                 Stability Of Factors 
               
               
                   
                 Presence Of Root 
                 Operating In Cells 
                 For Protein 
               
               
                   
                 And/Or Micro- 
                 Changes In 
                 Synthesis And 
               
               
                   
                 Organismal 
                 Metabolism 
                 Degradation 
               
               
                   
                 Symbionts 
                 Inhibition of root 
                 Metabolic Enzymes 
               
               
                   
                   
                 gravitropism 
               
               
                   
               
            
           
         
       
     
     Changes in the function or development of roots are the result of modulation of the activities of one or more of these many root genes and gene products. These genes and/or products are responsible for effects on traits such as plant vigor and seed yield, especially when plants are growing in the presence of soil borne biotic or abiotic stresses or when they are growing in barren conditions or in soils depleted of certain minerals. 
     Root genes, gene components and gene products can act alone or in combination as described in the introduction. Of particular interest are combinations of these genes and gene products with those that modulate stress tolerance and/or metabolism. Stress tolerance and metabolism genes and gene products are described in more detail in the sections below. 
     Use of Promoters of Root Genes 
     Promoters of root genes, as described in the Reference tables, for example, can be used to modulate transcription that is induced by root development or any of the root biological processes or activities above. For example, when a selected polynucleotide sequence is operably linked to a promoter of a root gene, then the selected sequence is transcribed in the same or similar temporal, development or environmentally-specific patterns as the root gene from which the promoter was taken. The root promoters can also be used to activate antisense copies of any coding sequence to achieve down regulation of its protein product in roots. They can also be used to activate sense copies of mRNAs by RNA interference or sense suppression in roots. 
     III.A.2. Root Hair Genes, Gene Components and Products 
     Root hairs are specialized outgrowths of single epidermal cells termed trichoblasts. In many and perhaps all species of plants, the trichoblasts are regularly arranged around the perimeter of the root. In  Arabidopsis , for example, trichoblasts tend to alternate with non-hair cells or atrichoblasts. This spatial patterning of the root epidermis is under genetic control, and a variety of mutants have been isolated in which this spacing is altered or in which root hairs are completely absent. 
     III.A.2.a. Identification of Root Hair Genes 
     Root hair genes identified herein are defined as genes, gene components and products capable of modulating one or more processes in or the function of root hairs as described below. Root hairs are capable of controlling or influencing many plant traits, also as shown below. Examples of such root hair development genes and gene products are shown in the Reference and Sequence Tables. The protein products of many of these genes are also identified in these Tables. 
     Root Hair Genes Identified by Differential Expression 
     These genes were discovered and characterized from a much larger set of genes by experiments designed to find genes whose mRNA products are associated specifically with root hairs. These experiments made use of the  arabidopsis  mutant “root hairless” (rhl), which does not develop root hairs. By comparing gene expression profiles of rhl roots with those of wild type roots grown in identical conditions, genes specifically expressed in root hairs were revealed. The MA_diff Table(s) reports the transcript levels of the experiment (see EXPT ID: 108594, 108433). For transcripts that had higher levels in the samples than the control, a “+” is shown. A “−” is shown for when transcript levels were reduced in root tips as compared to the control. For more experimental detail see the Example section below. 
     Root Hairs genes are those sequences that showed differential expression as compared to controls, namely those sequences identified in the MA_diff tables with a “+” or “−” indication. 
     Root Hairs Genes Identified by Cluster Analyses of Differential Expression 
     Root Hairs Genes Identified by Correlation to Genes that are Differentially Expressed 
     As described above, the transcription profiles of genes that act together are well correlated. Applicants not only have identified the genes that are differentially expressed in the microarray experiments, but also have identified the genes that act in concert with them. The MA_clust table indicates groups of genes that have well correlated transcription profiles and therefore participate in the same pathway or network. 
     A pathway or network of Root Hairs genes is any group in the MA_clust that comprises a cDNA ID that also appears in Expt ID 108594, 108433 the MA_diff table(s). 
     Root Hairs Genes Identified by Correlation to Genes that Cause Physiological Consequences 
     Additionally, the differential expression data and the phenotypic observations can be merged to identify pathways or networks of Root Hairs genes. A group in the MA_clust is considered a Root Hairs pathway or network if the group comprises a cDNA ID that also appears in Knock-in or Knock-out tables that causes one or more of the phenotypes described in section above. 
     Root Hairs Genes Identified by Amino Acid Sequence Similarity 
     Root Hairs genes from other plant species typically encode polypeptides that share amino acid similarity to the sequences encoded by corn and  Arabidopsis  Root Hairs genes. Groups of Root Hairs genes are identified in the Protein Group table. In this table, any protein group that comprises a peptide ID that corresponds to a cDNA ID member of a Root Hairs pathway or network is a group of proteins that also exhibits Root Hairs functions/utilities. 
     Examples of phenotypes, biochemical activities, and transcript profiles that can be modulated by these genes and gene products are described above and below. 
     III.A.2.b. Use of Root Hair Development Genes to Modulate Phenotypes 
     The root hair development genes of the instant invention are useful to modulate one or more processes of root hair structure and/or function including (1) development; (2) interaction with the soil and soil contents; (3) uptake and transport in the plant; and (4) interaction with microorganisms. 
     1.) Development 
     The surface cells of roots can develop into single epidermal cells termed trichoblasts or root hairs. Some of the root hairs will persist for the life of the plant; others will gradually die back; some may cease to function due to external influences. The genes and gene products of this invention are useful to modulate any one or all of these growth and development process generally, as in root hair density or root hair growth; including rate, timing, direction, and size, for example. Processes that are regulated by these genes and gene products include cell properties such as cell size, cell division, rate and direction and number, cell elongation, cell differentiation, lignified cell walls, epidermal cells (including trichoblasts) and root apical meristem cells (growth and initiation); and root hair architecture such as leaf cells under the trichome, cells forming the base of the trichome, trichome cells, and root hair responses. 
     The genes and gene products of this invention are useful to modulate one or more of the growth and development processes in response to internal plant programs or environmental stimuli in, for example, the seminal system, nodal system, hormone responses, Auxin, root cap abscission, root senescence, gravitropism, coordination of root growth and development with that of other organs (including leaves, flowers, seeds, fruits, and stems), and changes in soil environment (including water, minerals, Ph, and microfauna and flora). 
     2.) Interaction with Soil and Soil Contents 
     Root hairs are sites of intense chemical and biological activity and as a result can strongly modify the soil they contact. Roots hairs can be coated with surfactants and mucilage to facilitate these activities. Specifically, roots hairs are responsible for nutrient uptake by mobilizing and assimilating water, reluctant ions, organic and inorganic compounds and chemicals. In addition, they attract and interact with beneficial microfauna and flora. Root hairs also help to mitigate the effects of toxic ions, pathogens and stress. Examples of root hair properties and activities that the genes and gene products of the invention are useful to modulate include root hair surfactant and mucilage (including composition and secretion rate and time); nutrient uptake (including water, nitrate and other sources of nitrogen, phosphate, potassium, and micronutrients (e.g. iron, copper, etc.); microbe and nematode associations (such as bacteria including nitrogen-fixing bacteria, mycorrhizae, nodule-forming and other nematodes, and nitrogen fixation); oxygen transpiration; detoxification effects of iron, aluminum, cadium, mercury, salt, and other soil constituents; pathogens (including chemical repellents) glucosinolates (GSL1), which release pathogen-controlling isothiocyanates; and changes in soil (such as Ph, mineral excess and depletion), and rhizosheath. 
     3.) Transport of Materials in Plants 
     Uptake of the nutrients by the root and root hairs contributes a source-sink effect in a plant. The greater source of nutrients, the more sinks, such as stems, leaves, flowers, seeds, fruits, etc. can draw sustenance to grow. Thus, root hair development genes and gene products are useful to modulate the vigor and yield of the plant overall as well as of distinct cells, organs, or tissues of a plant. The genes and gene products, therefore, can modulate Vigor, including plant nutrition, growth rate (such as whole plant, including height, flowering time, etc., seedling, coleoptile elongation, young leaves, stems, flowers, seeds and fruit) and yield, including biomass (fresh and dry weight during any time in plant life, including maturation and senescence), number of flowers, number of seeds, seed yield, number, size, weight and harvest index (content and composition, e.g. amino acid, jasmonate, oil, protein and starch) and fruit yield (number, size, weight, harvest index, and post harvest quality). 
     Additional Uses of Plants with Modified Root Hairs 
     Plants with root hairs modified in one or more of the properties described above are used to provide:
         A. Higher vigor and yield of plant and harvested products due to pathogen resistance from conditioning the soil with plant-derived chemicals and/or more tolerance to stresses such as drought, flooding and anoxia   B. Better Animal (Including Human) Nutrition   C. Improved Dietary Mineral Nutrition   D. Increased Plant Survival By Decreasing Lodging   E. Better Plant Survival By:
           (a) Decreased Lodging   (b) More Efficient Transport   (c) More Efficient Physiology   (d) More Efficient Metabolism   
           F. Increased Yield Of Valuable Molecules       

     Root Hair Modulation 
     To regulate any of the phenotype(s) above, activities of one or more of the root hair genes or gene products is modulated and tested by screening for the desired trait. Specifically, the gene, mRNA levels, or protein levels are altered in a plant utilizing the procedures described herein and the phenotypes can be assayed. As an example, a plant can be transformed according to Bechtold and Pelletier (1998, Methods. Mol. Biol. 82:259-266) and/or screened for variants as in Winkler et al. (1998) Plant Physiol 118: 743-50 and visually inspected for the desired phenotype or metabolically and/or functionally assayed according to Dolan et al. (1993, Development 119: 71-84), Dolan et al. (1997, Development 124: 1789-98), Crawford and Glass (1998, Trends Plant Science 3: 389-95), Wang et al. (1998, PNAS USA 95: 15134-39), Gaxiola et al. (1998, PNAS USA 95: 4046-50), Apse et al. (1999, Science 285: 1256-58), Fisher and Long (1992, Nature 357: 655-60), Schneider et al. (1998, Genes Devel 12: 2013-21) and Hirsch (1999, Curr Opin Plant Biol. 2: 320-326). 
     III.A.2.c. Use of Root Hair Development Genes to Modulate Biochemical Activities 
     The activities of one or more of the root hair development genes can be modulated to change biochemical or metabolic activities and/or pathways such as those noted below. Such biological activities can be measured according to the citations included in the table below: 
     
       
         
           
               
               
               
             
               
                   
               
               
                   
                 Biochemical Or 
                   
               
               
                   
                 Metabolic 
               
               
                   
                 Activities 
                 Citations Including 
               
               
                 Process 
                 And/Or Pathways 
                 Assays 
               
               
                   
               
             
            
               
                 Association 
                 Functions Associated 
                 Gage et al. (1996) J 
               
               
                 Of Root Hair 
                 With Root Hair Curling 
                 Bacteriol 178: 7159-66 
               
               
                 With Nitrogen 
                 And Signal Transduction 
               
               
                 Fixing Bacteria 
               
               
                 Root Hair 
                   
                 Schneider et al. (1998) 
               
               
                 Spacing 
                   
                 Genes Devel 12: 2013-21 
               
               
                 Initiation 
               
               
                 Elongation 
               
               
                 Metabolism 
                 Organic Molecule Export 
                 Moody et al. (1988) 
               
               
                   
                   
                 Phytochemistry 27: 
               
               
                   
                   
                 2857-61 
               
               
                   
                 Ion Export 
                 Uozumi et al. (2000) Plant 
               
               
                   
                   
                 Physiol 122: 1249-59 
               
               
                   
                   
                 Frachisse et al. (2000) Plant 
               
               
                   
                   
                 J 21: 361-71 
               
               
                 Nutrient 
                 Nutrient Uptake 
                 Frachisse et al. (2000) Plant 
               
               
                 Uptake 
                   
                 J 21: 361-71 
               
               
                   
                   
                 Uozumio et al. (2000) Plant 
               
               
                   
                   
                 Physiol 122: 1249-59 
               
               
                   
               
            
           
         
       
     
     Other biological activities that can be modulated by the root hair genes and gene products are listed in the Reference tables. Assays for detecting such biological activities are described in the Protein Domain table. 
     III.A.2.d. Use of Root Hair Genes, Gene Components and Product to Modulate Transcription Levels 
     Many genes are “up regulated” or “down regulated” in root hairs or associated with root hair formation because genes are regulated in networks. Thus some root hairs genes are useful to regulate the activities of many other genes, directly or indirectly to influence complex phenotypes. Examples of transcription profiles of root genes are described in the Table below with associated biological activities. “Up regulated” profiles are those where the mRNA levels are higher when the rhl gene is inhibited as compared to when rhl gene is not inhibited; and vice-versa for “down-regulated” profiles. 
     
       
         
           
               
               
               
               
             
               
                   
               
               
                   
                   
                   
                 Examples Of 
               
               
                 Transcript 
                   
                 Physiological 
                 Biochemical 
               
               
                 Levels 
                 Type Of Genes 
                 Consequences 
                 Activity 
               
               
                   
               
             
            
               
                 Down Regulated 
                 Genes Expressed In 
                 Root Hair Formation 
                 Transporters 
               
               
                 Transcripts 
                 Root Hair 
                 Microorganism 
                 Metabolic Enzymes 
               
               
                   
                 Development 
                 Perception 
                 Change In Cell 
               
               
                   
                 Responders To 
                 Entrapment Of 
                 Membrane Structure 
               
               
                   
                 Micro-Organismal 
                 Microorganismal 
                 And Potential 
               
               
                   
                 Symbionts And 
                 Symbionts 
                 Kinases, 
               
               
                   
                 Parasites 
                 Nutrient Uptake 
                 Phosphatases, G- 
               
               
                   
                   
                 Synthesis Of 
                 Proteins 
               
               
                   
                   
                 Metabolites And/Or 
                 Transcription 
               
               
                   
                   
                 Proteins 
                 Activators 
               
               
                   
                   
                 Modulation Of 
                 Change In Chromatin 
               
               
                   
                   
                 Transduction 
                 Structure And/Or 
               
               
                   
                   
                 Pathways 
                 Localized DNA 
               
               
                   
                   
                 Specific Gene 
                 Topology 
               
               
                   
                   
                 Transcription 
                 Cell Wall Proteins 
               
               
                   
                   
                 Initiation 
               
               
                   
                   
                 Nutrient Uptake 
               
               
                   
                   
                 Enhancement 
               
               
                 Up-Regulated 
                 Genes Repressed In 
                 Negative Regulation 
                 Transcription Factors 
               
               
                 Transcripts 
                 Roots Making 
                 Of Hair Production 
                 Kinases, 
               
               
                   
                 Hairs 
                 Released 
                 Phosphatases, G- 
               
               
                   
                 Responders To 
                 Changes In 
                 Proteins 
               
               
                   
                 Micro-Organismal 
                 Pathways And 
                 Change In Chromatin 
               
               
                   
                 Symbionts And 
                 Processes Operating 
                 Structure And/Or 
               
               
                   
                 Parasites 
                 In Cells 
                 DNA Topology 
               
               
                   
                 Genes With 
                 Changes In 
                 Stability Of Factors 
               
               
                   
                 Discontinued 
                 Metabolism 
                 For Protein Synthesis 
               
               
                   
                 Expression Or 
                   
                 And Degradation 
               
               
                   
                 UnsTable mRNAIn 
                   
                 Metabolic Enzymes 
               
               
                   
                 Presence Of Root 
                   
                 Cell Wall Proteins 
               
               
                   
                 Hairs And/Or 
               
               
                   
                 Micro-Organismal 
               
               
                   
                 Symbionts 
               
               
                   
               
            
           
         
       
     
     Changes in the patterning or development of root hairs are the result of modulation of the activities of one or more of these many root hair genes and gene products. These genes and/or products are responsible for effects on traits such as plant vigor and seed yield, especially when plants are growing in the presence of biotic or abiotic stresses or when they are growing in barren conditions or in soils depleted of certain minerals. 
     Root hair genes and gene products can act alone or in combination as described in the introduction. Of particular interest are combination of these genes and gene products with those that modulate stress tolerance and/or metabolism. Stress tolerance and metabolism genes and gene products are described in more detail in the sections below. 
     Use of Promoters of Root Hair Genes 
     Promoters of root hair development genes, as described in the Reference tables, for example, are useful to modulate transcription that is induced by root hair development or any of the following phenotypes or biological activities above. For example, any desired sequence can be transcribed in similar temporal, tissue, or environmentally-specific patterns as the root hair genes when the desired sequence is operably linked to a promoter of a root hair responsive gene. 
     III.A.3. Leaf Genes, Gene Components and Products 
     Leaves are responsible for producing most of the fixed carbon in a plant and are critical to plant productivity and survival. Great variability in leaf shapes and sizes is observed in nature. Leaves also exhibit varying degrees of complexity, ranging from simple to multi-compound. Leaf genes as defined here, not only modulate morphology, but also influence the shoot apical meristem, thereby affecting leaf arrangement on the shoot, internodes, nodes, axillary buds, photosynthetic capacity, carbon fixation, photorespiration and starch synthesis. Leaf genes elucidated here can be used to modify a number of traits of economic interest from leaf shape to plant yield, including stress tolerance, and to modify the efficiency of synthesis and accumulation of specific metabolites and macromolecules. 
     III.A.3.a. Identification of Leaf Gene, Gene Components and Products 
     Leaf genes identified herein are defined as genes, active or potentially active to greater extent in leaves than in some other organs of the plant or as genes that affect leaf properties. These genes and gene components are useful for modulating one or more processes in or functions of leaves, as described below, to improve plant traits ranging from yield to stress tolerance. Examples of such leaf genes and gene products are shown in the Reference and Sequence Tables and sequences encoding polypeptides of the Protein Group and Protein Group Matrix tables or fragments thereof, Knock-In, Knock-Out and MA_diff Tables. The biochemical functions of the protein products of many of these genes determined from comparisons with known proteins are also given in the Reference tables. 
     Leaf Genes Identified by Phenotypic Observations 
     Some leaf genes were discovered and characterized from a much larger set of genes by experiments designed to find genes that cause phenotypic changes in leaf, petiole, internode, and cotyledon morphology. 
     In these experiments, leaf genes were identified by either (1) ectopic expression of a cDNA in a plant or (2) mutagenesis of the plant genome. The plants were then cultivated and one or more of the following leaf phenotypes, which varied from the parental “wild-type”, were observed:
         A. Changes In Seedling Stage Cotyledons
           Cup Shaped   Curled   Horizontally Oblong   Long Petioles   Short Petioles   Silver   Tricot   Wilted   
           B. Changes In Rosette And Flowering Stage Leaf Shapes
           Cordate   Cup-Shaped   Curled   Fused   Lanceolate   Lobed   Long Petioles   Short Petioles   Oval   Ovate   Serrate   Trident   Undulate   Vertically Oblong   
           C. Changes in Cauline, Flowering Leaf Shape
           Misshapen   Other   
           D. Changes In Leaf Pigment
           Albino   Dark Green Pigment   High Anthocyanin   Interveinal Chlorosis   Yellow Pigment   
           E. Changes In Leaf Size   F. Changes In Seedling Stage Hypocotyl
           Long   Short   
           G. Changes In Leaf Number   H. Changes In Wax Deposition
           Glossy Rosette And Flowering Stage Leaves   Altered Wax Deposition On The Bolt   
               

     Leaf Genes Identified by Differential Expression 
     Also, leaf genes were identified in experiments in which the concentration of mRNA products in the leaf, or stem, or Knock-out mutant 3642-1 were compared with to a control. The MA_diff Table(s) reports the transcript levels of the experiment (see EXPT ID: 108477, 108512, 108497, 108498, 108598). For transcripts that had higher levels in the samples than the control, a “+” is shown. A “−” is shown for when transcript levels were reduced in root tips as compared to the control. For more experimental detail see the Example section below. 
     Leaf genes are those sequences that showed differential expression as compared to controls, namely those sequences identified in the MA_diff tables with a “+” or “−” indication. 
     Leaf Genes Identified by Cluster Analyses of Differential Expression 
     Leaf Genes Identified by Correlation to Genes that are Differentially Expressed 
     As described above, the transcription profiles of genes that act together are well correlated. Applicants not only have identified the genes that are differentially expressed in the microarray experiments, but also have identified the genes that act in concert with them. The MA_clust table indicates groups of genes that have well correlated transcription profiles and therefore participate in the same pathway or network. 
     A pathway or network of Leaf genes is any group in the MA_clust that comprises a cDNA ID that also appears in Expt ID 108477, 108512, 108497, 108498, 108598 of the MA_diff table(s). 
     Leaf Genes Identified by Correlation to Genes that Cause Physiological Consequences 
     Additionally, the differential expression data and the phenotypic observations can be merged to identify pathways or networks of Leaf genes. A group in the MA_clust is considered a Leaf pathway or network if the group comprises a cDNA ID that also appears in Knock-in or Knock-out tables that causes one or more of the phenotypes described in section above. 
     Leaf Genes Identified by Amino Acid Sequence Similarity 
     Leaf genes from other plant species typically encode polypeptides that share amino acid similarity to the sequences encoded by corn and  Arabidopsis  Leaf genes. Groups of Leaf genes are identified in the Protein Group table. In this table, any protein group that comprises a peptide ID that corresponds to a cDNA ID member of a Leaf pathway or network is a group of proteins that also exhibits Leaf functions/utilities. 
     It is assumed that (i) the genes preferentially expressed in leaves are concerned with specifying leaf structures and the synthesis of all the constituent molecules and (ii) that the genes repressed in leaves specify products that are not required in leaves or that could inhibit normal leaf development and function. 
     Examples of phenotypes, biochemical activities, and transcription profiles that are modulated by using selected members of these genes and gene products, singly or in combination, are described below. 
     III.A.3.b. Use of Leaf Genes, Genes Components and Products to Modulate Phenotypes 
     Leaves are critical for the performance and industrial utility of plants. There is extensive evidence that the number, size, shape, position, timing of synthesis, timing of senescence and chemical constitution are very important for agriculture, horticulture and uses of plants as chemical factories for making valuable molecules. Many improvements already demonstrated over past decades have involved genetic modifications to leaves. Therefore, the leaf genes and gene components of this invention offer considerable opportunities for further improving plants for industrial purposes. When the leaf genes and/or gene components are mutated or regulated differently, they are capable of modulating one or more of the processes determining leaf structure and/or function including (1) development; (2) interaction with the environment and (3) photosynthesis and metabolism. 
     1.) Development 
     The leaf genes, gene components and products of the instant invention are useful to modulate one or more processes of the stages of leaf morphogenesis including: stage 1—organogenesis that gives rise to the leaf primordium; stage 2—delimiting basic morphological domains; and stage 3—a coordinated processes of cell division, expansion, and differentiation. Leaf genes include those genes that terminate as well as initiate leaf development. Modulating any or all of the processes leads to beneficial effects either at specific locations or throughout the plant, such as in the cotyledons, major leaves, cauline leaves, or petioles. 
     Leaf genes, gene components and gene products are useful to modulate changes in leaf cell size, cell division (rate and direction), cell elongation, cell differentiation, stomata size, number, spacing and activity, trichome size and number, xylem and phloem cell numbers, cell wall composition, and all cell types. The leaf genese are also useful to modulate to change overall leaf architecture, including veination (such as improvements in photosynthetic efficiency, stress tolerance efficiency of solute and nutrient movement to and from the leaf are accomplished by increases or decreases in vein placement and number of cells in the vein); shape, either elongated versus rounded or symmetry, around either (e.g. abaxial-adaxial (dorsiventral) axis, apical-basal (proximodistal) axis, and margin-blade-midrib (lateral) axis; and branching (improved plant performance to biotic and abiotic stress in heavy density planting is achieved by increases or decreases in leaf branch position or leaf branch length). 
     Shoot apical meristem cells differentiate to become leaf primordia that eventually develop into leaves. The genes, gene components and gene products of this invention are useful to modulate any one or all of these growth and development processes, by affecting timing and rate or planes of cell divisions for example, in response to the internal plant stimuli and/or programs such as embryogenesis; germination; hormones like Auxin leaf senescence; phototropism; coordination of leaf growth and development with that of other organs (such as roots, flowers, seeds, fruits, and stems; and stress-related programs. 
     2.) Interaction with the Environment 
     Leaves are the main sites of photosynthesis and have various adaptations for that purpose. Flat laminae provide a large surface for absorbing sunlight; leaves are rich in chloroplasts and mitochondria; stomata in the lower surface of the laminae allow gases to pass into and out of the leaves including water; and an extensive network of veins brings water and minerals into the leaves and transports the sugar products produced by photosynthesis to the rest of the plant. Examples of leaf properties or activities that are modulated by leaf genes, gene components and their products to facilitate interactions between a plant and the environment including pigment accumulation; wax accumulation on the surface of leaves (e.g. improved protection of young leaves from water borne pathogen attack such as downey mildew with increased wax production); oxygen gain/loss control; carbon dioxide gain/loss control; water gain/loss control; nutrient transport; light harvesting; chloroplast biogenesis; circadian rhythm control; light/dark adaptation; defense systems against biotic and abiotic stresses; metabolite accumulation; and secondary metabolite production in leaf mesophyl, epidermis and trichomes (such as increases in antifeeding secondary metabolites such as strictosiden reduce herbivory and decreases in secondary metabolites improve plants as forage by reducing allergens or undigestible compounds). 
     3.) Photosynthesis and Metabolism 
     Many of the uses for plants depend on the success of leaves as the powerhouses for plant growth, their ability to withstand stresses and their chemical composition. Leaves are organs with many different cell types and structures. Most genes of a plant are active in leaves and therefore leaves have very diverse of pathways and physiological processes. Pathways and processes that are modulated by leaf genes, gene components and products include photosynthesis, sugar metabolism, starch synthesis, starch degradation, nitrate and ammonia metabolism, amino acid biosynthesis, transport, protein biosynthesis, dna replication, repair, lipid biosynthesis and breakdown, protein biosynthesis, storage and breakdown, nucleotide transport and metabolism, cell envelope biogenesis, membrane formation, mitochondrial and chloroplast biogenesis, transcription and RNA metabolism, vitamin biosynthesis, steroid and terpenoid biosynthesis, devise secondary metabolite synthesis, co-enzyme metabolism, flavonoid biosynthesis and degradation, synthesis of waxes, glyoxylate metabolism, and hormone perception and response pathways. 
     Uses of Plants that are Modified as Described Above 
     Altering leaf genes or gene products in a plant modifies one or more plant traits, to make the plants more useful for specific purposes in agriculture, horticulture and for the production of valuable molecules. The modified plant traits include A higher yield of leaves and their molecular constituents (due to different number, size, weight, harvest index, composition including and amounts and types of carbohydrates, proteins, oils, waxes, etc.; photosynthetic efficiency (e.g. reduced photorespiration), absorption of water and nutrients to enhance yields, including under stresses such as high light, herbicides, and heat, pathways to accumulate new valuable molecules); more optimal leaf shape and architecture—enhancing photosynthesis and enhancing appeal in ornamental species (including size, number, pigment, and aroma; a better overall plant architecture—enhancing photosynthesis and enhancing appeal in ornamental species petals, sepals, stamens, and carpels; better shade avoidance for maximizing photosynthesis by, for example, altering leaf placement, to improve light capture and photosynthetic efficiency, thereby increasing yields; Reduced negative effects of high planting density, by altering leaf placement to be more vertical instead of parallel to the ground, for instance; More resistance to the deleterious effects of wind and mechanical damage; Better stress tolerance (including without limitation drought resistance, by decreasing water loss, and pathogen resistance, including, for instance, insect resistance through internal insecticide levels and optimizing the leaf shape to prevent runoff of insecticides); and better overall yield and vigor. 
     Plant yield of biomass and of constituent molecules and plant vigor are modulated to create benefits by genetically changing the growth rate of the whole plant, (including height, flowering time, etc.), seedling, coleoptile elongation, young leaves flowers, seeds, and/or fruit, or by changing the biomass, including fresh and dry weight during any time in plant life, (including maturation and senescence), number of flowers, seed yield including for example, number, size, weight, harvest index, content and composition (e.g. amino acid, jasmonate, oil, protein and starch0, and fruit yield (such as number, size, weight, harvest index, content and composition, e.g. amino acid, jasmonate, oil, protein and starch). 
     To change any of the phenotype(s) in I, II, or III above, activities of one or more of the leaf genes or gene products are modulated in an organism and the consequence evaluated by screening for the desired trait. Specifically, the gene, mRNA levels, or protein levels are altered in a plant utilizing the procedures described herein and the phenotypes can be assayed. As an example, a plant can be transformed according to Bechtold and Pelletier (Methods. Mol. Biol. 82:259-266 (1998)) with leaf gene constructs and/or screened for variants as in Winkler et al., Plant Physiol. 118: 743-50 (1998) and visually inspected for the desired phenotype and metabolically and/or functionally assayed for altered levels of relevant molecules. 
     III.A.3.c. Use of Leaf Genes, Gene Components and Products to Modulate Biochemical Activities 
     Leaves are complex organs and their structure, function and properties result from the integration of many processes and biochemical activities. Some of these are known from the published literature and some can be deduced from the genes and their products described in this application. Leaf genes, and gene components are used singly or in combination to modify these processes and biochemical activities and hence modify the phenotypic and trait characteristics described above. Examples of the processes and metabolic activities are given in the Table below. The resulting changes are measured according to the citations included in the Table. 
     
       
         
           
               
               
               
             
               
                   
               
               
                   
                 BIOCHEMICAL OR 
                   
               
               
                   
                 METABOLIC 
               
               
                   
                 ACTIVITIES 
                 CITATIONS INCLUDING 
               
               
                 PROCESS 
                 AND/OR PATHWAYS 
                 ASSAYS 
               
               
                   
               
             
            
               
                 Metabolism - anabolic 
                 Farnesylation 
                 Pei et al.,  Science  282: 287-290 
               
               
                 and catabolic 
                 Cell Wall Biosynthesis 
                 (1998); Cutler et al., 
               
               
                   
                 Nitrogen Metabolism 
                   Science  273: 1239 (1996) 
               
               
                   
                 Secondary Metabolite 
                 Goupil et al.,  J Exptl. Botany   
               
               
                   
                 Biosynthesis and 
                 49: 1855-62 (1998) 
               
               
                   
                 Degradation 
                 Walch-Liu et al.,  J Exppt.   
               
               
                   
                   
                   Botany  51, 227-237 (2000) 
               
               
                 Water Conservation And 
                 Stomatal Development And 
                 Allen et al.,  Plant Cell  11: 
               
               
                 Resistance To Drought 
                 Physiology 
                 1785-1798 (1999) 
               
               
                 And Other Related 
                 Production of polyols 
                 Li et al.,  Science  287: 300-303 
               
               
                 Stresses 
                 Regulation of salt 
                 (2000) 
               
               
                 Transport Anion and 
                 concentration 
                 Burnett et al.,  J Exptl. Botany   
               
               
                 Cation Fluxes 
                 ABA response(s) 
                 51: 197-205 (2000) 
               
               
                   
                 Ca2+ Accumulation 
                 Raschke, In:  Stomatal   
               
               
                   
                 K+ Fluxes 
                   Function , Zeiger et al. Eds., 
               
               
                   
                 Na+ Fluxes 
                 253-279 (1987) 
               
               
                   
                 Receptor - ligand binding 
                 Lacombe et al.,  Plant Cell  12: 
               
               
                   
                 Anion and Cation fluxes 
                 837-51 (2000); 
               
               
                   
                   
                 Wang et al.,  Plant Physiol.   
               
               
                   
                   
                 118: 1421-1429 (1998); 
               
               
                   
                   
                 Shi et al.,  Plant Cell  11: 
               
               
                   
                   
                 2393-2406 (1999) 
               
               
                   
                   
                 Gaymard et al.,  Cell  94: 647-655 
               
               
                   
                   
                 (1998) 
               
               
                   
                   
                 Jonak et al.,  Proc. Natl. Acad.   
               
               
                   
                   
                   Sci.  93: 11274-79 (1996); 
               
               
                   
                   
                 Sheen,  Proc. Natl. Acad. Sci.   
               
               
                   
                   
                 95: 975-80 (1998); 
               
               
                   
                   
                 Allen et al.,  Plant Cell  11: 
               
               
                   
                   
                 1785-98 (1999) 
               
               
                 Carbon Fixation 
                 Calvin Cycle 
                 Wingler et al.,  Philo Trans R   
               
               
                   
                 Photorespiration 
                   Soe Lond B Biol Sci  355, 
               
               
                   
                 Oxygen evolution 
                 1517-1529 (2000); 
               
               
                   
                 RuBisCO 
                 Palecanda et al.,  Plant Mol   
               
               
                   
                 Chlorophyll metabolism 
                   Biol  46, 89-97 (2001); 
               
               
                   
                 Chloroplast Biogenesis and 
                 Baker et al.,  J Exp Bot  52, 
               
               
                   
                 Metabolism 
                 615-621 (2001) 
               
               
                   
                 Fatty Acid and Lipid 
                 Chen et al.,  Acta Biochim Pol   
               
               
                   
                 Biosynthesis 
                 41, 447-457 (1999) 
               
               
                   
                 Glyoxylate metabolism 
                 Imlau et al.,  PlantCell II , 309-322 
               
               
                   
                 Sugar Transport 
                 (1999) 
               
               
                   
                 Starch Biosynthesis and 
               
               
                   
                 Degradation 
               
               
                 Hormone Perception and 
                 Hormone Receptors and 
                 Tieman et al.,  Plant J  26, 47-58 
               
               
                 Growth 
                 Downstream Pathways for 
                 (2001) 
               
               
                   
                 ethylene 
                 Hilpert et al.,  Plant J  26, 435-446 
               
               
                   
                 jasmonic acid 
                 (2001) 
               
               
                   
                 brassinosteroid 
                 Wenzel et al.,  Plant Phys   
               
               
                   
                 gibberellin 
                 124, 813-822 (2000) 
               
               
                   
                 Auxin 
                 Dengler and Kang,  Curr Opin   
               
               
                   
                 cytokinin 
                   Plant Biol  4, 50-56 (2001) 
               
               
                   
                 Activation Of Specific 
                 Tantikanjana et al.,  Genes   
               
               
                   
                 Kinases And Phosphatases 
                   Dev  15, 1577-1580 (2001) 
               
               
                   
               
            
           
         
       
     
     Other biological activities that are modulated by the leaf genes and gene products are listed in the Reference tables. Assays for detecting such biological activities are described in the Protein Domain table, for example. 
     III.A.3.d. Use of Leaf Genes, Gene Components and Products to Modulate Transcription Levels 
     The expression of many genes is “upregulated” or downregulated” in leaves because some leaf genes and their products are integrated into complex networks that regulate transcription of many other genes. Some leaf genes, gene components and products are therefore useful for modifying the transcription of other genes and hence complex phenotypes, as described above. Profiles of leaf gene activities are described in the Table below with associated biological activities. “Up-regulated” profiles are those where the mRNA transcript levels are higher in leaves as compared to the plant as a whole. “Down-regulated” profiles represent higher transcript levels in the whole plant as compared to leaf tissue only. 
     
       
         
           
               
               
               
               
             
               
                   
               
               
                   
                   
                   
                 EXAMPLES OF 
               
               
                   
                 TYPE OF GENES 
                 PHYSIOLOGICAL 
                 BIOCHEMICAL 
               
               
                   
                 WHOSE 
                 CONSEQUENCES OF 
                 ACTIVITIES OF GENE 
               
               
                 TRANSCRIPT 
                 TRANSCRIPTS 
                 MODIFYING GENE 
                 PRODUCTS WITH 
               
               
                 LEVELS 
                 ARE CHANGED 
                 PRODUCT LEVELS 
                 MODIFIED LEVELS 
               
               
                   
               
             
            
               
                 Up Regulated 
                 Genes Involved In 
                 Leaf Cells 
                 Transcription 
               
               
                 Transcripts 
                 Leaf Cell 
                 Proliferate And 
                 Factors, Signal 
               
               
                   
                 Differentiation, Cell 
                 Differentiate; 
                 Transduction 
               
               
                   
                 Division, Cell 
                   
                 Proteins, Kinase 
               
               
                   
                 Expansion 
                   
                 And Phosphatases 
               
               
                   
                 Genes Involved In 
                 Leaf Structures 
                 Chromatin 
               
               
                   
                 Positive Regulation 
                 Form And Expand 
                 Remodeling 
               
               
                   
                 Of Leaf Genes 
                   
                 Hormone 
               
               
                   
                 Repressors Of Root 
                   
                 Biosynthesis 
               
               
                   
                 And Other Non Leaf 
                   
                 Enzymes 
               
               
                   
                 Cell Types 
                   
                 Receptors 
               
               
                   
                 Genes Involved In 
                 Photosynthesis And 
                 Light Harvesting 
               
               
                   
                 Photosynthesis 
                 Plastid 
                 Coupled To ATP 
               
               
                   
                   
                 Differentiation 
                 Production 
               
               
                   
                   
                   
                 Chlorophyll 
               
               
                   
                   
                   
                 Biosynthesis 
               
               
                   
                   
                 Calvin Cycle 
                 Ribulose 
               
               
                   
                   
                 Activated 
                 Bisphosphate 
               
               
                   
                   
                 Chloroplast 
                 Carboxylase 
               
               
                   
                   
                 Biogenesis And 
                 Chloroplast 
               
               
                   
                   
                 Plastid 
                 Membranes 
               
               
                   
                   
                 Differentiation 
                 Synthesis 
               
               
                   
                   
                 Activated 
                 Chloroplast 
               
               
                   
                   
                   
                 Ribosome 
               
               
                   
                   
                   
                 Biogenesis 
               
               
                   
                 Other Genes 
                 Starch Biosynthesis 
                 Starch Synthase 
               
               
                   
                 Involved In 
                 Lipid Biosynthesis 
                 Nitrate Reductase 
               
               
                   
                 Metabolism 
                 Nitrogen 
                 Terpenoid 
               
               
                   
                   
                 Metabolism - NO 3   
                 Biosynthesis 
               
               
                   
                   
                 Reduced And 
                 Transcription 
               
               
                   
                   
                 Amino Acids Made 
                 Factors 
               
               
                   
                   
                 Secondary 
                 Transporters 
               
               
                   
                   
                 Metabolites 
                 Kinases 
               
               
                   
                   
                 Produced 
                 Phosphatases And 
               
               
                   
                   
                   
                 Signal Transduction 
               
               
                   
                   
                   
                 Protein 
               
               
                   
                   
                   
                 Chromatin Structure 
               
               
                   
                   
                   
                 Modulators 
               
               
                 Down 
                 Genes Involved In 
                 Leaf Genes 
                 Transcription 
               
               
                 Regulated 
                 Negative Regulation 
                 Activated And Leaf 
                 Factors 
               
               
                 Genes 
                 Of Leaf Genes 
                 Functions Induced; 
                 Signal Transduction 
               
               
                   
                   
                 Dark-Adapted 
                 Proteins - Kinases 
               
               
                   
                   
                 Metabolism 
                 And Phosphatases 
               
               
                   
                   
                 Suppressed 
                 Metabolic Enzymes 
               
               
                   
                   
                 Meristematic Genes 
                 Chromatin 
               
               
                   
                   
                 Suppressed 
                 Remodeling Proteins 
               
               
                   
                   
                 Leaf Metabolic 
               
               
                   
                   
                 Pathways Induced 
               
               
                   
               
            
           
         
       
     
     While leaf polynucleotides and gene products are used singly, combinations of these polynucleotides are often better to optimize new growth and development patterns. Useful combinations include different leaf polynucleotides and/or gene products with a hormone responsive polynucleotide. These combinations are useful because of the interactions that exist between hormone-regulated pathways, nutritional pathways and development. 
     Use of Leaf Gene Promoters 
     Promoters of leaf genes are useful for transcription of desired polynucleotides, both plant and non-plant. If the leaf gene is expressed only in leaves, or specifically in certain kinds of leaf cells, the promoter is used to drive the synthesis of proteins specifically in those cells. For example, extra copies of carbohydrate transporter cDNAs operably linked to a leaf gene promoter and inserted into a plant increase the “sink” strength of leaves. Similarly, leaf promoters are used to drive transcription of metabolic enzymes that alter the oil, starch, protein, or fiber contents of a leaf. Alternatively, leaf promoters direct expression of non-plant genes that can, for instance, confer insect resistance specifically to a leaf. Additionally the promoters are used to synthesize an antisense mRNA copy of a gene to inactivate the normal gene expression into protein. The promoters are used to drive synthesis of sense RNAs to inactivate protein production via RNA interference. 
     III.A.4. Trichome Genes and Gene Components 
     Trichomes, defined as hair-like structures that extend from the epidermis of aerial tissues, are present on the surface of most terrestrial plants. Plant trichomes display a diverse set of structures, and many plants contain several types of trichomes on a single leaf. The presence of trichomes can increase the boundary layer thickness between the epidermal tissue and the environment, and can reduce heat and water loss. In many species, trichomes are thought to protect the plant against insect or pathogen attack, either by secreting chemical components or by physically limiting insect access to or mobility on vegetative tissues. The stellate trichomes of  Arabidopsis  do not have a secretory anatomy, but at a functional level, they might limit herbivore access to the leaf in the field. In addition, trichomes are known to secrete economically valuable substances, such as menthol in mint plants. 
     III.A.4.a. Identification of Trichome Genes, Gene Components and Products 
     Trichome genes identified herein are defined as genes or gene components capable of modulating one or more processes in or functions of a trichome, as described below. These genes, their components and products are useful for modulating diverse plant traits from production of secondary metabolites to pathogen resistance. Examples of such trichome genes and gene products are shown in the Reference and Sequence Tables and sequences encoding polypeptides of the Protein Group and Protein Group Matrix tables or fragments thereof, Knock-in, Knock-out, MA-diff and MA-clust. The biochemical functions of the protein products of many of these genes determined from comparisons with known proteins are also given in the Reference tables. 
     Trichome Genes Identified by Phenotypic Observation 
     Trichome genes were discovered and characterized from a much larger set of genes by experiments designed to find genes that cause phenotypic changes in trichome number and morphology on leaf, internode, cotyledon, petiole, and inflorescence. In these experiments, trichome genes were identified by either (1) ectopic expression of a cDNA in a plant or (2) mutagenesis of the plant genome. The plants were then cultivated and one or more of the following phenotypes, which varied from parental “wild-type”, were observed: (1) trichome number; (2) trichome spacing (clustering); or (3) trichome branching. The genes regulating trichome phenotypes are identified in the Knock-In and Kncok-Out Tables. 
     Trichome Genes Identified by Differential Expression 
     Trichome genes were also discovered and characterized from a much larger set of genes by experiments designed to find genes whose mRNA products are associated specifically or preferentially with trichomes. These experiments made use of an  Arabidopsis  glaborous mutant and a hairy mutant. By comparing gene expression profiles of the glabrous mutant with those of the hairy mutant grown under identical conditions, genes specifically or preferentially expressed in trichomes were revealed. The MA_diff Table(s) reports the transcript levels of the experiment (see EXPT ID: 108452). For transcripts that had higher levels in the samples than the control, a “+” is shown. A “−” is shown for when transcript levels were reduced in root tips as compared to the control. For more experimental detail see the Example section below. 
     Trichome genes are those sequences that showed differential expression as compared to controls, namely those sequences identified in the MA_diff tables with a “+” or “−” indication. 
     Trichome Genes Identified by Cluster Analyses of Differential Expression 
     Trichome Genes Identified by Correlation to Genes that are Differentially Expressed 
     As described above, the transcription profiles of genes that act together are well correlated. Applicants not only have identified the genes that are differentially expressed in the microarray experiments, but also have identified the genes that act in concert with them. The MA_clust table indicates groups of genes that have well correlated transcription profiles and therefore participate in the same pathway or network. 
     A pathway or network of Trichome genes is any group in the MA_clust that comprises a cDNA ID that also appears in Expt ID 108452 of the MA_diff table(s). 
     Trichome Genes Identified by Correlation to Genes that Cause Physiological Consequences 
     Additionally, the differential expression data and the phenotypic observations can be merged to identify pathways or networks of Trichome genes. A group in the MA_clust is considered a Trichome pathway or network if the group comprises a cDNA ID that also appears in Knock-in or Knock-out tables that causes one or more of the phenotypes described in section above. 
     Trichome Genes Identified by Amino Acid Sequence Similarity 
     Trichome genes from other plant species typically encode polypeptides that share amino acid similarity to the sequences encoded by corn and  Arabidopsis  Trichome genes. Groups of Trichome genes are identified in the Protein Group table. In this table, any protein group that comprises a peptide ID that corresponds to a cDNA ID member of a Trichome pathway or network is a group of proteins that also exhibits Trichome functions/utilities. 
     It is assumed that the genes differentially expressed in trichomes or leaves producing trichomes are concerned with specifying trichomes and their functions and therefore modulations of such genes and their products modify trichomes and their products. 
     Examples of phenotypes, biochemical activities, and transcription profiles that can be modulated by selected numbers of these genes and gene products singly or in combinations are described above and below. 
     III.A.4.b. Use of Trichome Genes, Gene Components and Products To Modulate Phenotypes 
     Trichome genes of the instant invention, when mutated or activated differently, are useful for modulating one or more processes of trichome structure and/or function including: (1) development; (2) plant stress tolerance; and (3) biosynthesis or secretion of trichome-specific molecules. Trichome genes, components and gene products are useful to alter or modulate one or more of the following phenotypes: 
     1.) Development 
     Trichome differentiation is integrated with leaf development, hormone levels and the vegetative development phase. The first trichome at the leaf tip appears only after the leaf grows to ˜100 μm in length. Subsequent events proceed basipetally as the leaf grows. As leaf development progresses, cell division patterns become less regular and islands of dividing cells can be observed among differentiated pavement cells with their characteristic lobed morphology. Trichome initiation in the expanding leaf occurs within these islands of cells and often defines points along the perimeter of a circle, with an existing trichome defining the center. 
     Once a cell enters the trichome pathway it undergoes an elaborate morphogenesis program that has been divided into different stages based on specific morphological hallmarks. The trichome genes, gene components and gene products of this invention are useful to modulate any one or all of these growth and development processes by affecting rate, timing, direction and size, for example. Trichome genes can also affect trichome number and the organs on which they occur, type of trichomes such as glandular trichomes and stellate trichomes; cell properties such as cell size, cell division rate and direction, cell elongation, cell differentiation, secretory cells, trichome number (average trichome number per leaf for mint: 13,500,000), cell walls, cell death, and response to reactive oxygen species; trichome architecture such as trichome cell structure, placement on leaf, and secretory systems; and trichome responses. Trichome genes, gene components and gene products of this invention are useful to modulate one or more of the growth and development processes above; as in timing and rate, for example. In addition, the polynucleotides and polypeptides of the invention can control the response of these processes to internal plant programs and signaling molecules such as leaf development, hormones (including abscisic acid, Auxin, cytokinin, gibberellins, and brassinosteroids, apoptosis; and coordinated trichome growth and development in flowers, stems, petioles, cotyledons, and hypocotyls. 
     2.) Plant Stress Tolerance 
     The physical characteristics of trichomes as well as the substances secreted by trichomes are useful in protecting the plant from both biotic and abiotic attacks. Thus, selected trichome genes and gene products can be used to help protect distinct cells, organs, or tissues as well as overall plant yield and vigor. Examples of stresses, tolerances to which are modulated by trichome genes and gene products are drought (e.g., trichome number variation can decrease the surface area that allows evaporation), heat (e.g., trichomes can produce shade and provide protection for meristems), salt, insects (e.g., trichomes can prevent insects from settling on plant surfaces), herbivory (e.g., trichomes can produce harmful chemicals), and ultraviolet light. 
     3.) Biosynthesis, Accumulation or Secretion of Metabolites 
     The glandular trichomes from various species are shown to secrete and, sometimes, locally synthesize a number of substances including salt, monoterpenes and sesquiterpenes, terpenoids, exudate, insect entrapping substances, antifeedants, pheromones, and others. Therefore, trichome genes can be used to modulate the synthesis, accumulation and secretion of a large number of metabolites especially related to trichome biology. Some are synthesized in response to biotic and abiotic stresses. For a more detailed description of these metabolites see the section “Use of Trichome Genes to Modulate Biochemical Activities” below. 
     Uses of Plants that are Modified as Described Above 
     Altering trichome properties is useful for modifying one or more plant traits making the plants more useful in agriculture, horticulture and for the production of valuable molecules. These plant traits include Production of specific carbohydrates, proteins, oils, aromas, flavors, pigments, secondary metabolites such as menthol (and other monoterpenes), etc., that can be used in situ or purified and used in a wide variety of industries; Increased production of molecules synthesized in trichomes by increasing the trichome number on different plant organs, such as cotyledons, leaves, hypocotyls, stems, petioles, etc.; Increased cotton fibers per boll due to decreased numbers of trichomes that reduces insect hiding and contamination; More optimal growth rate of a whole plant or specific parts of a plant due to more optimal trichome cellular development and the better resistance to biotic/abiotic stresses (including plant parts such as whole plant seedling, coleoptile elongation, young leaves, flowers, seeds, and fruit); increased harvested yield of plants, organs and their constituent molecules including biomass (such as fresh and dry weight during any time in plant life, including maturation and senescence, number of flowers, seed yield in terms of number, size, weight, harvest index, content and composition, e.g. amino acid, jasmonate, oil, protein and starch, and fruit yield in terms of number, size, weight, harvest index, post harvest quality, content and composition, e.g. amino acid, jasmonate, oil, protein and starch). 
     To regulate any of the phenotype(s) above, activities of one or more of the trichome genes or gene products can be modulated in an organism and tested by screening for the desired trait. Specifically, the gene, mRNA levels, or protein levels can be altered in a plant utilizing the procedures described herein and the phenotypes can be assayed. As an example, a plant can be transformed according to Bechtold and Pelletier ( Methods. Mol. Biol.  82:259-266 (1998)) and/or screened for variants as in Winkler et al.,  Plant Physiol.  118: 743-50 (1998) and visually inspected for the desired phenotype or metabolically and/or functionally assayed. 
     III.A.4.c. Use of Trichome Genes, Gene Components and Products to Modulate Biochemical Activities 
     The phenotype traits outlined above result from the integration of many cellular trichome associated processes and biochemical activities. Some of these are known from published literature and some can be deduced from the genes discovered in the MA Tables, etc. One or more of these trichome genes, gene components and products are useful to modulate these cellular processes, biochemical or metabolic activities and/or pathways such as those noted below. Such biological activities can be measured according to the citations included in the table below: 
     
       
         
           
               
               
               
             
               
                   
               
               
                   
                 BIOCHEMICAL OR 
                   
               
               
                   
                 METABOLIC 
               
               
                   
                 ACTIVITIES 
                 CITATIONS INCLUDING 
               
               
                 PROCESS 
                 AND/OR PATHWAYS 
                 ASSAYS 
               
               
                   
               
             
            
               
                 Growth, Differentiation 
                 Cell wall biosynthetic 
                 Molhoj et. al. (2001). Plant 
               
               
                 And Development 
                 enzymes 
                 Mol. Biol. 46, 263-275 
               
               
                   
                 Cell fate determination 
                 Krishnakumar and 
               
               
                   
                 proteins 
                 Oppenheimer (1999). 
               
               
                   
                 Major pathways of carbon 
                 Development 1221, 3079-3088. 
               
               
                   
                 and nitrogen metabolism 
                 Kroumova et al. (1994). 
               
               
                   
                   
                 PNAS 91, 11437-11441 
               
               
                 Water 
                 Cytoskeleton and Trichome 
                 Schnittger et al. (1999). 
               
               
                 Conservation And 
                 morphology and spacing 
                 Plant Cell 11, 1105-1116 
               
               
                 Resistance To 
                 controls 
                 Hulskamp et al (1994). Cell 
               
               
                 Drought And 
                   
                 76, 555-566 
               
               
                 Other Related 
               
               
                 Stresses 
               
               
                 Trichome exudate 
                 Insect repellant 
                 Insects and The Plant 
               
               
                   
                   
                 Surface, pp 151-172, 
               
               
                   
                   
                 Edward Arnold, London 
               
               
                   
                   
                 (1986) 
               
               
                 Terpenoid 
                 Terpenoid biosynthesis 
                 Alonso et al. (1992). J. Biol. 
               
               
                 biosynthesis 
                 enzymes including: 
                 Chem. 267, 7582-7587 
               
               
                 including 
                 Farnesyltranstransferase 
                 Rajonarivony et al (1992). 
               
               
                 monoterpenes and 
                 Geranylgeranyl- 
                 Arch. Biochem. Biophys. 
               
               
                 sesquiterpenes 
                 diphosphate synthase 
                 299, 77-82 
               
               
                   
                 Geranyltranstransferase 
               
               
                   
                 Farnesyl-diphosphate 
               
               
                   
                 synthase 
               
               
                   
                 Dimethylallyltranstransferase 
               
               
                   
                 Geranyl-diphosphate 
               
               
                   
                 synthase 
               
               
                 H 2 O 2   
                 NADPH oxidase (subunit) 
                 Alverez et al (1998) Cell 92, 
               
               
                 accumulation and 
                 synthesis and function 
                 773-784 
               
               
                 activation of SAR 
                   
                 Grant Orozco-Cardenas and 
               
               
                   
                   
                 Ryan (1999) PNAS 96, 
               
               
                   
                   
                 6553-6557 
               
               
                 Antifeedants 
                 Lactone biosynthesis 
                 Paruch et al. (2000). J. 
               
               
                 biosynthesis and 
                 enzymes 
                 Agric. Food Chem. 48, 
               
               
                 secretion 
                   
                 4973-4977 
               
               
                 Pheromone 
                 Farnesine biosynthesis 
                 Teal et al. (1999) Arch. 
               
               
                 biosynthesis and 
                 enzymes 
                 Insect Biochem Physiol. 42, 
               
               
                 secretion 
                   
                 225-232 
               
               
                 Endoreplication 
                 Cyclin and cyclin dependant 
                 De Veylder et al. (2001) 
               
               
                   
                 kinases 
                 Plant Cell 13, 1653-1668 
               
               
                   
                   
                 De Veylder et al. (2001) 
               
               
                   
                   
                 Plant J. 25, 617-626 
               
               
                   
               
            
           
         
       
     
     Specific enzyme and other activities associated with the functions of individual trichome genes that can be modulated by the trichome genes and gene products are listed in the Reference tables where the functions of individual genes and their products are listed. Assays for detecting such biological activities are described in the Protein Domain table, for example. 
     III.A.4.d. Use of Trichome Genes, Gene Components and Products to Modulate Phenotypes by Modulating Transcription Levels of Other Genes 
     Many of the genes are “up regulated” or “down regulated” in trichomes because they are regulated as members of networks or cascade of genes under the control of regulatory genes. Thus some trichome genes are useful to influence levels of other genes and so orchestrate the complex phenotypes. Examples of the types of genes with altered transcript levels in trichomes are described in the Table below, together with associated biological activities. “Up-regulated” profiles are those where the mRNA levels are higher in the glaborous plants as compared to the“hairy” plant. “Down-regulated” profiles represent higher transcript levels in the “hairy” plant as compared to the glaborous plant. 
     
       
         
           
               
               
               
               
             
               
                   
               
               
                   
                   
                 PHYSIOLOGICAL 
                 EXAMPLES OF 
               
               
                   
                 TYPE OF GENES 
                 CONSEQUENCES 
                 BIOCHEMICAL 
               
               
                   
                 WHOSE 
                 OF MODIFYING 
                 ACTIVITIES WHOSE 
               
               
                 TRANSCRIPT 
                 TRANSCRIPTS ARE 
                 GENE PRODUCT 
                 TRANSCRIPTS ARE 
               
               
                 LEVELS 
                 CHANGED 
                 LEVELS 
                 CHANGED 
               
               
                   
               
             
            
               
                 Up Regulated 
                 Genes active in 
                 Changes in 
                 Transcription 
               
               
                 Transcripts 
                 suppressing trichome 
                 Hormone 
                 Factors 
               
               
                   
                 formation 
                 Perception 
                 Transporters 
               
               
                   
                   
                 Changes in 
                 Change In Cell G- 
               
               
                   
                   
                 Hormone 
                 proteins 
               
               
                   
                   
                 Biosynthesis 
                 Kinases And 
               
               
                   
                   
                 Changes in 
                 Phosphatases 
               
               
                   
                   
                 Specific Gene 
                 Transcription 
               
               
                   
                   
                 Transcription 
                 factors 
               
               
                   
                   
                 Initiation 
                 Ca-binding proteins 
               
               
                   
                   
                 Changes in 
                 Transcription 
               
               
                   
                   
                 cytoskeleton and 
                 Activators 
               
               
                   
                   
                 cell wall 
                 Change In 
               
               
                   
                   
                 assembly and 
                 Chromatin 
               
               
                   
                   
                 structure 
                 Structure And/Or 
               
               
                   
                   
                   
                 Localized DNA 
               
               
                   
                   
                   
                 Topology 
               
               
                   
                   
                   
                 Specific Factors 
               
               
                   
                   
                   
                 (Initiation And 
               
               
                   
                   
                   
                 Elongation) For 
               
               
                   
                   
                   
                 Protein Synthesis 
               
               
                   
                   
                   
                 Maintenance Of 
               
               
                   
                   
                   
                 mRNA Stability 
               
               
                   
                   
                   
                 Maintenance Of 
               
               
                   
                   
                   
                 Protein Stability 
               
               
                   
                   
                   
                 Maintenance Of 
               
               
                   
                   
                   
                 Protein-Protein 
               
               
                   
                   
                   
                 Interaction 
               
               
                 Down-Regulated 
                 Genes active in 
                 Changes in 
                 Transcription 
               
               
                 Transcripts 
                 inducing formation of 
                 Hormone 
                 Factors 
               
               
                   
                 trichomes 
                 Perception 
                 Change In Protein 
               
               
                   
                   
                 Changes in 
                 Structure By 
               
               
                   
                   
                 Hormone 
                 Phosphorylation 
               
               
                   
                   
                 Biosynthesis 
                 (Kinases) Or 
               
               
                   
                   
                 Changes in 
                 Dephosphorylation 
               
               
                   
                   
                 Specific Gene 
                 (Phosphatases) 
               
               
                   
                   
                 Transcription 
                 Change In 
               
               
                   
                   
                 Initiation 
                 Chromatin 
               
               
                   
                   
                 Changes in 
                 Structure And/Or 
               
               
                   
                   
                 cytoskeleton and 
                 DNA Topology 
               
               
                   
                   
                 cell wall 
                 G-proteins, Ca2+- 
               
               
                   
                   
                 assembly and 
                 binding proteins 
               
               
                   
                   
                 structure 
               
               
                   
                 Genes associated with 
                 Changes in cell 
               
               
                   
                 Trichome 
                 size, cell shape 
               
               
                   
                 differentiation and 
               
               
                   
                 structure 
               
               
                   
                 Genes associated with 
                 Changes in 
               
               
                   
                 trichome-specific 
                 terpenoid 
               
               
                   
                 metabolic pathways 
                 biosynthesis 
               
               
                   
                   
                 Changes in 
               
               
                   
                   
                 antifeedant and 
               
               
                   
                   
                 pheromone 
               
               
                   
                   
                 biosynthesis 
               
               
                   
               
            
           
         
       
     
     While trichome polynucleotides and gene products can act alone, combinations of these polynucleotides also affect growth, development and leaf biochemistry. Combinations of trichome polynucleotide(s) and/or gene product(s) with genes or gene products involved in leaf development, hormone responses, or vegetative development are useful because trichome development is integrated with these processes. 
     Use of Promoters of Trichome Genes 
     Promoters of trichome genes are useful for facilitating transcription of desired polynucleotides, both plant and non-plant in trichomes. For example, extra copies of existing terpenoid synthesis coding sequences can be operably linked to a trichome gene promoter and inserted into a plant to increase the terpenoids in the trichome. Alternatively, trichome promoters can direct expression of non-plant genes or genes from another plant species that can, for instance, lead to new terpenoids being made. The promoters can also be operably linked to antisense copies of coding sequences to achieve down regulation of these gene products in cells. 
     III.A5. Chloroplast Genes, Gene Components and Products 
     The chloroplast is a complex and specialized organelle in plant cells. Its complexity comes from the fact that it has at least six suborganellar compartments subdivided by double-membrane envelope and internal thylakoid membranes. It is specialized to carry out different biologically important processes including photosynthesis and amino acid and fatty acid biosynthesis. The biogenesis and development of chloroplast from its progenitor (the proplasptid) and the conversion of one form of plastid to another (e.g., from chloroplast to amyloplast) depends on several factors that include the developmental and physiological states of the cells. 
     One of the contributing problems that complicate the biogenesis of chloroplast is the fact that some, if not most, of its components must come from the outside of the organelle itself. The import mechanisms must take into account to what part within the different sub-compartments the proteins are being targeted; hence the proteins being imported from the cytoplasm must be able to cross the different internal membrane barriers before they can reach their destinations. The import mechanism must also take into account how to tightly coordinate the interaction between the plastid and the nucleus such that both nuclear and plastidic components are expressed in a synchronous and orchestrated manner. Changes in the developmental and physiological conditions within or surrounding plant cells can consequently change this tight coordination and therefore change how import mechanisms are regulated as well. Manipulation of these conditions and modulation of expression of the import components and their function can have critical and global consequences to the development of the plant and to several biochemical pathways occurring outside the chloroplast. Expression patterns of such genes have been determined using microarray technology. 
     Microarray technology allows monitoring of gene expression levels for thousands of genes in a single experiment. This is achieved by hybridizing labeled fluorescent cDNA pools to glass slides that contain spots of DNA (Schena et al. (1995) Science 270: 467-70). The US  Arabidopsis  Functional Genomics Consortium (AFGC) has recently made public the results from such microarray experiments conducted with AFGC chips containing about 10,000 non-redundant ESTs, selected from about 37,000 randomly sequenced ESTs generated from mRNA of different tissues and developmental stages. 
     The sequences of the ESTs showing at least two-fold increases or decreases in a mutant in a mutant (CiA2) of  Arabidopsis thaliana , that is distributed in chloroplast biogenesis relative to wild type grown in the same conditions were identified, compared to the Ceres full length cDNA and genomic sequence databanks, and equivalent Ceres clones identified. The MA_diff table reports the results of this analysis, indicating those Ceres clones which are up or down regulated over controls, thereby indicating the Ceres clones that are involved in the import of proteins to chloroplast and chloroplast biogenesis. 
     Examples of genes and gene products that are involved in the import of proteins to chloroplast are shown in the Reference, Sequence, Protein Group, and Protein Group Matrix tables. While chloroplast protein import polynucleotides and gene products can act alone, combinations of these polynucleotides also affect growth and development. Useful combinations include different chloroplast protein import responsive polynucleotides and/or gene products that have similar transcription profiles or similar biological activities, and members of the same or functionally related biochemical pathways. Whole pathways or segments of pathways are controlled by transcription factor proteins and proteins controlling the activity of signal transduction pathways. Manipulation of one or more chloroplast protein import gene activities are useful to modulate the biological processes and/or phenotypes listed below. Chloroplast protein import responsive genes and gene products can act alone or in combination. Useful combinations include chloroplast protein import responsive genes and/or gene products with similar transcription profiles, similar biological activities, or members of the same or functionally related biochemical pathways. Here, in addition to polynucleotides having similar transcription profiles and/or biological activities, useful combinations include polynucleotides that may have different transcription profiles but which participate in common or overlapping pathways. Whole pathways or segments of pathways are controlled by transcription factor proteins and proteins controlling the activity of signal transduction pathways. Therefore, manipulation of such protein levels is especially useful for altering phenotypes and biochemical activities of plants. Manipulation of one or more chloroplast protein import gene activities are useful to modulate the biological processes and/or phenotypes listed below. 
     Such chloroplast protein import responsive genes and gene products can function to either increase or dampen the above phenotypes or activities in response to changes in the regulation of import mechanisms. Further, promoters of chloroplast protein transport responsive genes, as described in the Reference tables, for example, are useful to modulate transcription that is induced by chloroplast protein transport or any of the following phenotypes or biological activities below. Further, any desired sequence can be transcribed in similar temporal, tissue, or environmentally specific patterns as the chloroplast protein transport responsive genes when the desired sequence is operably linked to a promoter of a chloroplast protein transport responsive gene. The MA_diff Table(s) reports the transcript levels of the experiment (see EXPT ID: Chloroplast (relating to SMD 8093, SMD 8094)). For transcripts that had higher levels in the samples than the control, a “+” is shown. A “−” is shown for when transcript levels were reduced in root tips as compared to the control. For more experimental detail see the Example section below. 
     Chloroplast genes are those sequences that showed differential expression as compared to controls, namely those sequences identified in the MA_diff tables with a “+” or “−” indication. 
     Chloroplast Genes Identified by Cluster Analyses of Differential Expression Chloroplast 
     Genes Identified by Correlation to Genes that are Differentially Expressed 
     As described above, the transcription profiles of genes that act together are well correlated. Applicants not only have identified the genes that are differentially expressed in the microarray experiments, but also have identified the genes that act in concert with them. The MA_clust table indicates groups of genes that have well correlated transcription profiles and therefore participate in the same pathway or network. 
     A pathway or network of Chloroplast genes is any group in the MA_clust that comprises a cDNA ID that also appears in Expt ID Chloroplast (relating to SMD 8093, SMD 8094) of the MA_diff table(s). 
     Chloroplast Genes Identified by Correlation to Genes that Cause Physiological Consequences 
     Additionally, the differential expression data and the phenotypic observations can be merged to identify pathways or networks of Chloroplast genes. A group in the MA_clust is considered a Chloroplast pathway or network if the group comprises a cDNA ID that also appears in Knock-in or Knock-out tables that causes one or more of the phenotypes described in section above. 
     Chloroplast Genes Identified by Amino Acid Sequence Similarity 
     Chloroplast genes from other plant species typically encode polypeptides that share amino acid similarity to the sequences encoded by corn and  Arabidopsis  Chloroplast genes. Groups of Chloroplast genes are identified in the Protein Group table. In this table, any protein group that comprises a peptide ID that corresponds to a cDNA ID member of a Chloroplast pathway or network is a group of proteins that also exhibits Chloroplast functions/utilities. 
     III.A.5.a. Use of Chloroplast Protein Import Responsive Genes to Modulate Phenotypes 
     Chloroplast protein import responsive genes and gene products are useful to or modulate one or more phenotypes, including growth, roots, stems, and leaves; development, including plastid biogenesis, plastid division, plastid development and thylakoid membrane structures differentiation including plastid/chloroplast differentiation; photosynthesis including carbon dioxide fixation; transport including transcription/translation regulation within transport complex, phosphate translocation, and targeted starch deposition and accumulation; and biosynthesis of essential compounds such as lipid biosynthesis, riboflavin biosynthesis, carotenoid biosynthesis, and aminoacid biosynthesis. 
     To improve any of the phenotype(s) above, activities of one or more of the chloroplast protein import responsive genes or gene products can be modulated and the plants tested by screening for the desired trait. Specifically, the gene, mRNA levels, or protein levels can be altered in a plant utilizing the procedures described herein and the phenotypes can be assayed. As an example, a plant can be transformed according to Bechtold and Pelletier (1998, Methods. Mol. Biol. 82:259-266) and/or screened for variants as in Winkler et al. (1998) Plant Physiol 118: 743-50 and visually inspected for the desired phenotype or metabolically and/or functionally assayed according to Saito et al. (1994, Plant Physiol. 106: 887-95), Takahashi et al (1997, Proc. Natl. Acad. Sci. USA 94: 11102-07) and Koprivova et al. (2000, Plant Physiol. 122: 737-46). 
     III.A.5.b. Use of Chloroplast Protein Import-Responsive Genes to Modulate Biochemical Activities 
     The activities of one or more of the chloroplast protein import responsive genes can be modulated to change biochemical or metabolic activities and/or pathways such as those noted below. Such biological activities can be measured according to the citations included in the table below: 
     
       
         
           
               
               
               
             
               
                   
               
               
                   
                 BIOCHEMICAL OR 
                   
               
               
                   
                 METABOLIC 
               
               
                   
                 ACTIVITIES 
                 CITATIONS INCLUDING 
               
               
                 GENERAL CATEGORY 
                 AND/OR PATHWAYS 
                 ASSAYS 
               
               
                   
               
             
            
               
                 Cell Growth and 
                 Regulation of Leaf 
                 Reinbothe et al. (1997) Proc. 
               
               
                 Differentiation 
                 Development Including 
                 Natl. Acad. Sci. USA. 
               
               
                   
                 Photosynthetic 
                 94: 8890-8894 
               
               
                   
                 Apparatus 
                 Eggink and Hoober (2000) J. 
               
               
                   
                   
                 Biol. Chem. 275: 9087-9090 
               
               
                   
                   
                 Jagtap et al. (1998) J Exptl 
               
               
                   
                   
                 Botany 49: 1715-1721 
               
               
                   
                 Regulation of Plastid 
                 Lawrence and Kindle (1997) 
               
               
                   
                 Biogenesis and Plastid 
                 J. Biol. Chem. 272: 20357-20363 
               
               
                   
                 Division 
                 Lahiri and Allison (2000) 
               
               
                   
                   
                 Plant Physiol. 123: 883-894 
               
               
                   
                 Development of Plastid 
                 Kouranov et al. (1999) J. 
               
               
                   
                 Inner/Outer and 
                 Biol. Chem. 274: 25181-25186 
               
               
                   
                 thylakoid Membrane 
                 Jackson et al. (1998) J. Biol. 
               
               
                   
                 Structures 
                 Chem. 273: 16583-16588 
               
               
                   
                   
                 Li and Chen (1997) J. Biol. 
               
               
                   
                   
                 Chem. 272: 10968-10974 
               
               
                   
                   
                 Lawrence and Kindle (1997) 
               
               
                   
                   
                 J. Biol. Chem. 272: 20357-20363 
               
               
                   
                   
                 Silva-Filho et al. (1997) J. 
               
               
                   
                   
                 Biol. Chem. 272: 15264-15269 
               
               
                   
                 Regulation of 
                 May and Soll (2000) Plant 
               
               
                   
                 transcription and/or 
                 Cell 12: 53-63 
               
               
                   
                 translation related to 
                 Caliebe et al. (1997) EMBO 
               
               
                   
                 maintenance of stability 
                 J. 16: 7342-7350 
               
               
                   
                 of protein-protein 
               
               
                   
                 interaction within 
               
               
                   
                 transport complex 
               
               
                 Physiology 
                 Modulation of 
                 Sung and Krieg (1979) Plant 
               
               
                   
                 Photosynthesis 
                 Physiol 64: 852-56 
               
               
                   
                 Regulation of Lipid 
                 Bourgis et al. (1999) Plant 
               
               
                   
                 Biosynthesis 
                 Physiol. 120: 913-922 
               
               
                   
                   
                 Reverdatto et al. (1999) 
               
               
                   
                   
                 Plant Physiol. 119: 961-978 
               
               
                   
                   
                 Roesler et al. (1997) Plant 
               
               
                   
                   
                 Physiol. 113: 75-81 
               
               
                   
                 Regulation of Riboflavin 
                 Jordan et al. (1999) J. Biol. 
               
               
                   
                 (Vitamin B) biosynthesis 
                 Chem. 274: 22114-22121 
               
               
                   
                 Regulation of phosphate 
                 Flugge (1999) Annu. Rev. 
               
               
                   
                 translocation across 
                 Plant Physiol. Plant Mol. 
               
               
                   
                 chloroplast membrane 
                 Biol. 50: 27-45 
               
               
                   
                   
                 Silva-Filho et al. 
               
               
                   
                   
                 (1997) J. Biol. Chem. 
               
               
                   
                   
                 272: 15264-15269 
               
               
                   
                 Regulation of targeted 
                 Yu et al. (1998) Plant 
               
               
                   
                 starch depostion and 
                 Physiol. 116: 1451-1460 
               
               
                   
                 accumulation 
               
               
                   
                 Modulation of protein 
                 Summer and Cline (1999) 
               
               
                   
                 targeting and 
                 Plant Physiol. 119: 575-584 
               
               
                   
                 translocation across 
                 Dabney-Smith et al. (1999) 
               
               
                   
                 chloroplast membrane 
                 J. Biol. Chem. 274: 32351-32359 
               
               
                   
                   
                 Hinnah et al. (1997) EMBO 
               
               
                   
                   
                 J. 16: 7351-7360 
               
               
                   
                 Regulation of carotenoid 
                 Bonk et al. (1996) Plant 
               
               
                   
                 biosynthesis 
                 Physiol. 111: 931-939 
               
               
                   
                 Regulation of amino acid 
                 Flugge (1999) Annu. Rev. 
               
               
                   
                 biosynthesis 
                 Plant Physiol. Plant Mol. 
               
               
                   
                   
                 Biol. 50: 27-45 
               
               
                   
                 Regulation of secondary 
                 Flugge (1999) Annu. Rev. 
               
               
                   
                 metabolism 
                 Plant Physiol. Plant Mol. 
               
               
                   
                   
                 Biol. 50: 27-45 
               
               
                 Signal Transduction 
                 Regulation of gene 
                 Chen et al. (2000) Plant 
               
               
                   
                 transcriptional activity 
                 Physiol. 122: 813-822. 
               
               
                   
                 specific to chloroplast 
                 Macasev et al. (2000) Plant 
               
               
                   
                 protein import 
                 Physiol. 123: 811-816. 
               
               
                   
                 Regulation of protein 
                 Lang et al. (1998) J. Biol. 
               
               
                   
                 target signal cleavage 
                 Chem. 273: 30973-30978 
               
               
                   
                 and protein degradation 
                 Jackson et al. (1998) J. Biol. 
               
               
                   
                   
                 Chem. 273: 16583-16588 
               
               
                   
                   
                 Richter and Lamppa (1998) 
               
               
                   
                   
                 Proc. Natl. Acad. Sci. USA. 
               
               
                   
                   
                 95: 7463-7468 
               
               
                   
                 Regulation of ion 
                 Van der Wijngaard and 
               
               
                   
                 channel conformation 
                 Vredenberg (1999) J. Biol. 
               
               
                   
                 and activity 
                 Chem. 274: 25201-25204 
               
               
                   
                 Regulation of kinase and 
                 Waegemann and Soll (1996) 
               
               
                   
                 phosphatases synthesis 
                 J. Biol. Chem. 271: 6545-6554 
               
               
                   
                 and activity 
                 Li et al. (2000) Science 287-300-303 
               
               
                   
                   
                 Muller et al. (2000) J. Biol. 
               
               
                   
                   
                 Chem. 275: 19475-19481 
               
               
                   
                 Modulation of Molecular 
                 Bonk et al. (1996) Plant 
               
               
                   
                 Chaperone and Other 
                 Physiol. 111: 931-939 
               
               
                   
                 Protein Folding Activity 
                 Walker et al. (1996) J. Biol. 
               
               
                   
                   
                 Chem. 271: 4082-4085 
               
               
                   
                   
                 Kessler and Blobel (1996). 
               
               
                   
                   
                 Proc. Natl. Acad. Sci. USA 
               
               
                   
                   
                 93: 7684-7689 
               
               
                   
                   
                 Jackson et al. (1998) J. Biol. 
               
               
                   
                   
                 Chem. 273: 16583-16588 
               
               
                   
               
            
           
         
       
     
     Other biological activities that can be modulated by the chloroplast protein import responsive genes and gene products are listed in the Reference tables. Assays for detecting such biological activities are described in the Protein Domain table. 
     Chloroplast protein import responsive genes are characteristically differentially transcribed in response to fluctuating chloroplast protein import levels or concentrations, whether internal or external to an organism or cell. The MA_diff reports the changes in transcript levels of various chloroplast protein import responsive genes that are differentially expressed among the mutants and the wild type. 
     Profiles of some of these chloroplast protein import responsive genes are shown in the Table below together with examples of the kinds of associated biological activities. 
                                                     EXAMPLES OF       TRANSCRIPT       PHYSIOLOGICAL   BIOCHEMICAL       LEVELS   TYPE OF GENES   CONSEQUENCES   ACTIVITY                  Up regulated   Responders to   Chloroplast   Transporters       transcripts   defective chloroplast   protein import   Metabolic enzymes           protein import   regulation   Change in cell           Genes induced by   Chloroplast   membrane structure           defective import   protein import and   and potential               transport   Kinases and               Chloroplast   phosphatases               import   Transcription               metabolism   activators               Synthesis of   Change in               secondary   chromatin structure               metabolites and/or   and/or localized               proteins   DNA topology               Modulation of   Redox control               chloroplast import   Metabolic enzymes               response   concerned with               transduction   chloroplast               pathways   biochemistry               Changes in   Organelle gene               chloroplast   expression and               membranes   translation               Specific gene               transcription               initiation               Chloroplast and               non-chloroplast               metabolic               pathways       Down-regulated   Responders to   Regulation of   Transcription       transcripts   defective chloroplast   chloroplast protein   factors           protein import.   import pathways   Change in protein           Genes repressed by   released   structure by           defective chloroplast   Chloroplast   phosphorylation           protein import   protein import and   (kinases) or           Genes with unsTable   transport   dephosphoryaltion           mRNAs when   Chloroplast   (phosphatases)           chloroplast import is   import   Change in           defective   metabolism   chromatin structure           Genes with   Changes in   and/or DNA           discontinued   pathways and   topology           expression or   processes   Stability factors for           unsTable mRNA in   operating in   protein mRNA           presence of   chloroplasts   synthesis and           chloroplast protein   Changes in   degradation           import   organelle   Organelle               membranes   transcription and               Loss of organelle   translation proteins               gene expression,   Metabolic enzymes               RNA and protein               synthesis               Changes in               metabolism other               than chloroplast               protein import               pathways               Chloroplast               import               metabolism                    
Use of Promoters of Chloroplast Genes
 
     Promoters of Chloroplast genes are useful for transcription of any desired polynucleotide or plant or non-plant origin. Further, any desired sequence can be transcribed in a similar temporal, tissue, or environmentally specific patterns as the Chloroplast genes where the desired sequence is operably linked to a promoter of a Chloroplast gene. The protein product of such a polynucleotide is usually synthesized in the same cells, in response to the same stimuli as the protein product of the gene from which the promoter was derived. Such promoter are also useful to produce antisense mRNAs to down-regulate the product of proteins, or to produce sense mRNAs to down-regulate mRNAs via sense suppression 
     III.A.6. Reproduction Genes, Gene Components and Products 
     Reproduction genes are defined as genes or components of genes capable of modulating any aspect of sexual reproduction from flowering time and inflorescence development to fertilization and finally seed and fruit development. These genes are of great economic interest as well as biological importance. The fruit and vegeTable industry grosses over $1 billion USD a year. The seed market, valued at approximately $15 billion USD annually, is even more lucrative. 
     Expression of many reproduction genes and gene products is orchestrated by internal programs or the surrounding environment of a plant, as described below. These genes and/or products have great importance in determining traits such as fruit and seed yield. Examples of such reproduction genes and gene products are shown in the Reference, Sequence, Protein Group, Protein Group Matrix tables, Knock-in, Knock-out, MA-diff and MA-clust. The biochemical functions of the protein products of many of these genes determined from comparisons with known proteins are also given in the Reference tables. 
     Reproduction Genes Identified by Phenotypic Observation 
     Reproduction genes were discovered and characterized from a much larger set of genes by experiments designed to find genes that cause phenotypic changes in flower, silique, and seed morphology. In these experiments, reproduction genes were identified by either (1) ectopic expression of a cDNA in a plant or (2) mutagenesis of the plant genome. The plants were then cultivated and phenotypes, which varied from the parental “wild-type”, were observed. 
     One particular example of reproductive genes are those that are regulated by AP2. AP2 is a transcription factor that regulates many genes, both as a repressor of some genes and as an activator of others. Some of these genes are those which establish the floral meristem or those which regulate floral organ identity and development. As such, AP2 has an effect on reproduction. This is, loss of AP2 activity is correlated with decreased male and female reproduction. AP2 is also known to have an effect on seed mass, and therefore on yield. That is, overexpression of AP2 is correlated with smaller seeds or seedless fruit while repression of AP2 correlates with larger seeds (see, e.g. U.S. Pat. No. 5,994,622). 
     Another example of reproduction genes are those that are regulated by PISTILLATA (PI). PI is a transcription factor that regulates many genes both as a repressor and activator. Some of these genes are those which regulate floral organ identity and development, in conjunction with other transcription factors such as AP2 and AGAMOUS. As such, PI has an effect on reproduction in that loss of PI activity is correlated with decreased male reproduction. PI is also known to have an effect on carpel number, and therefore potentially on ovule/seed number and yield. Specifically, repression of PI results in increased carpel number and therefore ovule number. 
     Yet another example of reproductive genes are those that are regulated by MEDEA (MEA). MEA is a SET-domain containing protein that associates with other proteins to form complexes that affect chromatin structure and therefore gene expression. As such, loss of MEA function is correlated with global gene activation and repression leading to many phenotypes including decreased female reproduction and therefore reduced seed set and yield. 
     In the characterization of these and other reproduction genes, the following phenotypes were scored:
         I. Flower
           Size
               Large   Small   
               Shape
               Abnormal organ numbers   Agamous   AP-2 like   
               Color   Number   Fused Sepals   
           II. Silique
           Size   Seed number
               Reduced   Absent   
               Seed color   
               

     The identified genes regulating reproduction are identified in the Knock-in and Knock-out Tables. 
     Reproduction Genes Identified by Differential Expression 
     Reproduction genes were also identified in experiments designed to discover genes whose mRNA products were in different concentrations in whole flowers, flower parts, and siliques relative to the plant as a whole. The MA_diff Table(s) reports the transcript levels of the experiment (see EXPT ID: 108473, 108474, 108429, 108430, 108431, 108475, 108476, 108501). For transcripts that had higher levels in the samples than the control, a “+” is shown. A “−” is shown for when transcript levels were reduced in root tips as compared to the control. For more experimental detail see the Example section below. 
     Reproduction genes are those sequences that showed differential expression as compared to controls, namely those sequences identified in the MA_diff tables with a “+” or “−” indication. 
     Reproduction Genes Identified by Cluster Analyses of Differential Expression 
     Reproduction Genes Identified by Correlation to Genes that are Differentially Expressed 
     As described above, the transcription profiles of genes that act together are well correlated. Applicants not only have identified the genes that are differentially expressed in the microarray experiments, but also have identified the genes that act in concert with them. The MA_clust table indicates groups of genes that have well correlated transcription profiles and therefore participate in the same pathway or network. 
     A pathway or network of Reproduction genes is any group in the MA_clust that comprises a cDNA ID that also appears in Expt ID 108473, 108474, 108429, 108430, 108431, 108475, 108476, 108501 of the MA_diff table(s). 
     Reproduction Genes Identified by Correlation to Genes that Cause Physiological Consequences 
     Additionally, the differential expression data and the phenotypic observations can be merged to identify pathways or networks of Reproduction genes. A group in the MA_clust is considered a Reproduction pathway or network if the group comprises a cDNA ID that also appears in Knock-in or Knock-out tables that causes one or more of the phenotypes described in section above. 
     Reproduction Genes Identified by Amino Acid Sequence Similarity 
     Reproduction genes from other plant species typically encode polypeptides that share amino acid similarity to the sequences encoded by corn and  Arabidopsis  Reproduction genes. Groups of Reproduction genes are identified in the Protein Group table. In this table, any protein group that comprises a peptide ID that corresponds to a cDNA ID member of a Reproduction pathway or network is a group of proteins that also exhibits Reproduction functions/utilities. 
     It is assumed that the reproduction genes differentially expressed in floral parts and seeds are concerned with specifying flowers and seeds and their functions, and therefore modulations of such genes produce variant flowers and seeds. 
     Reproductive genes and gene products can function to either increase or dampen the phenotypes, biochemical activities and transcription profiles, either in response to changes of internal plant programs or to external environmental fluctuations. 
     III.A.5.a. Use of Reproduction Genes, Gene Components and Products to Modulate Phenotypes 
     The reproduction genes of the instant invention, when mutated or activated differently, are capable of modulating one or more processes of flower, seed and fruit development. They are thus useful for improving plants for agriculture and horticulture and for providing seeds with a better chemical composition for diverse industries including the food, feed and chemical industries. Reproduction genes, gene components and products are useful to alter the following traits and properties of plants, including development, such as flowering time and number of inflorescences, flower development (including anther, stamen, pollen, style, stigma, ovary, ovule, and gametes), pollination and fertilization (including sporogenesis gametogenesis, zygote formation, embryo development, endosperm development, and male sterility, hybrid breeding systems and heterosis); cellular properties, such as cell size, cell shape, cell death, cell division, cell elongation, cell differentiation, and meiosis; organ characteristics, such as flowers, receptacle, sepals, petals, and tepals color, shape, and size, number, and petal drop); androecium, such as stamen (including anther size, pollen sterile, size, shape, weight and color, number, and filament size), gynoecium, such as carpel, ovary, number, and length) and style (stigma, ovule, size, shape, and number); pedicel and peduncle (size and shape), seeds, such as placenta, embryo, cotyledon, endosperm, suspensor, seed coat (testa), aleurone, development, including apomixis (gametophytic, apospory, diplospory), dormancy and germination; fruits, such as pericarp—thickness, texture (exocarp, mesocarp, endocarp); development (seed set, fruit set, false fruit, fruit elongation and maturation, and dehiscence), and fruit drop; plant seed yield, such as increased biomass, better harvest index, attraction of favorable insects, better seed quality, and better yield of constituent chemicals; and plant population features, such as architecture (shade avoidance and planting density). 
     To regulate any of the phenotype(s) above, activities of one or more of the reproduction genes or gene products can be modulated in an organism and tested by screening for the desired trait. Specifically, the gene, mRNA levels or protein levels can be altered in a plant using the procedures described herein and the phenotypes can be assayed. As an example, a plant can be transformed according to Bechtold and Pelletier ( Methods Mol. Biol.  82:259-266 (1998)) and/or screened for variants as in Winkler et al. ( Plant Physiol  118:743-50 (1998)) and visually inspected for the desired phenotype or metabolically and/or functionally assayed. 
     III.A.5.b. Use of Reproduction Genes to Modulate Biochemical Activities 
     The activities of one or more of the reproduction genes can be modulated to change biochemical or metabolic activities and/or pathways such as those examples noted below. Such biological activities can be measured according to the citations included in the Table below: 
     
       
         
           
               
               
               
             
               
                   
               
               
                   
                 EXAMPLES OF 
                   
               
               
                   
                 BIOCHEMICAL/MOLECULAR 
               
               
                 FUNCTION/PROCESS 
                 ACTIVITIES 
                 Reference AND ASSAY 
               
               
                   
               
             
            
               
                 Metabolism 
                 Energy production and 
                 Ap Rees, T. (1974). In 
               
               
                   
                 conversion 
                 “Plant Biochemistry. 
               
               
                   
                 Glucosyl-transferase 
                 Biochemistry, Series One”, 
               
               
                   
                 (CLONE_ID 1040) 
                 Vol. 11. (H. L. Kornberg and 
               
               
                   
                 Heme-binding protein 
                 D. C. Phillips, eds.), 
               
               
                   
                 (putative cytochrom 
                 Butterworths, London. 
               
               
                   
                 B5) 
                 Juliano, B. O. and Varner, J. E. 
               
               
                   
                 (CLONE_ID 3743) 
                 (1969). Plant Physiol. 
               
               
                   
                 Storage protein synthesis 
                 44, 886-892. 
               
               
                   
                 Inorganic ion transport and 
                 Bewley et al. (1993). Plant 
               
               
                   
                 metabolism 
                 Physiol. Biochem. 31, 483-490. 
               
               
                   
                 Peroxidase 
                 Hills, M. J. and Beevers, H. 
               
               
                   
                 (CLONE_ID 100990) 
                 (1987). Plant Physiol. 84, 
               
               
                   
                 Cystathione beta 
                 272-276. 
               
               
                   
                 synthase 
                 Olsen, L. J. and Harada, J. J. 
               
               
                   
                 (CLONE_ID 21847) 
                 (1991). In “Molecular 
               
               
                   
                 Amino acid transport and 
                 Approaches to 
               
               
                   
                 metabolism 
                 Compartmentalization and 
               
               
                   
                 l-asparaginase 
                 Metabolic Regulation (A. H. C. Huang 
               
               
                   
                 (CLONE_ID 92780) 
                 and L. Taiz, eds.), 
               
               
                   
                 Putative peptide/amino 
                 ASPP, Rockville, Md. 
               
               
                   
                 acid 
                 Mitsuhashi, W. and Oaks, A. 
               
               
                   
                 transporter 
                 (1994). Plant Physiol. 
               
               
                   
                 (CLONE_ID 113723) 
                 104, 401-407. 
               
               
                   
                 Carbohydrate transport and 
                 Walker-Smith, D. J., and 
               
               
                   
                 metabolism 
                 Payne, J. W. (1985). Planta 
               
               
                   
                 Glucose transport 
                 164, 550-556. 
               
               
                   
                 protein 
                 Salmenkallio, M. and 
               
               
                   
                 (CLONE_ID 33727) 
                 Sopanen, T. (1989). Plant 
               
               
                   
                 Putative sugar 
                 Physiol. 89, 1285-1291. 
               
               
                   
                 transporter 
                 Baumgartner, B. and 
               
               
                   
                 (CLONE_ID 3250) 
                 Chrispeels, M. J. (1976). 
               
               
                   
                 Starch biosynthesis 
                 Plant Physiol. 58, 1-6. 
               
               
                   
                 Coenzyme metabolism 
                 Elpidina, E. N. et al. (1991). 
               
               
                   
                 Tyrosine 
                 Planta 185, 46-52. 
               
               
                   
                 aminotransferase 
                 Ericson, M. C. and 
               
               
                   
                 (ROOTY/SUPERROOT1) 
                 Chrispeels, M. J. (1973). 
               
               
                   
                 (CLONE_ID 14570) 
                 Plant Physiol. 52, 98-104. 
               
               
                   
                 Formate dehydrogenase 
                 Kern, R. and Chrispeels, M. J. 
               
               
                   
                 (CLONE_ID 7530) 
                 1978) Plant Physiol. 62, 
               
               
                   
                 Lipid metabolism 
                 815-819. 
               
               
                   
                 Branched chain α- 
                 Dilworth, M. F. and Dure, L. 
               
               
                   
                 ketoacid 
                 III. (1978). Plant Physiol. 
               
               
                   
                 dehydrogenase E2 
                 61, 698-702. 
               
               
                   
                 subunit 
                 Chrispeels, M. J. and Jones, R. L. 
               
               
                   
                 (CLONE_ID 25116) 
                 (1980/81). Isr. J. Bot. 
               
               
                   
                 Acyl carrier protein-1 
                 29, 222-245. 
               
               
                   
                 (CLONE_ID 14291) 
                 Gould, S. E. B., and Rees, D. A. 
               
               
                   
                 Lipid metabolic enzymes 
                 (1964). J. Sci. Food 
               
               
                   
                 Secretion 
                 Agric. 16, 702-709. 
               
               
                   
                 Sensor protein RcsC- 
               
               
                   
                 like 
               
               
                   
                 (CLONE_ID 16461) 
               
               
                   
                 Signal recognition 
               
               
                   
                 particle 
               
               
                   
                 RP54 (CLONE_ID 
               
               
                   
                 22158) 
               
               
                 Modulate floral organ 
                 Transcriptional control 
                 Elliot et al. (1996). Plant 
               
               
                 number 
                 ANT (AP2-domain) DNA 
                 Cell 8, 155-168. 
               
               
                   
                 binding protein 
                 Sakai et al. (2000). Plant 
               
               
                   
                 SUP (Zinc finger) 
                 Cell 12, 1607-1618. 
               
               
                   
                   
                 Jacobsen and Meyerowitz 
               
               
                   
                   
                 (1997). Science 277, 1100-1103. 
               
               
                 Floral organ size 
                 Transcriptional control 
                 Mizukami et al. (2000). 
               
               
                   
                 ANT (AP2-domain) DNA 
                 PNAS 97, 942-947. 
               
               
                   
                 binding protein 
                 Krizek (1999). 
               
               
                   
                   
                 Developmental Genetics 25, 
               
               
                   
                   
                 224-236. 
               
               
                 Female organ 
                 Membrane receptor kinase 
                 Clark and Meyerowitz 
               
               
                 number/Floral meristem 
                 signal transduction 
                 (1997). Cell 89, 575-585 
               
               
                 size 
                 CLV1 (LRR domain and 
                 Jeong et al. (1999). Plant 
               
               
                   
                 kinase domain) receptor 
                 Cell 11, 1925-1934. 
               
               
                   
                 CLV2 (LRR domain) 
                 Fletcher et al. (1999). 
               
               
                   
                 receptor 
                 Science 283, 1911-1914. 
               
               
                   
                 CLV3 (Receptor ligand) 
               
               
                 Female reproduction 
                 DNA binding protein 
                 Yanofsky et al. (1990). 
               
               
                   
                 AG (MADS domain) DNA 
                 Nature 346, 35-39. 
               
               
                   
                 binding protein 
               
               
                 Female reproduction 
                 Signal transduction 
                 Kieber et al. (1993). Cell 
               
               
                   
                 CTR1 (Raf kinase) 
                 72, 427-441. 
               
               
                 Male organ number 
                 DNA methylation 
                 Jacobsen and Meyerowitz 
               
               
                   
                 MET1 (DNA 
                 (1997). Science 277, 1100-1103. 
               
               
                   
                 methyltransferase) 
               
               
                 Seed size control 
                 DNA binding protein 
                 Jofuku et al. (1994). Plant 
               
               
                   
                 AP2 (AP2 domain) 
                 Cell 6, 1211-1225. 
               
               
                   
                 RAP2 (AP2 domain) 
                 U.S. Pat. No. #6,093,874; 
               
               
                   
                   
                 #5,994,622 
               
               
                 Seed size control 
                 Polycomb group protein 
                 Luo et al. (2000). PNAS 97, 
               
               
                   
                 complex 
                 10637-10642. 
               
               
                   
                 FIE, FIS2, MEA 
               
               
                 Seed size control 
                 DNA methylation 
                 Scott et al. (2000). 
               
               
                   
                 MET1 
                 Development 127, 2493-2502. 
               
               
                   
                   
                 Vinkenoog et al. (2000). 
               
               
                   
                   
                 Plant Cell 12, 2271-2282. 
               
               
                   
                   
                 Luo et al. (2000). PNAS 97, 
               
               
                   
                   
                 10637-10642. 
               
               
                 Embryo 
                 CAAT box binding complex 
                 Lotan et al. (1998). Cell 93, 
               
               
                 development/Embryo 
                 LEC1/HAP3 
                 1195. 
               
               
                 viability 
                 HAP2, HAP5 
                 U.S. Pat. No. #6,235,975 
               
               
                 Embryo development/Seed 
                 DNA binding proteins 
                 Finkelstein et al. (1998). 
               
               
                 dormancy 
                 ABI4 (AP2 domain) 
                 Plant Cell 10, 1043-1054. 
               
               
                   
                 FUS3 (B3 domain) 
                 Luerssen et al. (1998). Plant 
               
               
                   
                 VP1 (B3 domain) 
                 J. 15, 755-764. 
               
               
                 Embryo development 
                 Signal transduction 
                 Leung et al. (1994). Science 
               
               
                   
                 ABI1, ABI2 
                 264, 1448-1452. 
               
               
                   
                 [Serine/threonine protein 
                 Leung et al. (1997). Plant 
               
               
                   
                 phosphatase 2C (PP2C)] 
                 Cell 9, 759-771. 
               
               
                 Endosperm development 
                 Chromatin level control of 
                 Ohad et al. (1996). PNAS 
               
               
                   
                 gene activity 
                 93, 5319-5324. 
               
               
                   
                 Polycomb complex; FIE, 
                 U.S. Pat. No. #6,229,064 
               
               
                   
                 MEA, FIS2 
                 Kiyosue et al. (1999). 
               
               
                   
                   
                 PNAS 96, 4186-4191. 
               
               
                   
                   
                 Grossniklaus et al. (1998). 
               
               
                   
                   
                 Science 280, 446-450. 
               
               
                   
                   
                 Chaudhury et al. (1997) 
               
               
                   
                   
                 PNAS 94, 4223-4228. 
               
               
                 Integument 
                 DNA binding 
                 Jofuku et al. (1994). Plant 
               
               
                 development/Seed coat 
                 AP2, ANT (AP2 domain) 
                 Cell 6, 1211-1225. 
               
               
                 development 
                 BEL1 (Homeodomain) 
                 Klucher et al. Plant Cell 8, 
               
               
                   
                   
                 137-153. 
               
               
                   
                   
                 Reiser et al. (1995). Cell 83, 
               
               
                   
                   
                 735-742. 
               
               
                 Anthocyanin production 
                 Secondary transporter 
                 Debeaujon et al. (2001). 
               
               
                   
                 TT12 (MATE; multidrug and 
                 Plant Cell 13, 853-872. 
               
               
                   
                 toxic compound extrusion) 
               
               
                 Anthocyanin production 
                 DNA binding protein 
                 Nesi et al. (2000). Plant Cell 
               
               
                   
                 TT8 (Basic helix-loop-helix 
                 12, 1863-1878. 
               
               
                   
                 domain) 
               
               
                 Fruit development 
                 Chromatin level control of 
                 Ohad et al. (1996). PNAS 
               
               
                   
                 gene activity 
                 93, 5319-5324. 
               
               
                   
                 Polycomb complex; FIE, 
                 Kiyosue et al. (1999). 
               
               
                   
                 MEA, FIS2 
                 PNAS 96, 4186-4191. 
               
               
                   
                   
                 Grossniklaus et al. (1998). 
               
               
                   
                   
                 Science 280, 446-450. 
               
               
                   
                   
                 Chaudhury et al. (1997) 
               
               
                   
                   
                 PNAS 94, 4223-4228. 
               
               
                 Fruit size control 
                 Signal transduction 
                 Frary et al. (2000). Science 
               
               
                   
                 FW2.2 (c-Ras P21) 
                 289, 85-88. 
               
               
                 Fruit development/Pod 
                 Transcriptional control 
                 Liljegren et al. (2000). 
               
               
                 shattering 
                 SHP1, SHP2, FUL (MADS 
                 Nature 404, 766-770. 
               
               
                   
                 domain) DNA binding 
                 Ferrandiz et al. (2000). 
               
               
                   
                 proteins 
                 Science 289, 436-438.. 
               
               
                 Transcription and 
                 Transcription 
                 Delseny, M. et al. (1977). 
               
               
                 Posttranscription 
                 SRF-domain AGL11 
                 Planta 135, 125-128. 
               
               
                   
                 (CLONE_ID 32791) 
                 Lalonde, L. and Bewley, J. D. 
               
               
                   
                 AP2-domain containing 
                 (1986). J. Exp. Bot. 37, 
               
               
                   
                 protein (CLONE_ID 
                 754-764. 
               
               
                   
                 332) 
                 Walling, L. et al. (1986). 
               
               
                   
                 Myb-DNA binding 
                 PNAS 83, 2123-2125. 
               
               
                   
                 protein 
                 Okamuro, J. K. and 
               
               
                   
                 (CLONE_ID 94597) 
                 Goldberg, R. B. (1989). In 
               
               
                   
                 Transcription factors 
                 “Biochemistry of Plants, 
               
               
                   
                 Signal transduction 
                 Vol 15.” Academic Press, 
               
               
                   
                 mechanisms 
                 Inc. 
               
               
                   
                 Protein-kinases 
                 Wong, J. et al. (1995). 
               
               
                   
                 Phosphatases 
                 Genes Dev. 9, 2696-2711. 
               
               
                   
                 meiosis proteins 
                 Dimitrov et al. (1994). J. 
               
               
                   
                 Chromatin remodeling 
                 Cell Biol. 126, 591-601. 
               
               
                   
                 proteins 
                 Landsberger, N. and 
               
               
                   
                 Chaperones 
                 Wolffe, A. P. (1997). 
               
               
                   
                 Chalcone synthase 
                 EMBO J. 16, 4361-4373. 
               
               
                   
                 Putative Ser/Thr protein 
                 Bogdanove, A. J. and 
               
               
                   
                 kinase (CLONE_ID 
                 Martin, G. G. (2000). PNAS 
               
               
                   
                 31383) 
                 97, 8836-8840. 
               
               
                   
                 ER6-like protein 
                 Zhu, H. et al. Science Jul. 
               
               
                   
                 (implicated in ethylene 
                 26, 2001: 
               
               
                   
                 signal transduction) 
                 10.1126/science.1062191 
               
               
                   
                 (CLONE_ID 7474) 
                 (Reports). 
               
               
                   
                 Translation, ribosomal 
               
               
                   
                 structure and biogenesis 
               
               
                   
                 Ribosomal proTein 
               
               
                   
                 S15A 
               
               
                   
                 (CLONE_ID 17466) 
               
               
                   
                 Translation initiation 
               
               
                   
                 factor 
               
               
                   
                 (CLONE_ID 103464) 
               
               
                   
                 Posttranslational 
               
               
                   
                 modification, protein 
               
               
                   
                 turnover, chaperones 
               
               
                   
                 DnaJ-domain containing 
               
               
                   
                 protein (CLONE_ID 
               
               
                   
                 4150) 
               
               
                   
                 Cyclophilin-like protein 
               
               
                   
                 (CLONE_ID 35643) 
               
               
                 Cell division and Repair 
                 Cell division and 
                 Rogan, P. G. and Simon, E. W. 
               
               
                   
                 chromosome partitioning 
                 (1975). New Phytol. 74, 
               
               
                   
                 Protein of unknown 
                 273-275. 
               
               
                   
                 function 
                 Morahashi, Y. and Bewley, J. D. 
               
               
                   
                 with tropomyosin-, 
                 (1980). Plant Physiol 
               
               
                   
                 myosin 
                 66, 70-73. 
               
               
                   
                 tail- and filament- 
                 Morahashi, Y. et al. (1981). 
               
               
                   
                 domains 
                 Plant Physiol. 68, 318-323. 
               
               
                   
                 (CLONE_ID 15546) 
                 Morahashi, Y. (1986). 
               
               
                   
                 Actin-1 
                 Physiol. Plant. 66, 653-658. 
               
               
                   
                 (CLONE_ID 25785) 
                 Zlatanova, J. et al. (1987). 
               
               
                   
                 DNA replication, 
                 Plant Mol. Biol. 10, 139-144. 
               
               
                   
                 recombination and repair 
                 Zlatanova, J. and Ivanov, P. 
               
               
                   
                 Proliferating cell 
                 (1988). Plant Sci. 58, 71-76. 
               
               
                   
                 nuclear 
               
               
                   
                 antigen-1 (axillary 
               
               
                   
                 protein, 
               
               
                   
                 DNA polymerase I 
               
               
                   
                 delta) 
               
               
                   
                 (CLONE_ID 28554) 
               
               
                   
                 AAA-type ATPase, 
               
               
                   
                 cdc48 
               
               
                   
                 (CLONE_ID 100292) 
               
               
                   
                 Cell envelope biogenesis, 
               
               
                   
                 outer membrane 
               
               
                   
                 dTDP-D-glucose 4,6- 
               
               
                   
                 dehydratase 
               
               
                   
                 (CLONE_ID 28597) 
               
               
                   
                 Putative cinnamoyl- 
               
               
                   
                 CoA 
               
               
                   
                 reductase 
               
               
                   
                 (CLONE_ID 109228) 
               
               
                   
               
            
           
         
       
     
     Other biological activities that are modulated by the reproductive genes and gene products are listed in the Reference tables. Assays for detecting such biological activities are described in the Protein Domain table, for example. 
     III.5.A.c. Use of Reproduction Genes, Gene Components and Products to Modulate Transcription Levels 
     Reproduction genes are characteristically differentially transcribed in response to cell signals such as fluctuating hormone levels or concentrations, whether internal or external to an organism or cell. Many reproduction genes belong to networks or cascades of genes under the control of regulatory genes. Thus some reproduction genes are useful to modulate the expression of other genes. Examples of transcription profiles of reproduction genes are described in the Table below with associated biological activities. “Up-regulated” profiles are those where the mRNA transcript levels are higher in flowers, flower parts or siliques as compared to the plant as a whole. “Down-regulated” profiles represent higher transcript levels in the whole plant as compared to flowers, flower parts or siliques alone. 
     
       
         
           
               
               
               
               
             
               
                   
               
               
                   
                   
                   
                 EXAMPLES OF 
               
               
                   
                   
                 PHYSIOLOGICAL 
                 BIOCHEMICAL 
               
               
                   
                   
                 CONSEQUENCES 
                 ACTIVITIES OF 
               
               
                   
                 TYPE OF GENES 
                 OF ALTERING 
                 GENES WITH 
               
               
                 TRANSCRIPT 
                 WITH ALTERED 
                 GENE 
                 ALTERED 
               
               
                 LEVELS 
                 ACTIVITY 
                 EXPRESSION 
                 EXPRESSION 
               
               
                   
               
             
            
               
                 Up Regulated 
                 Genes that control 
                 Flowers form from 
                 Transcription Factors 
               
               
                 Transcripts 
                 flower differentiation, 
                 flower meristem 
                 Signal transduction 
               
               
                 Flower 
                 number and size 
                 Floral organs mature 
                 Membrane Structure 
               
               
                 Reproduction 
                 Genes that promote 
                 Flavonoid pathways 
                 Protein kinases 
               
               
                 Genes 
                 petal, stamen and 
                 induced 
                 Phosphatases 
               
               
                   
                 carpel formation 
                   
                 Meiosis proteins 
               
               
                   
                 Genes controlling 
                   
                 Chromatin 
               
               
                   
                 flower-specific 
                   
                 remodeling proteins 
               
               
                   
                 metabolism such as 
                   
                 Chaperones 
               
               
                   
                 petal pigments 
                   
                 Chalcone synthase 
               
               
                   
                 Genes that promote 
                   
                 Amino acid transport 
               
               
                   
                 ovule formation 
                   
                 and metabolism 
               
               
                   
                 Genes that promote 
                   
                 Storage protein 
               
               
                   
                 fertilization, seed, 
                   
                 synthesis 
               
               
                   
                 embryo and 
                   
                 Lipid metabolic 
               
               
                   
                 endosperm formation 
                   
                 enzymes 
               
               
                   
                   
                   
                 Carbohydrate 
               
               
                   
                   
                   
                 transport and 
               
               
                   
                   
                   
                 metabolism 
               
               
                   
                   
                   
                 Starch biosynthesis 
               
               
                 AP2 
                 Genes activated by 
                 Many steps and 
                 Proteins associated 
               
               
                 Reproduction 
                 AP2 transcription 
                 pathways induced, 
                 with: 
               
               
                 Genes 
                 factors 
                 developmental and 
                 Energy production 
               
               
                   
                 Genes that induce 
                 metabolic 
                 and conversion 
               
               
                   
                 petal and stamen 
                 No petals or stamens 
                 Amino acid transport 
               
               
                   
                 formation 
                 produced 
                 and metabolism 
               
               
                   
                   
                   
                 Carbohydrate 
               
               
                   
                   
                   
                 transport and 
               
               
                   
                   
                   
                 metabolism 
               
               
                   
                   
                   
                 Lipid metabolism 
               
               
                   
                   
                   
                 Transcription and 
               
               
                   
                   
                   
                 signal transduction 
               
               
                   
                   
                   
                 Poor translational 
               
               
                   
                   
                   
                 modification 
               
               
                   
                   
                   
                 DNA replication 
               
               
                   
                   
                   
                 Chromatin 
               
               
                   
                   
                   
                 remodeling 
               
               
                 Down-Regulated 
                 Genes that repress 
                 Flowers form from 
                 Transcritipion factors 
               
               
                 Transcripts 
                 flower development 
                 flower meristem 
                 Signal transduction 
               
               
                 Flower 
                 Genes that induce 
                 Non-floral organs are 
                 pathways 
               
               
                 Reproduction 
                 stem, leaf and other 
                 repressed 
                 Kinases and 
               
               
                 Genes 
                 organ differentiation 
                 Flower-specific 
                 phosphatases 
               
               
                 AP2 Reproduction 
                 Genes that negatively 
                 pathways are induced 
                 Chromatin 
               
               
                 Genes 
                 regulate flower 
                 Many steps and 
                 remodeling proteins 
               
               
                   
                 specific metabolism 
                 pathways induced, 
                 Proteins associated 
               
               
                   
                 Genes that negatively 
                 developmental and 
                 with: 
               
               
                   
                 regulate ovule 
                 metabolic 
                 Energy production 
               
               
                   
                 formation, meiosis, 
                 No petals or stamens 
                 and conversion 
               
               
                   
                 fertilization and seed 
                 produced 
                 Amino acid transport 
               
               
                   
                 development 
                   
                 and metabolism 
               
               
                   
                 Genes activated by 
                   
                 Carbohydrate 
               
               
                   
                 AP2 transcription 
                   
                 transport and 
               
               
                   
                 factors 
                   
                 metabolism 
               
               
                   
                 Genes that induce 
                   
                 Lipid metabolism 
               
               
                   
                 petal and stamen 
                   
                 Transcription and 
               
               
                   
                 formation 
                   
                 signal transduction 
               
               
                   
                   
                   
                 Poor translational 
               
               
                   
                   
                   
                 modification 
               
               
                   
                   
                   
                 DNA replication 
               
               
                   
                   
                   
                 Chromatin 
               
               
                   
                   
                   
                 remodeling 
               
               
                   
               
            
           
         
       
     
     While polynucleotides and gene products modulating reproduction can act alone, combinations of these polynucleotides also affect growth and development. Useful combinations include different polynucleotides and/or gene products of the instant invention that have similar transcription profiles or similar biological activities, and members of the same or similar biochemical pathways. In addition, the combination of a polynucleotide and/or gene product(s) capable of modulating reproduction with a hormone responsive polynucleotide, particularly one affected by gibberellic acid and/or Auxin, is also useful because of the interactions that exist between hormone-regulated pathways, and development. Here, in addition to polynucleotides having similar transcription profiles and/or biological activities, useful combinations include polynucleotides that may have different transcription profiles but which participate in common or overlapping pathways. 
     Use of Promoters and Reproduction Genes 
     Promoter of reproduction genes are useful for transcription of desired polynucleotides, both plant and non-plant. For example, extra copies of carbohydrate transporter genes can be operably linked to a reproduction gene promoter and inserted into a plant to increase the “sink” strength of flowers or siliques. Similarly, reproduction gene promoters can be used to drive transcription of metabolic enzymes capable of altering the oil, starch, protein or fiber of a flower or silique. Alternatively, reproduction gene promoters can direct expression of non-plant genes that can, for instance confer insect resistance specifically to a flower. 
     III.A.7. Ovule Genes, Gene Components and Products 
     The ovule is the primary female sexual reproductive organ of flowering plants. It contains the egg cell and, after fertilization occurs, contains the developing seed. Consequently, the ovule is at times comprised of haploid, diploid and triploid tissue. As such, ovule development requires the orchestrated transcription of numerous polynucleotides, some of which are ubiquitous, others that are ovule-specific and still others that are expressed only in the haploid, diploid or triploid cells of the ovule. 
     Although the morphology of the ovule is well known, little is known of these polynucleotides and polynucleotide products. Mutants allow identification of genes that participate in ovule development. As an example, the pistillata (PI) mutant replaces stamens with carpels, thereby increasing the number of ovules present in the flower. Accordingly, comparison of transcription levels between the wild-type and PI mutants allows identification of ovule-specific developmental polynucleotides. 
     Changes in the concentration of ovule-specific polynucleotides during development results in the modulation of many polynucleotides and polynucleotide products. Examples of such ovule-specific responsive polynucleotides and polynucleotide products are shown in the Reference, Sequence, Protein Group, Protein Group Matrix, MA_diff, and MA_clust tables. These polynucleotides and/or products are responsible for effects on traits such as fruit production and seed yield. 
     While ovule-specific developmentally responsive polynucleotides and polynucleotide products can act alone, combinations of these polynucleotides also affect fruit and seed growth and development. Useful combinations include different ovule-specific developmentally responsive polynucleotides and/or polynucleotide products that have similar transcription profiles or similar biological activities, and members of the same or similar biochemical pathways. In addition, the combination of an ovule-specific developmentally responsive polynucleotide and/or polynucleotide product with an environmentally responsive polynucleotide is also useful because of the interactions that exist between development, hormone-regulated pathways, stress pathways and nutritional pathways. Here, in addition to polynucleotides having similar transcription profiles and/or biological activities, useful combinations include polynucleotides that may have different transcription profiles but which participate in a common pathway. The MA_diff Table(s) reports the transcript levels of the experiment (see EXPT ID: 108595). For transcripts that had higher levels in the samples than the control, a “+” is shown. A “−” is shown for when transcript levels were reduced in root tips as compared to the control. For more experimental detail see the Example section below. 
     Ovule genes are those sequences that showed differential expression as compared to controls, namely those sequences identified in the MA_diff tables with a “+” or “−” indication. 
     Ovule Genes Identified by Cluster Analyses of Differential Expression 
     Ovule Genes Identified By Correlation To Genes That Are Differentially Expressed 
     As described above, the transcription profiles of genes that act together are well correlated. Applicants not only have identified the genes that are differentially expressed in the microarray experiments, but also have identified the genes that act in concert with them. The MA_clust table indicates groups of genes that have well correlated transcription profiles and therefore participate in the same pathway or network. 
     A pathway or network of Ovule genes is any group in the MA_clust that comprises a cDNA ID that also appears in Expt ID 108595 of the MA_diff table(s). 
     Ovule Genes Identified by Correlation to Genes that Cause Physiological Consequences 
     Additionally, the differential expression data and the phenotypic observations can be merged to identify pathways or networks of Ovule genes. A group in the MA_clust is considered a Ovule pathway or network if the group comprises a cDNA ID that also appears in Knock-in or Knock-out tables that causes one or more of the phenotypes described in section above. 
     Ovule Genes Identified by Amino Acid Sequence Similarity 
     Ovule genes from other plant species typically encode polypeptides that share amino acid similarity to the sequences encoded by corn and  Arabidopsis  Ovule genes. Groups of Ovule genes are identified in the Protein Group table. In this table, any protein group that comprises a peptide ID that corresponds to a cDNA ID member of a Ovule pathway or network is a group of proteins that also exhibits Ovule functions/utilities. 
     Such ovule-specific developmentally responsive polynucleotides and polynucleotide products can function to either increase or dampen the above phenotypes or activities either in response to transcript changes during ovule development or in the absence of ovule-specific polynucleotide fluctuations. More specifically, ovule-specific developmentally responsive polynucleotides and polynucleotide products are useful to or modulate one or more of the phenotypes, including egg cell, maturation (for development of parthenogenic embryos), metabolism, polar nuclei, fusion (for development of parthenogenic endosperm), central cell, maturation, metabolism (for alteration of endosperm metabolism), synergids, maturation, programmed cell death, nucellus, maturation, integuments, maturation,  funiculus , extension (for increased seed), cuticle, maturation, tensile properties (for increased seed size), ovule, modulation of ovule senescence, and shaping (for increased seed number). 
     To produce the desired phenotype(s) above, one or more of the ovule-specific developmentally responsive polynucleotides and polynucleotide products can be tested by screening for the desired trait. Specifically, the polynucleotide, mRNA levels, or protein levels can be altered in a plant utilizing the procedures described herein and the phenotypes can be assayed. As an example, a plant can be transformed according to Bechtold and Pelletier (1998, Methods. Mol. Biol. 82:259-266) and visually inspected for the desired phenotype or metabolically and/or functionally assayed according to Weigel et al. (2000, Plant Physiol 122: 1003-14) and Winkler et al. (1998, Plant Physiol 118: 743-50). 
     Alternatively, the activities of one or more of the ovule-specific developmentally responsive polynucleotides and polynucleotide products can be modulated to change biochemical or metabolic activities and/or pathways such as those noted below. Such biological activities can be measured according to the citations included in the Table below: 
     
       
         
           
               
               
               
             
               
                   
               
               
                   
                 BIOCHEMICAL OR 
                   
               
               
                 GENERAL 
                 METABOLIC ACTIVITIES 
               
               
                 CATEGORY 
                 AND/OR PATHWAYS 
                 ASSAY 
               
               
                   
               
             
            
               
                 Cell Growth and 
                 Programmed Cell Death 
                 Pennell and Lamb 
               
               
                 Differentiation 
                 DNA Methylation and 
                 (1997) Plant Cell 9, 
               
               
                   
                 Imprinting 
                 1157-1168 
               
               
                   
                   
                 Adams et al. (2000) 
               
               
                   
                   
                 Development 127: 
               
               
                   
                   
                 2493-502 
               
               
                 Organ Growth and 
                 Ovule Growth and 
                 De Martinis and 
               
               
                 Development 
                 Development 
                 Mariani (1999) 
               
               
                   
                 Ethylene Response 
                 Plant Cell 11: 
               
               
                   
                 Megagametophyte 
                 1061-72 
               
               
                   
                 Development 
                 Christensen et al. 
               
               
                   
                 Seed Growth and 
                 (1997) Sexual Plant 
               
               
                   
                 Development 
                 Reproduc 10: 49-64 
               
               
                   
                 Fertilization 
                 Scott et al. (1998) 
               
               
                   
                 Independent 
                 Development 125: 
               
               
                   
                 Seed Development 
                 3329-41 
               
               
                   
                   
                 Ohad et al. (1996) 
               
               
                   
                   
                 PNAS USA 93: 
               
               
                   
                   
                 5319-24 
               
               
                   
                   
                 Chaudhury et al. 
               
               
                   
                   
                 (1997) PNAS USA 
               
               
                   
                   
                 94: 4223-28 
               
               
                 Signal Transduction 
                 Ethylene Metabolism 
                 DeMartinis and 
               
               
                   
                 Protein Remodeling 
                 Mariani (1999) 
               
               
                   
                 Sucrose Mobilization 
                 Plant Cell 11: 
               
               
                   
                 and 
                 1061-1072 
               
               
                   
                 Partitioning 
                 Winkler et al. 
               
               
                   
                 Pollen Tube Adhesion 
                 (1998) Plant 
               
               
                   
                 Jasmonic Acid 
                 Physiol 118: 
               
               
                   
                 Biosynthesis 
                 743-750 
               
               
                 Senescence and Cell 
                 Apomixis 
               
               
                 Death 
               
               
                 Environmental 
                 Wound and Defense 
                 Epple and 
               
               
                 Responses 
                 Response Gene 
                 Bohlmann (1997) 
               
               
                   
                 Expression 
                 Plant Cell 9: 509-20 
               
               
                   
                 Stress Response 
                 He et al. (1998) 
               
               
                   
                   
                 Plant J. 14: 55-63 
               
               
                   
               
            
           
         
       
     
     Other biological activities that can be modulated by the ovule-specific developmentally responsive polynucleotides and polynucleotide products are listed in the Reference tables. Assays for detecting such biological activities are described in the Protein Domain table section. 
     Ovule-specific developmentally responsive polynucleotides are characteristically differentially transcribed in response to fluctuating developmental-specific polynucleotide levels or concentrations, whether internal or external to a cell. The MA_diff Table reports the changes in transcript levels of various ovule-specific developmentally responsive polynucleotides in ovules. 
     These data can be used to identify a number of types of ovule-specific developmentally responsive polynucleotides. Profiles of these different ovule-specific developmentally responsive polynucleotides are shown in the Table below with examples of associated biological activities. 
                                                     EXAMPLES OF       TRANSCRIPTS       PHYSIOLOGICAL   BIOCHEMICAL       AFFECTED BY   TYPES OF GENES   CONSEQUENCES   ACTIVITY                  Ethylene Signals   Responders to   Ethylene Perception   Transcription       Protein   Ethylene   Ethylene Uptake   Factors       Remodeling       Modulation of Ethylene   Transporters               Response Transduction   Inhibit Transport of               Pathways   Abscissic acid               Specific Gene   Degradation               Transcription Initiation               Repression of Pathways               to Optimize Abscissic               acid Response Pathways       Lower at 1 hours   High Abscissic acid   Negative Regulation of   Abscissic acid       than 6 hours   Responders   Abscissic acid Pathways   Metabolic Pathways           Repressor of Abscissic           acid Deprivation           Pathways                    
Use of Promoters of Ovule Genes
 
     Promoters of Ovule genes are useful for transcription of any desired polynucleotide or plant or non-plant origin. Further, any desired sequence can be transcribed in a similar temporal, tissue, or environmentally specific patterns as the Ovule genes where the desired sequence is operably linked to a promoter of a Ovule gene. The protein product of such a polynucleotide is usually synthesized in the same cells, in response to the same stimuli as the protein product of the gene from which the promoter was derived. Such promoter are also useful to produce antisense mRNAs to down-regulate the product of proteins, or to produce sense mRNAs to down-regulate mRNAs via sense suppression. 
     III.A.8. Seed and Fruit Development Genes, Gene Components and Products 
     The ovule is the primary female sexual reproductive organ of flowering plants. At maturity it contains the egg cell and one large central cell containing two polar nuclei encased by two integuments that, after fertilization, develops into the embryo, endosperm, and seed coat of the mature seed, respectively. As the ovule develops into the seed, the ovary matures into the fruit or silique. As such, seed and fruit development requires the orchestrated transcription of numerous polynucleotides, some of which are ubiquitous, others that are embryo-specific and still others that are expressed only in the endosperm, seed coat, or fruit. Such genes are termedfruit development responsive genes. 
     Changes in the concentration of fruit-development responsive polynucleotides during development results in the modulation of many polynucleotides and polynucleotide products. Examples of such fruit development responsive polynucleotides and polynucleotide products relative to leaves and floral stem are shown in the Reference, Sequence, Protein Group, Protein Group Matrix, MA_diff, MA_clust, Knock-in and Knock-out tables. The polynucleotides were discovered by isolating fruits at developmental stages from  Arabidopsis  wild-type ecotype “Wassilewskija”, and measuring the mRNAs expressed in them relative to those in a leaf and floral stem sample. These polynucleotides and/or products are responsible for effects on traits such as seed size, seed yield, seed composition, seed dormancy, fruit ripening, fruit production, and pod shattering. 
     While fruit development responsive polynucleotides and polynucleotide products can act alone, combinations of these polynucleotides also affect fruit and seed growth and development. Useful combinations include different polynucleotides and/or polynucleotide products that have similar transcription profiles or similar biological activities, and members of the same or functionally similar biochemical pathways. In particular, modulation of transcription factors and/or signal transduction pathways are likely to be useful for manipulating whole pathways and hence phenotypes. In addition, the combination of ovule-developmentally responsive polynucleotides and/or polynucleotide products with environmentally responsive polynucleotides is also useful because of the interactions that exist between development, hormone-regulated pathways, stress and pathogen induced pathways and nutritional pathways. Here, useful combinations include polynucleotides that may have different transcription profiles, and participate in common or overlapping pathways but combine to produce a specific, phenotypic change. 
     Such fruit development responsive polynucleotides and polynucleotide products can function to either increase or dampen the above phenotypes or activities either in response to transcript changes in fruit development or in the absence of fruit development polynucleotide fluctuations. 
     The MA_diff Table(s) reports the transcript levels of the experiment (see EXPT ID: 108436, 108437, 108438). For transcripts that had higher levels in the samples than the control, a “+” is shown. A “−” is shown for when transcript levels were reduced in root tips as compared to the control. For more experimental detail see the Example section below. 
     Fruit genes are those sequences that showed differential expression as compared to controls, namely those sequences identified in the MA_diff tables with a “+” or “−” indication. 
     Fruit Genes Identified by Cluster Analyses of Differential Expression 
     Fruit Genes Identified by Correlation to Genes that are Differentially Expressed 
     As described above, the transcription profiles of genes that act together are well correlated. Applicants not only have identified the genes that are differentially expressed in the microarray experiments, but also have identified the genes that act in concert with them. The MA_clust table indicates groups of genes that have well correlated transcription profiles and therefore participate in the same pathway or network. 
     A pathway or network of Fruit genes is any group in the MA_clust that comprises a cDNA ID that also appears in Expt ID 108436, 108437, 108438 of the MA_diff table(s). 
     Fruit Genes Identified by Correlation to Genes that Cause Physiological Consequences 
     Additionally, the differential expression data and the phenotypic observations can be merged to identify pathways or networks of Fruit genes. A group in the MA_clust is considered a Fruit pathway or network if the group comprises a cDNA ID that also appears in Knock-in or Knock-out tables that causes one or more of the phenotypes described in section above. 
     Fruit Genes Identified by Amino Acid Sequence Similarity 
     Fruit genes from other plant species typically encode polypeptides that share amino acid similarity to the sequences encoded by corn and  Arabidopsis  Fruit genes. Groups of Fruit genes are identified in the Protein Group table. In this table, any protein group that comprises a peptide ID that corresponds to a cDNA ID member of a Fruit pathway or network is a group of proteins that also exhibits Fruit functions/utilities. 
     Use of Fruit Development Responsive Genes to Modulate Phenotypes 
     Manipulation of the polynucleotides in the mature ovule, developing embryo, endosperm, seed coat and fruit enables many features of seed and fruit to be improved including the following:
         Female fertility, megasporogenesis, embryo and endosperm development, ovule size, endosperm size, embryo size, seed size, seed yield, seed protein, seed oil, seed starch, seed cell number, cell size, seed coat development, organ size, dormancy and acquisition of desiccation tolerance, seed storage and longevity, seed germination, apomixis, production of seedless fruit and vegetables and hybrid seed production.       

     To improve any of the phenotype(s) above, activities of one or more of the fruit development responsive polynucleotides and polynucleotide products can be modulated and the plants can be tested by screening for the desired trait. Specifically, the polynucleotide, mRNA levels, or protein levels can be altered in a plant utilizing the procedures described herein and the phenotypes can be assayed. As an example, a plant can be transformed according to Bechtold and Pelletier (1998, Methods. Mol. Biol. 82:259-266) and visually inspected for the desired phenotype or metabolically and/or functionally assayed. 
     Use of Fruit Development Responsive Genes to Modulate Biochemical Activities 
     The activities of one or more of the fruit-expressed polynucleotides and polynucleotide products can be modulated to change biochemical or metabolic activities and/or pathways such as those noted below. Such biological changes can be achieved and measured according to citations such as the following:
     1. Winkler et al. (1998). Plant Physiol. 118, 743-750   2. Weigel et al. (2000). Plant Physiol. 122, 1003-1014   3. Cosgrove (1997). Plant Cell 9, 1031-1041   4. Jacobs (1997). Plant Cell 9, 1021-1029   5. Reismeier et al. (1994). EMBO J. 13, 1-7   6. Carland et al. (1999). Plant Cell 11, 2123-2138   7. Cheng et al. (1996). Plant Cell 8, 971-983   8. Weber et al. (1995). Plant Cell 7, 1835-1846   9. Leyser and Furner (1992). Development 116, 397-403   10. Hayashi et al. (1998). Plant Cell 10, 183-196.   11. Pyke (1999). Plant Cell 11, 549-556   12. Lotan et al. (1998). Cell 93, 1195-1205   13. Lending and Larkins (1989). Plant Cell 1, 1011-1023   14. Hong et al. (1996). Development 122, 2051-2058.   15. Fernandez et al. (2000). Science 289, 436-438   16. D&#39;Aoust et al. (1999). Plant Cell 11, 2407-2418   17. Bewley (1997). Plant Cell 9, 1055-1066   18. Heath et al. (1986). Planta 169, 304-312   19. Browse et al. (1986). Anal. Biochem. 152, 141-145   20. D&#39;Aoust et al. (1999). Plant Cell 11, 2407-2418   

     Other biological activities that can be modulated by the fruit-specific developmentally responsive polynucleotides and polynucleotide products are listed in Reference Tables. Assays for detecting such biological activities are described in the table as well as in the Protein Domain tables. 
     
       
         
           
               
               
               
               
               
               
             
               
                   
                   
               
               
                   
                 BIOLOGICAL 
                   
                   
                   
                   
               
               
                   
                 FUNCTION 
                 UTILITY 
                 CITATION 
                 ASSAY 
                 CITATION 
               
               
                   
                   
               
             
            
               
                   
               
            
           
           
               
               
               
               
               
               
            
               
                 Ovule 
                 Ethylene and 
                 Manipulate 
                 De Martinis 
                 Analyze 
                 Winkler et al. 
               
               
                 Growth, 
                 ethylene signal 
                 female 
                 and Mariani 
                 ovule and 
                 (1998). Plant 
               
               
                 Ovule 
                 transduction 
                 fertility. 
                 (1999). Plant 
                 seed 
                 Physiol. 118, 
               
               
                 Development 
                 pathway 
                 Manipulate 
                 Cell 11, 1061-1072. 
                 development 
                 743-750. 
               
               
                 and Seed 
                 Examples: AP2 
                 megasporo- 
                 Silencing 
                 by light 
                 Systematic 
               
               
                 Growth and 
                 domain DNA 
                 genesis. 
                 gene 
                 microscopy 
                 reverse 
               
               
                 Development 
                 binding 
                 Manipulate 
                 expression of 
                 or by 
                 genetics of 
               
               
                   
                 proteins; 
                 female 
                 the ethylene- 
                 confocal 
                 transfer- 
               
               
                   
                 EREBP, EBF 
                 gametophyte 
                 forming 
                 microscopy. 
                 DNA-tagged 
               
               
                   
                 Example: 
                 development. 
                 enzyme results 
                 Test for 
                 lines of 
               
               
                   
                 Leucine-rich 
                 Manipulate 
                 in a reversible 
                 fertilization 
                   Arabidopsis . 
               
               
                   
                 receptor kinase; 
                 fertilization 
                 inhibition of 
                 independent 
                 Weigel et al. 
               
               
                   
                 ETR-like 
                 independent 
                 ovule 
                 endosperm 
                 (2000). Plant 
               
               
                   
                 Example: Raf 
                 endosperm 
                 development in 
                 development. 
                 Physiol 122, 
               
               
                   
                 kinase; CTR 
                 development. 
                 transgenic 
                 Test for 
                 1003-1014. 
               
               
                   
                   
                 Manipulate 
                 tobacco plants. 
                 fertilization 
                 Activation 
               
               
                   
                   
                 fertilization 
                 Christensen et 
                 independent 
                 tagging in 
               
               
                   
                   
                 independent 
                 al. (1997). 
                 embryo 
                   Arabidopsis . 
               
               
                   
                   
                 embryo 
                 Sexual Plant 
                 development. 
                 Ohad et al. 
               
               
                   
                   
                 development. 
                 Reproduc. 10, 
                 Test for 
                 (1996). PNAS 
               
               
                   
                   
                 Manipulate 
                 49-64. 
                 fertilization 
                 USA 93, 
               
               
                   
                   
                 fertilization 
                 Megagametogenesis 
                 independent 
                 5319-5324. A 
               
               
                   
                   
                 independent 
                 in 
                 seed 
                 mutation that 
               
               
                   
                   
                 seed 
                 
                   Arabidopsis 
                 
                 production. 
                 allows 
               
               
                   
                   
                 development. 
                 wild type and 
                 Analyze seed 
                 endosperm 
               
               
                   
                   
                 Manipulate 
                 the Gf mutant. 
                 size. 
                 development 
               
               
                   
                   
                 ovule size. 
                 Christiansen 
                 Analyze seed 
                 without 
               
               
                   
                   
                 Manipulate 
                 and Drews, 
                 yield. 
                 fertilization 
               
               
                   
                   
                 endosperm 
                 unpublished 
                 Analyze seed 
                 Chaudhury et 
               
               
                   
                   
                 size. 
                   
                 composition. 
                 al. (1997). 
               
               
                   
                   
                 Manipulate 
                   
                 Analyze fruit 
                 PNAS USA 
               
               
                   
                   
                 embryo size. 
                   
                 size. 
                 94, 4223-4228. 
               
               
                   
                   
                 Manipulate 
                   
                   
                 Fertilization- 
               
               
                   
                   
                 seed size. 
                   
                   
                 independent 
               
               
                   
                   
                 Manipulate 
                   
                   
                 seed 
               
               
                   
                   
                 seed yield. 
                   
                   
                 development 
               
               
                   
                   
                 Manipulate 
                   
                   
                 in  Arabidopsis   
               
               
                   
                   
                 seed protein. 
                   
                   
                 
                   thaliana 
                 
               
               
                   
                   
                 Manipulate 
                   
                   
                 De Martinis 
               
               
                   
                   
                 seed oil. 
                   
                   
                 and Mariani 
               
               
                   
                   
                 Manipulate 
                   
                   
                 (1999). Plant 
               
               
                   
                   
                 starch 
                   
                   
                 Cell 11, 1061-1072. 
               
               
                   
                   
                 production. 
                   
                   
                 Silencing 
               
               
                   
                   
                 Manipulate 
                   
                   
                 gene 
               
               
                   
                   
                 cell number. 
                   
                   
                 expression of 
               
               
                   
                   
                 Manipulate 
                   
                   
                 the ethylene- 
               
               
                   
                   
                 cell size. 
                   
                   
                 forming 
               
               
                   
                   
                 Produce 
                   
                   
                 enzyme results 
               
               
                   
                   
                 seedless fruit 
                   
                   
                 in a reversible 
               
               
                   
                   
                 and 
                   
                   
                 inhibition of 
               
               
                   
                   
                 vegetables 
                   
                   
                 ovule 
               
               
                   
                   
                 Manipulate 
                   
                   
                 development in 
               
               
                   
                   
                 fruit size. 
                   
                   
                 transgenic 
               
               
                   
                   
                   
                   
                   
                 tobacco plants. 
               
               
                   
                   
                   
                   
                   
                 Christensen et 
               
               
                   
                   
                   
                   
                   
                 al. (1997). 
               
               
                   
                   
                   
                   
                   
                 Sexual Plant 
               
               
                   
                   
                   
                   
                   
                 Reproduc. 10, 
               
               
                   
                   
                   
                   
                   
                 49-64. 
               
               
                   
                   
                   
                   
                   
                 Megagametogenesis 
               
               
                   
                   
                   
                   
                   
                 in 
               
               
                   
                   
                   
                   
                   
                 
                   Arabidopsis 
                 
               
               
                   
                   
                   
                   
                   
                 wild type and 
               
               
                   
                   
                   
                   
                   
                 the Gf mutant. 
               
               
                   
                   
                   
                   
                   
                 Scott et al. 
               
               
                   
                   
                   
                   
                   
                 (1998). 
               
               
                   
                   
                   
                   
                   
                 Development 
               
               
                   
                   
                   
                   
                   
                 125, 3329-3341. 
               
               
                   
                   
                   
                   
                   
                 Parent- 
               
               
                   
                   
                   
                   
                   
                 of-origin 
               
               
                   
                   
                   
                   
                   
                 effects on 
               
               
                   
                   
                   
                   
                   
                 seed 
               
               
                   
                   
                   
                   
                   
                 development 
               
               
                   
                   
                   
                   
                   
                 in 
               
               
                   
                   
                   
                   
                   
                 
                   Arabidopsis 
                 
               
               
                   
                   
                   
                   
                   
                 
                   thaliana 
                 
               
               
                   
                   
                   
                   
                   
                 Heath et al. 
               
               
                   
                   
                   
                   
                   
                 (1986). 
               
               
                   
                   
                   
                   
                   
                 Planta 169, 
               
               
                   
                   
                   
                   
                   
                 304-312. 
               
               
                   
                   
                   
                   
                   
                 Browse et al. 
               
               
                   
                   
                   
                   
                   
                 (1986). Anal. 
               
               
                   
                   
                   
                   
                   
                 Biochem. 
               
               
                   
                   
                   
                   
                   
                 152, 141-145. 
               
               
                   
                   
                   
                   
                   
                 D&#39;Aoust et al. 
               
               
                   
                   
                   
                   
                   
                 (1999). Plant 
               
               
                   
                   
                   
                   
                   
                 Cell 11, 
               
               
                   
                   
                   
                   
                   
                 2407-2418. 
               
               
                   
                 2. Growth and 
                 Manipulate 
                 Wilson et al. 
                 Analyze ovule 
                 Winkler et al. 
               
               
                   
                 developmental 
                 female 
                 (1996). Plant 
                 and seed 
                 (1998). Plant 
               
               
                   
                 control genes 
                 fertility. 
                 Cell 8, 659-671. A 
                 development 
                 Physiol. 118, 
               
               
                   
                 — 
                 Manipulate 
                 dissociation 
                 by light 
                 743-750. 
               
               
                   
                 Upregulated 
                 megasporo- 
                 insertion 
                 microscopy or 
                 Systematic 
               
               
                   
                 genes 
                 genesis. 
                 causes a 
                 by confocal 
                 reverse 
               
               
                   
                 Example: DNA 
                 Manipulate 
                 semidominant 
                 microscopy. 
                 genetics of 
               
               
                   
                 binding 
                 female 
                 mutation that 
                 Test for 
                 transfer- 
               
               
                   
                 proteins; tiny- 
                 gametophyte 
                 increases 
                 fertilization 
                 DNA-tagged 
               
               
                   
                 like, AGL1, 
                 development. 
                 expression of 
                 independent 
                 lines of 
               
               
                   
                 FBP2, AGL9, 
                 Manipulate 
                 TINY, an 
                 endosperm 
                   Arabidopsis . 
               
               
                   
                 AP3, CPC-like 
                 fertilization 
                 
                   Arabidopsis 
                 
                 development. 
                 Weigel et al. 
               
               
                   
                 myb. 
                 independent 
                 gene related to 
                 Test for 
                 (2000). Plant 
               
               
                   
                 Example: 
                 endosperm 
                 APETALA2. 
                 fertilization 
                 Physiol 122, 
               
               
                   
                 Protein kinase; 
                 development. 
                 Zhao et al 
                 independent 
                 1003-1014. 
               
               
                   
                 ASK1. 
                 Manipulate 
                 (1999). 
                 embryo 
                 Activation 
               
               
                   
                 Example: Auxin 
                 fertilization 
                 Developmental 
                 development. 
                 tagging in 
               
               
                   
                 conjugating 
                 independent 
                 Genetics 25, 
                 Test for 
                   Arabidopsis . 
               
               
                   
                 enzyme; indole- 
                 embryo 
                 209-223. The 
                 fertilization 
                 Ohad et al. 
               
               
                   
                 3-acetate beta- 
                 development. 
                 ASK1 gene 
                 independent 
                 (1996). PNAS 
               
               
                   
                 glucosyltransferase. 
                 Manipulate 
                 regulates 
                 seed 
                 USA 93, 
               
               
                   
                 Example: S/T 
                 fertilization 
                 development 
                 production. 
                 5319-5324. A 
               
               
                   
                 protein kinase; 
                 independent 
                 and interacts 
                 Analyze seed 
                 mutation that 
               
               
                   
                 APK1. 
                 seed 
                 with the UFO 
                 size. 
                 allows 
               
               
                   
                 Example: 
                 development. 
                 gene to 
                 Analyze seed 
                 endosperm 
               
               
                   
                 Leucine-rich 
                 Manipulate 
                 control floral 
                 yield. 
                 development 
               
               
                   
                 receptor kinase; 
                 ovule size. 
                 organ identity 
                 Analyze seed 
                 without 
               
               
                   
                 CLV1, ER, 
                 Manipulate 
                 in 
                 composition. 
                 fertilization 
               
               
                   
                 BRI, Cf-2-like. 
                 endosperm 
                   Arabidopsis . 
                 Analyze fruit 
                 Chaudhury et 
               
               
                   
                 — 
                 size. 
                 Flanagan et 
                 size. 
                 al. (1997). 
               
               
                   
                 Downregulated 
                 Manipulate 
                 al. (1996). 
                 Analyze 
                 PNAS USA 
               
               
                   
                 genes 
                 embryo size. 
                 Plant J. 10, 
                 seedling size. 
                 94, 4223-4228. 
               
               
                   
                 Example: 
                 Manipulate 
                 343-53. 
                 Analyze 
                 Fertilization- 
               
               
                   
                 Cyclin- 
                 organ size 
                 Specific 
                 seedling 
                 independent 
               
               
                   
                 dependent 
                 and number. 
                 expression of 
                 viability. 
                 seed 
               
               
                   
                 kinase; cdc2. 
                 Manipulate 
                 the AGL1 
                 Screen for 
                 development 
               
               
                   
                   
                 seed size. 
                 MADS-box 
                 changes in 
                 in 
               
               
                   
                   
                 Manipulate 
                 gene suggests 
                 shatter time. 
                 
                   Arabidopsis 
                 
               
               
                   
                   
                 seed yield. 
                 regulatory 
                 Screen for 
                 
                   thaliana 
                 
               
               
                   
                   
                 Manipulate 
                 functions in 
                 changes in 
                 De Martinis 
               
               
                   
                   
                 seedling size 
                 
                   Arabidopsis 
                 
                 germination 
                 and Mariani 
               
               
                   
                   
                 through seed 
                 
                   gynoecium 
                 
                 frequency. 
                 (1999). Plant 
               
               
                   
                   
                 size. 
                 and ovule 
                 Screen for 
                 Cell 11, 1061-1072. 
               
               
                   
                   
                 Manipulate 
                 development. 
                 seed longevity 
                 Silencing 
               
               
                   
                   
                 seedling 
                 Angenent et 
                 and viability. 
                 gene 
               
               
                   
                   
                 vigor 
                 al. (1994). 
                   
                 expression of 
               
               
                   
                   
                 through seed 
                 Plant J 1994. 
                   
                 the ethylene- 
               
               
                   
                   
                 size. 
                 5, 33-44. Co- 
                   
                 forming 
               
               
                   
                   
                 Manipulate 
                 suppression of 
                   
                 enzyme results 
               
               
                   
                   
                 seed protein. 
                 the petunia 
                   
                 in a reversible 
               
               
                   
                   
                 Manipulate 
                 homeotic gene 
                   
                 inhibition of 
               
               
                   
                   
                 seed oil. 
                 fbp2 affects 
                   
                 ovule 
               
               
                   
                   
                 Manipulate 
                 the identity of 
                   
                 development in 
               
               
                   
                   
                 starch 
                 the generative 
                   
                 transgenic 
               
               
                   
                   
                 production. 
                 meristem. 
                   
                 tobacco plants. 
               
               
                   
                   
                 Manipulate 
                 AGL9 web 
                   
                 Christensen et 
               
               
                   
                   
                 integument 
                 page. 
                   
                 al. (1997). 
               
               
                   
                   
                 development. 
                 Wada et al. 
                   
                 Sexual Plant 
               
               
                   
                   
                 Manipulate 
                 (1997) 
                   
                 Reproduc. 10, 
               
               
                   
                   
                 seedcoat 
                 Science 277, 
                   
                 49-64. 
               
               
                   
                   
                 development. 
                 1113-6. 
                   
                 Megagametogenesis 
               
               
                   
                   
                 Manipulate 
                 Epidermal cell 
                   
                 in 
               
               
                   
                   
                 cell size. 
                 differentiation 
                   
                 
                   Arabidopsis 
                 
               
               
                   
                   
                 Manipulate 
                 in  Arabidopsis   
                   
                 wild type and 
               
               
                   
                   
                 cell number. 
                 determined by 
                   
                 the Gf mutant. 
               
               
                   
                   
                 Manipulate 
                 a Myb 
                   
                 Scott et al. 
               
               
                   
                   
                 homeotic 
                 homolog 
                   
                 (1998). 
               
               
                   
                   
                 gene 
                 CPC. 
                   
                 Development 
               
               
                   
                   
                 expression. 
                 Szerszen et al. 
                   
                 125, 3329-3341. 
               
               
                   
                   
                 Manipulate 
                 (1994). 
                   
                 Parent- 
               
               
                   
                   
                 organ size. 
                 Science 16, 
                   
                 of-origin 
               
               
                   
                   
                 Manipulate 
                 1699-1701. 
                   
                 effects on 
               
               
                   
                   
                 meristem 
                 iaglu, a gene 
                   
                 seed 
               
               
                   
                   
                 size. 
                 from  Zea   
                   
                 development 
               
               
                   
                   
                 Produce 
                 
                   mays 
                 
                   
                 in 
               
               
                   
                   
                 seedless fruit 
                 involved in 
                   
                 
                   Arabidopsis 
                 
               
               
                   
                   
                 and 
                 conjugation of 
                   
                 
                   thaliana. 
                 
               
               
                   
                   
                 vegetables 
                 growth 
                   
                 Heath et al. 
               
               
                   
                   
                 Manipulate 
                 hormone 
                   
                 (1986). 
               
               
                   
                   
                 fruit size. 
                 indole-3- 
                   
                 Planta 169, 
               
               
                   
                   
                 Manipulate 
                 acetic acid. 
                   
                 304-312. 
               
               
                   
                   
                 time of seed 
                 Ito et al. 
                   
                 Browse et al. 
               
               
                   
                   
                 dispersal. 
                 (1997). Plant 
                   
                 (1986). Anal. 
               
               
                   
                   
                 Manipulate 
                 Cell Physiol. 
                   
                 Biochem. 
               
               
                   
                   
                 seed viability 
                 38, 248-258. A 
                   
                 152, 141-145. 
               
               
                   
                   
                 upon storage. 
                 serine/threonine 
                   
                 D&#39;Aoust et al. 
               
               
                   
                   
                 Manipulate 
                 protein 
                   
                 (1999). Plant 
               
               
                   
                   
                 germination frequency. 
                 kinase gene 
                   
                 Cell 11, 2407-2418. 
               
               
                   
                   
                   
                 isolated by an 
               
               
                   
                   
                   
                 in vivo 
               
               
                   
                   
                   
                 binding 
               
               
                   
                   
                   
                 procedure 
               
               
                   
                   
                   
                 using the 
               
               
                   
                   
                   
                 
                   Arabidopsis 
                 
               
               
                   
                   
                   
                 floral 
               
               
                   
                   
                   
                 homeotic 
               
               
                   
                   
                   
                 gene product, 
               
               
                   
                   
                   
                 AGAMOUS. 
               
               
                   
                   
                   
                 Clark et al. 
               
               
                   
                   
                   
                 (1997). Cell 
               
               
                   
                   
                   
                 89, 575-585. 
               
               
                   
                   
                   
                 The 
               
               
                   
                   
                   
                 CLAVATA1 
               
               
                   
                   
                   
                 gene encodes 
               
               
                   
                   
                   
                 a putative 
               
               
                   
                   
                   
                 receptor 
               
               
                   
                   
                   
                 kinase that 
               
               
                   
                   
                   
                 controls shoot 
               
               
                   
                   
                   
                 and floral 
               
               
                   
                   
                   
                 meristem size 
               
               
                   
                   
                   
                 in 
               
               
                   
                   
                   
                   Arabidopsis . 
               
               
                   
                   
                   
                 Torii et al. 
               
               
                   
                   
                   
                 (1996). Plant 
               
               
                   
                   
                   
                 Cell 8, 735-746. 
               
               
                   
                   
                   
                 The 
               
               
                   
                   
                   
                 
                   Arabidopsis 
                 
               
               
                   
                   
                   
                 ERECTA 
               
               
                   
                   
                   
                 gene encodes 
               
               
                   
                   
                   
                 a putative 
               
               
                   
                   
                   
                 receptor 
               
               
                   
                   
                   
                 protein kinase 
               
               
                   
                   
                   
                 with 
               
               
                   
                   
                   
                 extracellular 
               
               
                   
                   
                   
                 leucine-rich 
               
               
                   
                   
                   
                 repeats. 
               
               
                   
                   
                   
                 Li and Chory 
               
               
                   
                   
                   
                 (1997). Cell 
               
               
                   
                   
                   
                 90, 929-38. A 
               
               
                   
                   
                   
                 putative 
               
               
                   
                   
                   
                 leucine-rich 
               
               
                   
                   
                   
                 repeat 
               
               
                   
                   
                   
                 receptor 
               
               
                   
                   
                   
                 kinase 
               
               
                   
                   
                   
                 involved in 
               
               
                   
                   
                   
                 brassinosteroid 
               
               
                   
                   
                   
                 signal 
               
               
                   
                   
                   
                 transduction. 
               
               
                   
                 3. Cell 
                 Manipulate 
                 Solomon et al. 
                 Analyze ovule 
                 Winkler et al. 
               
               
                   
                 senescence and 
                 female 
                 (1999). Plant 
                 and seed 
                 (1998). Plant 
               
               
                   
                 cell death 
                 fertility. 
                 Cell 11, 431-444. 
                 development 
                 Physiol. 118, 
               
               
                   
                 Example: 
                 Manipulate 
                 The 
                 by light 
                 743-750. 
               
               
                   
                 Cystatin 
                 seed set. 
                 involvement of 
                 microscopy or 
                 Systematic 
               
               
                   
                 Example: 
                 Manipulate 
                 cysteine 
                 by confocal 
                 reverse 
               
               
                   
                 WIPK 
                 seed yield. 
                 proteases and 
                 microscopy. 
                 genetics of 
               
               
                   
                   
                 Manipulate 
                 protease 
                 Analyze seed 
                 transfer- 
               
               
                   
                   
                 seed size. 
                 inhibitor genes 
                 set. 
                 DNA-tagged 
               
               
                   
                   
                 Manipulate 
                 in the 
                 Analyze seed 
                 lines of 
               
               
                   
                   
                 fruit set. 
                 regulation of 
                 size. 
                   Arabidopsis . 
               
               
                   
                   
                 Promote 
                 programmed 
                 Analyze seed 
                 Weigel et al. 
               
               
                   
                   
                 apomixis. 
                 cell death in 
                 yield. 
                 (2000). Plant 
               
               
                   
                   
                 Produce 
                 plants. 
                 Analyze fruit 
                 Physiol 122, 
               
               
                   
                   
                 Seedless fruit 
                 Zhang et al. 
                 set. 
                 1003-1014. 
               
               
                   
                   
                 and 
                 (2000). Plant J. 
                 Screen for 
                 Activation 
               
               
                   
                   
                 vegetables. 
                 23, 339-347. 
                 fertilization 
                 tagging in 
               
               
                   
                   
                   
                 Multiple levels 
                 independent 
                   Arabidopsis . 
               
               
                   
                   
                   
                 of tobacco 
                 seed 
                 Ohad et al. 
               
               
                   
                   
                   
                 WIPK 
                 development. 
                 (1996). PNAS 
               
               
                   
                   
                   
                 activation 
                   
                 USA 93, 
               
               
                   
                   
                   
                 during the 
                   
                 5319-5324. A 
               
               
                   
                   
                   
                 induction of cell 
                   
                 mutation that 
               
               
                   
                   
                   
                 death by fungal 
                   
                 allows 
               
               
                   
                   
                   
                 elicitins. 
                   
                 endosperm 
               
               
                   
                   
                   
                   
                   
                 development 
               
               
                   
                   
                   
                   
                   
                 without 
               
               
                   
                   
                   
                   
                   
                 fertilization 
               
               
                   
                 4. Protein 
                 Manipulate 
                 Christensen et 
                 Test for 
                 Winkler et al. 
               
               
                   
                 remodeling 
                 female 
                 al. (1997). 
                 altered female 
                 (1998). Plant 
               
               
                   
                 Example: DNA-J 
                 fertility. 
                 Sexual Plant 
                 fertility, seed 
                 Physiol. 118, 
               
               
                   
                 protein/chaperones 
                 Manipulate 
                 Reproduc. 10, 
                 set, seed 
                 743-750. 
               
               
                   
                   
                 female 
                 49-64. 
                 yield. 
                 Systematic 
               
               
                   
                   
                 gametophyte 
                 Megagametogenesis 
                 Analyze ovule 
                 reverse 
               
               
                   
                   
                 development. 
                 in 
                 development 
                 genetics of 
               
               
                   
                   
                 Promote 
                 
                   Arabidopsis 
                 
                 by light 
                 transfer- 
               
               
                   
                   
                 apomixis. 
                 wild type and 
                 microscopy or 
                 DNA-tagged 
               
               
                   
                   
                 Manipulate 
                 the Gf mutant. 
                 by confocal 
                 lines of 
               
               
                   
                   
                 endosperm 
                 Cory 
                 microscopy. 
                   Arabidopsis . 
               
               
                   
                   
                 development. 
                 Christiansen 
                 Analyze seed 
                 Weigel et al. 
               
               
                   
                   
                 Manipulate 
                 and Gary 
                 size. 
                 (2000). Plant 
               
               
                   
                   
                 embryo 
                 Drews, 
                 Analyze seed 
                 Physiol 122, 
               
               
                   
                   
                 development. 
                 unpublished 
                 yield. 
                 1003-1014. 
               
               
                   
                   
                 Manipulate 
                   
                 Analyze seed 
                 Activation 
               
               
                   
                   
                 seed size. 
                   
                 composition. 
                 tagging in 
               
               
                   
                   
                 Manipulate 
                   
                   
                   Arabidopsis . 
               
               
                   
                   
                 seed yield. 
                   
                   
                 Christensen et 
               
               
                   
                   
                 Manipulate 
                   
                   
                 al. (1997). 
               
               
                   
                   
                 seed protein. 
                   
                   
                 Sexual Plant 
               
               
                   
                   
                 Manipulate 
                   
                   
                 Reproduc. 10, 
               
               
                   
                   
                 seed oil. 
                   
                   
                 49-64. 
               
               
                   
                   
                 Manipulate 
                   
                   
                 Megagametogenesis 
               
               
                   
                   
                 starch. 
                   
                   
                 in 
               
               
                   
                   
                 Produce 
                   
                   
                 
                   Arabidopsis 
                 
               
               
                   
                   
                 seedless fruit 
                   
                   
                 wild type and 
               
               
                   
                   
                 and 
                   
                   
                 the Gf mutant. 
               
               
                   
                   
                 vegetables. 
                   
                   
                 Ohad et al. 
               
               
                   
                   
                   
                   
                   
                 (1996). PNAS 
               
               
                   
                   
                   
                   
                   
                 USA 93, 
               
               
                   
                   
                   
                   
                   
                 5319-5324. A 
               
               
                   
                   
                   
                   
                   
                 mutation that 
               
               
                   
                   
                   
                   
                   
                 allows 
               
               
                   
                   
                   
                   
                   
                 endosperm 
               
               
                   
                   
                   
                   
                   
                 development 
               
               
                   
                   
                   
                   
                   
                 without 
               
               
                   
                   
                   
                   
                   
                 fertilization 
               
               
                   
                   
                   
                   
                   
                 Scott et al. 
               
               
                   
                   
                   
                   
                   
                 (1998). 
               
               
                   
                   
                   
                   
                   
                 Development 
               
               
                   
                   
                   
                   
                   
                 125, 3329-3341. 
               
               
                   
                   
                   
                   
                   
                 Parent- 
               
               
                   
                   
                   
                   
                   
                 of-origin 
               
               
                   
                   
                   
                   
                   
                 effects on 
               
               
                   
                   
                   
                   
                   
                 seed 
               
               
                   
                   
                   
                   
                   
                 development 
               
               
                   
                   
                   
                   
                   
                 in 
               
               
                   
                   
                   
                   
                   
                 
                   Arabidopsis 
                 
               
               
                   
                   
                   
                   
                   
                   thaliana . 
               
               
                   
                   
                   
                   
                   
                 Heath et al. 
               
               
                   
                   
                   
                   
                   
                 (1986). 
               
               
                   
                   
                   
                   
                   
                 Planta 169, 
               
               
                   
                   
                   
                   
                   
                 304-312. 
               
               
                   
                   
                   
                   
                   
                 Browse et al. 
               
               
                   
                   
                   
                   
                   
                 (1986). Anal. 
               
               
                   
                   
                   
                   
                   
                 Biochem. 
               
               
                   
                   
                   
                   
                   
                 152, 141-145. 
               
               
                   
                   
                   
                   
                   
                 D&#39;Aoust et al. 
               
               
                   
                   
                   
                   
                   
                 (1999). Plant 
               
               
                   
                   
                   
                   
                   
                 Cell 11, 
               
               
                   
                   
                   
                   
                   
                 2407-2418. 
               
               
                   
                 5. Sucrose 
                 Manipulate 
                 Mapping of 
                 Analyze ovule 
                 Winkler et al. 
               
               
                   
                 mobilization and 
                 female 
                 tomato genes 
                 and seed 
                 (1998). Plant 
               
               
                   
                 partitioning 
                 fertility. 
                 associated 
                 development 
                 Physiol. 118, 
               
               
                   
                 Example: 
                 Manipulate 
                 with sugar 
                 by light 
                 743-750. 
               
               
                   
                 Invertase 
                 ovule 
                 metabolism. 
                 microscopy or 
                 Systematic 
               
               
                   
                 inhibitor 
                 development. 
                 Tomato 
                 by confocal 
                 reverse 
               
               
                   
                 Example: bZIP 
                 Manipulate 
                 Genetics Co- 
                 microscopy. 
                 genetics of 
               
               
                   
                 transcription 
                 seed 
                 op Report 48, 
                 Determine 
                 transfer-DNA- 
               
               
                   
                 factor 
                 development. 
                 22-23 (1998) 
                 female 
                 tagged lines of 
               
               
                   
                 (translation of 
                 Manipulate 
                 Ikeda et al. 
                 fertility. 
                   Arabidopsis . 
               
               
                   
                 bZIP protein is 
                 endosperm 
                 (1999). Plant 
                 Analyze seed 
                 Weigel et al. 
               
               
                   
                 inhibited by 
                 development. 
                 Physiol 121, 
                 mass. 
                 (2000). Plant 
               
               
                   
                 sucrose levels 
                 Manipulate 
                 813-820. 
                 Analyze seed 
                 Physiol 122, 
               
               
                   
                 greater than 25 mM) 
                 embryo 
                 Sucrose and 
                 yield. 
                 1003-1014. 
               
               
                   
                 Example: 
                 development. 
                 Cytokinin 
                 Analyze seed 
                 Activation 
               
               
                   
                 Lipoxygenase 
                 Manipulate 
                 Modulation of 
                 composition. 
                 tagging in 
               
               
                   
                 — 
                 seed size. 
                 WPK4, a 
                 Analyze 
                   Arabidopsis . 
               
               
                   
                 Downregulated 
                 Manipulate 
                 Gene 
                 organ size. 
                 Christensen et 
               
               
                   
                 gene 
                 seed yield. 
                 Encoding a 
                 Analyze 
                 al. (1997). 
               
               
                   
                 Example: 
                 Manipulate 
                 SNF1-Related 
                 seedling size. 
                 Sexual Plant 
               
               
                   
                 SNF1-related 
                 seed protein. 
                 Protein 
                 Analyze 
                 Reproduc. 10, 
               
               
                   
                 protein kinase 
                 Manipulate 
                 Kinase from 
                 seedling 
                 49-64. 
               
               
                   
                   
                 seed oil. 
                 Wheat. 
                 viability. 
                 Megagametogenesis 
               
               
                   
                   
                 Manipulate 
                 Rook et al. 
                   
                 in 
               
               
                   
                   
                 starch. 
                 (1998). Plant 
                   
                 
                   Arabidopsis 
                 
               
               
                   
                   
                 Manipulate 
                 J. 15, 253-263. 
                   
                 wild type and 
               
               
                   
                   
                 cell size. 
                 Sucrose- 
                   
                 the Gf mutant. 
               
               
                   
                   
                 Manipulate 
                 specific 
                   
                 Ohad et al. 
               
               
                   
                   
                 cell number. 
                 signaling 
                   
                 (1996). PNAS 
               
               
                   
                   
                 Manipulate 
                 represses 
                   
                 USA 93, 
               
               
                   
                   
                 organ size. 
                 translation of 
                   
                 5319-5324. A 
               
               
                   
                   
                 Manipulate 
                 the 
                   
                 mutation that 
               
               
                   
                   
                 meristem 
                 
                   Arabidopsis 
                 
                   
                 allows 
               
               
                   
                   
                 size. 
                 ATB2 bZIP 
                   
                 endosperm 
               
               
                   
                   
                 Manipulate 
                 transcription 
                   
                 development 
               
               
                   
                   
                 seedling size 
                 factor gene. 
                   
                 without 
               
               
                   
                   
                 through seed 
                 Rook et al. 
                   
                 fertilization 
               
               
                   
                   
                 size. 
                 (1998). Plant 
                   
                 Scott et al. 
               
               
                   
                   
                 Manipulate 
                 Mol Biol 
                   
                 (1998). 
               
               
                   
                   
                 seedling 
                 37, 171-178. 
                   
                 Development 
               
               
                   
                   
                 viability 
                 The light- 
                   
                 125, 3329-3341. 
               
               
                   
                   
                 through seed 
                 regulated 
                   
                 Parent- 
               
               
                   
                   
                 size. 
                 
                   Arabidopsis 
                 
                   
                 of-origin 
               
               
                   
                   
                 Produce 
                 bZIP 
                   
                 effects on 
               
               
                   
                   
                 seedless fruit 
                 transcription 
                   
                 seed 
               
               
                   
                   
                 and 
                 factor gene 
                   
                 development 
               
               
                   
                   
                 vegetables. 
                 ATB2 
                   
                 in 
               
               
                   
                   
                 Translational 
                 encodes a 
                   
                 
                   Arabidopsis 
                 
               
               
                   
                   
                 control of 
                 protein with 
                   
                   thaliana . 
               
               
                   
                   
                 gene 
                 an unusually 
                   
                 6. Heath et al. 
               
               
                   
                   
                 expression in 
                 long leucine 
                   
                 (1986). 
               
               
                   
                   
                 ovule and 
                 zipper 
                   
                 Planta 169, 
               
               
                   
                   
                 seed by 
                 domain. 
                   
                 304-312. 
               
               
                   
                   
                 sucrose. 
                 Bunker et al. 
                   
                 7. Browse et 
               
               
                   
                   
                 Manipulate 
                 (1995). Plant 
                   
                 al. (1986). 
               
               
                   
                   
                 assimilate 
                 Cell 7, 1319-1331. 
                   
                 Anal. 
               
               
                   
                   
                 partitioning 
                 Sink 
                   
                 Biochem. 
               
               
                   
                   
                 in ovule and 
                 limitation 
                   
                 152, 141-145. 
               
               
                   
                   
                 seed 
                 induces the 
                   
                 8. D&#39;Aoust et 
               
               
                   
                   
                 development. 
                 expression of 
                   
                 al. (1999). 
               
               
                   
                   
                   
                 multiple 
                   
                 Plant Cell 11, 
               
               
                   
                   
                   
                 soybean 
                   
                 2407-2418. 
               
               
                   
                   
                   
                 vegetative 
               
               
                   
                   
                   
                 lipoxygenase 
               
               
                   
                   
                   
                 mRNAs while 
               
               
                   
                   
                   
                 the 
               
               
                   
                   
                   
                 endogenous 
               
               
                   
                   
                   
                 jasmonic acid 
               
               
                   
                   
                   
                 level remains 
               
               
                   
                   
                   
                 low. 
               
               
                   
                   
                   
                 Lowry et al. 
               
               
                   
                   
                   
                 (1998). Plant 
               
               
                   
                   
                   
                 Physiol. 116, 
               
               
                   
                   
                   
                 923-933. 
               
               
                   
                   
                   
                 Specific 
               
               
                   
                   
                   
                 soybean 
               
               
                   
                   
                   
                 lipoxygenases 
               
               
                   
                   
                   
                 localize to 
               
               
                   
                   
                   
                 discrete 
               
               
                   
                   
                   
                 subcellular 
               
               
                   
                   
                   
                 compartments 
               
               
                   
                   
                   
                 and their 
               
               
                   
                   
                   
                 mRNAs are 
               
               
                   
                   
                   
                 differentially 
               
               
                   
                   
                   
                 regulated by 
               
               
                   
                   
                   
                 source-sink 
               
               
                   
                   
                   
                 status. 
               
               
                   
                 6. Jasmonic 
                 Targeted 
                 Sanders et al. 
                 Test for 
                 Winkler et al. 
               
               
                   
                 acid 
                 death of cells 
                 (2000). Plant 
                 altered female 
                 (1998). Plant 
               
               
                   
                 biosynthesis 
                 belonging to 
                 Cell 12, 1041-1062. 
                 fertility. 
                 Physiol. 118, 
               
               
                   
                 and signal 
                 the female 
                 The 
                 Analyze male 
                 743-750. 
               
               
                   
                 transduction 
                 gametophyte, 
                 
                   Arabidopsis 
                 
                 fertility. 
                 Systematic 
               
               
                   
                 pathway 
                 ovule or 
                 DELAYED 
                 Screen for 
                 reverse 
               
               
                   
                 Example: 
                 integuments. 
                 DEHISCENCE1 
                 enhanced 
                 genetics of 
               
               
                   
                 Biosynthetic 
                 Delay 
                 gene 
                 expression of 
                 transfer- 
               
               
                   
                 enzyme; FMN 
                 senescence 
                 encodes an 
                 pathogen 
                 DNA-tagged 
               
               
                   
                 oxidoreductase 
                 of 
                 enzyme in the 
                 defense 
                 lines of 
               
               
                   
                 12-oxophyto- 
                 unfertilized 
                 jasmonic acid 
                 response 
                 
                   Arabidopsis 
                 
               
               
                   
                 dienoate 
                 female 
                 synthesis 
                 genes. 
                 Weigel et al. 
               
               
                   
                 reductase, 
                 gametophyte, 
                 pathway. 
                   
                 (2000). Plant 
               
               
                   
                 OPR1, OPR1- 
                 ovule or 
                 Vijayan et al. 
                   
                 Physiol 122, 
               
               
                   
                 like. 
                 integuments. 
                 (1998). A role 
                   
                 1003-1014. 
               
               
                   
                 Example: 
                 Manipulate 
                 for jasmonate 
                   
                 Activation 
               
               
                   
                 Signal 
                 female 
                 in pathogen 
                   
                 tagging in 
               
               
                   
                 transduction 
                 fertility 
                 defense of 
                   
                   Arabidopsis . 
               
               
                   
                 pathway kinase 
                 Coordinate 
                   Arabidopsis . 
               
               
                   
                 WIPK. 
                 female with 
                 PNAS USA 
               
               
                   
                   
                 male 
                 95, 7209-7214. 
               
               
                   
                   
                 reproduction. 
                 Seo et al. 
               
               
                   
                   
                 Manipulate 
                 (1999). Plant 
               
               
                   
                   
                 male fertility. 
                 Cell 11, 289-298. 
               
               
                   
                   
                 Enhanced 
                 Jasmonate- 
               
               
                   
                   
                 defense 
                 based wound 
               
               
                   
                   
                 response in 
                 signal 
               
               
                   
                   
                 ovules and 
                 transduction 
               
               
                   
                   
                 seed 
                 requires 
               
               
                   
                   
                   
                 activation of 
               
               
                   
                   
                   
                 WIPK, a 
               
               
                   
                   
                   
                 tobacco 
               
               
                   
                   
                   
                 mitogen- 
               
               
                   
                   
                   
                 activated 
               
               
                   
                   
                   
                 protein 
               
               
                   
                   
                   
                 kinase. 
               
               
                 Environmental 
                 1. Wound and 
                 Pathogen 
                 Song et al. 
                 Resistance to 
                 Winkler et al. 
               
               
                 responses 
                 defense 
                 resistant 
                 (1995). 
                 
                   Xanthamonas 
                 
                 (1998). Plant 
               
               
                   
                 response gene 
                 ovules. 
                 Science 270, 
                 sp. 
                 Physiol. 118, 
               
               
                   
                 expression 
                 Pathogen 
                 1804-1806. A 
                 Resistance to 
                 743-750. 
               
               
                   
                 Example: 
                 resistant 
                 receptor 
                 known 
                 Systematic 
               
               
                   
                 Leucine rich 
                 seeds. 
                 kinase-like 
                 
                   arabidopsis 
                 
                 reverse 
               
               
                   
                 receptor S/T 
                 Pathogen 
                 protein 
                 pathogens in 
                 genetics of 
               
               
                   
                 kinase; Xa21- 
                 resistant 
                 encoded by the 
                 ovules, seed 
                 transfer-DNA- 
               
               
                   
                 like and TMK- 
                 fruit. 
                 rice disease 
                 and fruit. 
                 tagged lines of 
               
               
                   
                 like. 
                   
                 resistance 
                   
                   Arabidopsis . 
               
               
                   
                 Example: Cell 
                   
                 gene, Xa21. 
                   
                 Weigel et al. 
               
               
                   
                 wall-associated 
                   
                 Seo et al. 
                   
                 (2000). Plant 
               
               
                   
                 protein kinase 
                   
                 (1995). Science 
                   
                 Physiol 122, 
               
               
                   
                 WAK1. 
                   
                 270, 1988-1992. 
                   
                 1003-1014. 
               
               
                   
                 Example: 
                   
                 Tobacco 
                   
                 Activation 
               
               
                   
                 Thionins. 
                   
                 MAP kinase: a 
                   
                 tagging in 
               
               
                   
                   
                   
                 possible 
                   
                   Arabidopsis . 
               
               
                   
                   
                   
                 mediator in 
                   
                 Epple and 
               
               
                   
                   
                   
                 wound signal 
                   
                 Bohlmann 
               
               
                   
                   
                   
                 transduction 
                   
                 (1997). Plant 
               
               
                   
                   
                   
                 pathways. 
                   
                 Cell 9, 509-520. 
               
               
                   
                   
                   
                 He et al. 
                   
                 Overexpression 
               
               
                   
                   
                   
                 (1998). Plant J. 
                   
                 of an 
               
               
                   
                   
                   
                 14, 55-63. 
                   
                 endogenous 
               
               
                   
                   
                   
                 Requirement 
                   
                 thionin 
               
               
                   
                   
                   
                 for the induced 
                   
                 enhances 
               
               
                   
                   
                   
                 expression of a 
                   
                 resistance of 
               
               
                   
                   
                   
                 cell wall 
                   
                 
                   Arabidopsis 
                 
               
               
                   
                   
                   
                 associated 
                   
                 against 
               
               
                   
                   
                   
                 receptor kinase 
                   
                 
                   Fusarium 
                 
               
               
                   
                   
                   
                 for survival 
                   
                   oxysporum . 
               
               
                   
                   
                   
                 during the 
                   
                 He et al. 
               
               
                   
                   
                   
                 pathogen 
                   
                 (1998). Plant 
               
               
                   
                   
                   
                 response. 
                   
                 J. 14, 55-63. 
               
               
                   
                   
                   
                 He et al. 
                   
                 Requirement 
               
               
                   
                   
                   
                 (1999). Plant 
                   
                 for the 
               
               
                   
                   
                   
                 Mol. Biol. 39, 
                   
                 induced 
               
               
                   
                   
                   
                 1189-1196. A 
                   
                 expression of 
               
               
                   
                   
                   
                 cluster of five 
                   
                 a cell wall 
               
               
                   
                   
                   
                 cell wall- 
                   
                 associated 
               
               
                   
                   
                   
                 associated 
                   
                 receptor 
               
               
                   
                   
                   
                 receptor kinase 
                   
                 kinase for 
               
               
                   
                   
                   
                 genes, Wak1-5, 
                   
                 survival 
               
               
                   
                   
                   
                 are expressed 
                   
                 during the 
               
               
                   
                   
                   
                 in specific 
                   
                 pathogen 
               
               
                   
                   
                   
                 organs of 
                   
                 response. 
               
               
                   
                   
                   
                   Arabidopsis . 
               
               
                   
                   
                   
                 Epple and 
               
               
                   
                   
                   
                 Bohlmann 
               
               
                   
                   
                   
                 (1997). Plant 
               
               
                   
                   
                   
                 Cell 9, 509-520. 
               
               
                   
                   
                   
                 Overexpression 
               
               
                   
                   
                   
                 of an 
               
               
                   
                   
                   
                 endogenous 
               
               
                   
                   
                   
                 thionin 
               
               
                   
                   
                   
                 enhances 
               
               
                   
                   
                   
                 resistance of 
               
               
                   
                   
                   
                 
                   Arabidopsis 
                 
               
               
                   
                   
                   
                 against 
               
               
                   
                   
                   
                 
                   Fusarium 
                 
               
               
                   
                   
                   
                   oxysporum . 
               
               
                   
                   
                   
                 Ichimura et al. 
               
               
                   
                   
                   
                 (1998). DNA 
               
               
                   
                   
                   
                 Res. 5,341-5348. 
               
               
                   
                   
                   
                 Molecular 
               
               
                   
                   
                   
                 cloning and 
               
               
                   
                   
                   
                 characterization 
               
               
                   
                   
                   
                 of three cDNAs 
               
               
                   
                   
                   
                 encoding 
               
               
                   
                   
                   
                 putative 
               
               
                   
                   
                   
                 mitogen- 
               
               
                   
                   
                   
                 activated 
               
               
                   
                   
                   
                 protein kinase 
               
               
                   
                   
                   
                 kinases 
               
               
                   
                   
                   
                 (MAPKKs) in 
               
               
                   
                   
                   
                 
                   Arabidopsis 
                 
               
               
                   
                   
                   
                   thaliana . 
               
               
                   
                 2. Stress 
                 Manipulate 
                 Close, T. J. 
                 Test for 
                 Winkler et al. 
               
               
                   
                 response to 
                 drought 
                 (1996). 
                 enhanced 
                 (1998). Plant 
               
               
                   
                 cold, drought, 
                 resistance. 
                 Physiol. Plant 
                 sensitivity to 
                 Physiol. 118, 
               
               
                   
                 salinity, seed 
                 Manipulate 
                 97, 795-803. 
                 drought, 
                 743-750. 
               
               
                   
                 maturation, 
                 desiccation 
                 Dehydrins: 
                 dessication, 
                 Systematic 
               
               
                   
                 embryo 
                 tolerance in 
                 emergence of 
                 cold, salinity, 
                 reverse 
               
               
                   
                 development, 
                 flowers, 
                 a biochemical 
                 in ovules, 
                 genetics of 
               
               
                   
                 ABA. 
                 ovules and 
                 role of a 
                 developing 
                 transfer- 
               
               
                   
                 Example: 
                 seeds. 
                 family of 
                 seed and 
                 DNA-tagged 
               
               
                   
                 Dehydrins 
                 Manipulate 
                 plant 
                 seedlings. 
                 lines of 
               
               
                   
                 Example: 
                 cold 
                 dehydration 
                 Test for 
                   Arabidopsis . 
               
               
                   
                 NPK1-like 
                 tolerance in 
                 proteins. 
                 enhanced 
                 Weigel et al. 
               
               
                   
                 protein kinase 
                 flowers, 
                 Kovtun et al. 
                 tolerance to 
                 (2000). Plant 
               
               
                   
                 Example: DNA 
                 ovules, and 
                 (2000). PNAS 
                 drought, 
                 Physiol 122, 
               
               
                   
                 binding protein 
                 seeds. 
                 USA 97, 
                 dessication, 
                 1003-1014. 
               
               
                   
                 genes: CBF- 
                 Manipulate 
                 2940-2945. 
                 cold, salinity, 
                 Activation 
               
               
                   
                 like, DREB2A, 
                 seed 
                 Functional 
                 in ovules, 
                 tagging in 
               
               
                   
                 RAP2.1. 
                 dormancy. 
                 analysis of 
                 developing 
                   Arabidopsis . 
               
               
                   
                   
                 Manipulate 
                 oxidative 
                 seed and seed. 
               
               
                   
                   
                 germination 
                 stress- 
                 Test for 
               
               
                   
                   
                 frequency. 
                 activated 
                 changes in 
               
               
                   
                   
                 Manipulate 
                 mitogen- 
                 seed viability 
               
               
                   
                   
                 seed storage 
                 activated 
                 upon storage. 
               
               
                   
                   
                 and viability. 
                 protein kinase 
                 Test for 
               
               
                   
                   
                   
                 cascade in 
                 changes in 
               
               
                   
                   
                   
                 plants. 
                 germination 
               
               
                   
                   
                   
                   
                 frequencies. 
               
               
                   
                 3. Response to 
                 Altered 
                 Bender and 
                 Test for 
                 Winkler et al. 
               
               
                   
                 starvation, 
                 response to 
                 Fink (1998). 
                 enhanced 
                 (1998). Plant 
               
               
                   
                 wounding, and 
                 starvation. 
                 A myb 
                 sensitivity to 
                 Physiol. 118, 
               
               
                   
                 pathogen attack 
                 Altered 
                 homologue, 
                 starvation, 
                 743-750. 
               
               
                   
                 by tryptophan 
                 response to 
                 ATR1, 
                 wounding, 
                 Systematic 
               
               
                   
                 synthesis. 
                 wounding. 
                 activates 
                 and pathogen 
                 reverse 
               
               
                   
                 Example: DNA 
                 Altered 
                 tryptophan 
                 attack. 
                 genetics of 
               
               
                   
                 binding protein; 
                 response to 
                 gene 
                 Test for 
                 transfer- 
               
               
                   
                 ATR1-like 
                 pathogen 
                 expression in 
                 enhanced 
                 DNA-tagged 
               
               
                   
                 myb. 
                 attack. 
                   Arabidopsis . 
                 tolerance to 
                 lines of 
               
               
                   
                 Example: Auxin 
                   
                 PNAS USA 
                 starvation, 
                   Arabidopsis . 
               
               
                   
                 conjugating 
                   
                 95, 5655-5660. 
                 wounding, 
                 Weigel et al. 
               
               
                   
                 enzyme; indole- 
                   
                   
                 and pathogen 
                 (2000). Plant 
               
               
                   
                 3-acetate beta- 
                   
                   
                 attack. 
                 Physiol 122, 
               
               
                   
                 glucosyltransferase. 
                   
                   
                   
                 1003-1014. 
               
               
                   
                   
                   
                   
                   
                 Activation 
               
               
                   
                   
                   
                   
                   
                 tagging in 
               
               
                   
                   
                   
                   
                   
                   Arabidopsis . 
               
               
                 Cell 
                 Stearoyl-acyl 
                 Production of 
                 Merlo et al. 
                 Analyze seed 
                 Winkler et al. 
               
               
                 metabolism 
                 carrier protein 
                 oils high in 
                 (1998). Plant 
                 size. 
                 (1998). Plant 
               
               
                   
                 desaturase 
                 saturated 
                 Cell 10, 1603-1621. 
                 Analyze seed 
                 Physiol. 118, 
               
               
                   
                 Example: C18 
                 fatty acids 
                   
                 yield. 
                 743-750. 
               
               
                   
                 fatty acid 
                 Manipulate 
                   
                 Analyze seed 
                 Systematic 
               
               
                   
                 desaturation 
                 membrance 
                   
                 composition. 
                 reverse 
               
               
                   
                   
                 composition 
                   
                 Analyze seed 
                 genetics of 
               
               
                   
                   
                   
                   
                 oil by gas 
                 transfer- 
               
               
                   
                   
                   
                   
                 chromatography. 
                 DNA-tagged 
               
               
                   
                   
                   
                   
                   
                 lines of 
               
               
                   
                   
                   
                   
                   
                   Arabidopsis . 
               
               
                   
                   
                   
                   
                   
                 Weigel et al. 
               
               
                   
                   
                   
                   
                   
                 (2000). Plant 
               
               
                   
                   
                   
                   
                   
                 Physiol 122, 
               
               
                   
                   
                   
                   
                   
                 1003-1014. 
               
               
                   
                   
                   
                   
                   
                 Activation 
               
               
                   
                   
                   
                   
                   
                 tagging in 
               
               
                   
                   
                   
                   
                   
                   Arabidopsis . 
               
               
                   
                   
                   
                   
                   
                 Browse et al. 
               
               
                   
                   
                   
                   
                   
                 (1986). Anal. 
               
               
                   
                   
                   
                   
                   
                 Biochem. 
               
               
                   
                   
                   
                   
                   
                 152, 141-145. 
               
               
                   
                 2. Manipulate 
                 Manipulate 
                 Mathews and 
                 Analyze seed 
                 Winkler et al. 
               
               
                   
                 nitrogen 
                 asparagine 
                 Van Holde 
                 size. 
                 (1998). Plant 
               
               
                   
                 economy 
                 degradation 
                   
                 Analyze seed 
                 Physiol. 118, 
               
               
                   
                 Example: 
                 in ovules and 
                   
                 yield. 
                 743-750. 
               
               
                   
                 Asparaginase 
                 seeds. 
                   
                 Analyze seed 
                 Systematic 
               
               
                   
                   
                 Manipulate 
                   
                 composition. 
                 reverse 
               
               
                   
                   
                 endosperm 
                   
                   
                 genetics of 
               
               
                   
                   
                 production. 
                   
                   
                 transfer- 
               
               
                   
                   
                 Manipulate 
                   
                   
                 DNA-tagged 
               
               
                   
                   
                 embryo 
                   
                   
                 lines of 
               
               
                   
                   
                 development. 
                   
                   
                   Arabidopsis . 
               
               
                   
                   
                 Manipulate 
                   
                   
                 Weigel et al. 
               
               
                   
                   
                 ovule size. 
                   
                   
                 (2000). Plant 
               
               
                   
                   
                 Manipulate 
                   
                   
                 Physiol 122, 
               
               
                   
                   
                 seed size. 
                   
                   
                 1003-1014. 
               
               
                   
                   
                   
                   
                   
                 Activation 
               
               
                   
                   
                   
                   
                   
                 tagging in 
               
               
                   
                   
                   
                   
                   
                   Arabidopsis . 
               
               
                   
                   
                   
                   
                   
                 Heath et al. 
               
               
                   
                   
                   
                   
                   
                 (1986). 
               
               
                   
                   
                   
                   
                   
                 Planta 169, 
               
               
                   
                   
                   
                   
                   
                 304-312. 
               
               
                   
                   
                   
                   
                   
                 Browse et al. 
               
               
                   
                   
                   
                   
                   
                 (1986). Anal. 
               
               
                   
                   
                   
                   
                   
                 Biochem. 
               
               
                   
                   
                   
                   
                   
                 152, 141-145. 
               
               
                   
                   
                   
                   
                   
                 D&#39;Aoust et al. 
               
               
                   
                   
                   
                   
                   
                 (1999). Plant 
               
               
                   
                   
                   
                   
                   
                 Cell 11, 
               
               
                   
                   
                   
                   
                   
                 2407-2418. 
               
               
                   
               
            
           
         
       
     
     Fruit development responsive polynucleotides are characteristically differentially transcribed in response to fluctuating developmental-specific polynucleotide levels or other signals, whether internal or external to a cell. MA_diff reports the changes in transcript levels of various fruit development responsive polynucleotides in fruits. 
     These data can be used to identify a number of types of fruit development responsive polynucleotides. Profiles of some of these different fruit development responsive polynucleotides are shown in the table below with examples of the kinds of associated biological activities. Because development is a continuous process and many cell types are being examined together, the expression profiles of genes overlap between stages of development in the chart below. 
     
       
         
           
               
               
               
               
             
               
                   
               
               
                   
                   
                   
                 Examples of 
               
               
                   
                 Developmental 
                   
                 Biochemical 
               
               
                 Transcript Levels 
                 Process 
                 Metabolic Pathways 
                 Activity 
               
               
                   
               
             
            
               
                 (0-5 mm) &gt;&gt;  
                 Ovule Elongation 
                 Hormone Production, 
                 Transcription 
               
               
                 (5-10 mm) ≅  
                 Tissue Specialization 
                 Transport, Perception, 
                 Factors 
               
               
                 (&gt;10 mm) 
                 Vascular system 
                 Signalling, Response (e.g., 
                 Transporters 
               
               
                 (0-5 mm) &gt;&gt;  
                 Meristem 
                 Gibberellin, Ethylene, Auxin) 
                 Kinases 
               
               
                 (5-10 mm) &gt;  
                 Endosperm 
                 Cell wall Biosynthesis 
                 Changes in 
               
               
                 (&gt;10 mm) 
                 Seed coat 
                 Lipid Biosynthesis 
                 cytoskeletal 
               
               
                 (0-5 mm) &gt;  
                 Fruit 
                 Specific Gene Transcription 
                 protein activity 
               
               
                 (5-10 mm) ≅  
                   
                 Initiation 
                 modulating cell 
               
               
                 (&gt;10 mm) 
                   
                 Sucrose Mobilization and 
                 structure 
               
               
                   
                   
                 Partitioning 
                 Stability factors 
               
               
                   
                   
                 Sucrose Signaling 
                 for protein 
               
               
                   
                   
                 Lipoxygenase 
                 translation 
               
               
                   
                   
                 Localization 
                 Changes in cell 
               
               
                   
                   
                 Repressors of Metabolic 
                 wall/membrane 
               
               
                   
                   
                 Pathways 
                 structure 
               
               
                   
                   
                 Protein Remodeling 
                 Chromatin 
               
               
                   
                   
                   
                 structure and/or 
               
               
                   
                   
                   
                 DNA topology 
               
               
                   
                   
                   
                 Biosynthetic 
               
               
                   
                   
                   
                 enzymes 
               
               
                 (5-10 mm) &gt;&gt;  
                 Tissue Specialization 
                 Cell Wall Biosynthesis 
                 Transcription 
               
               
                 (0-5 mm) &gt;  
                 Vascular System 
                 Specific Gene Transcription  
                 Factors 
               
               
                 (&gt;10 mm) 
                 Organelle 
                 Initiation 
                 Transporters 
               
               
                 (5-10 mm) &gt; 
                 Differentiation 
                 Sucrose Mobilization and 
                 Kinases 
               
               
                 (0-5 mm) ≅  
                 Cotyledon Elongation 
                 Partitioning 
                 Chaperones 
               
               
                 (&gt;10 mm) 
                 (cell division) 
                 Sucrose Signaling 
                 Changes in 
               
               
                 (5-10 mm) &gt;&gt;  
                 Vacuome 
                 Repressors of Metabolic 
                 cytoskeletal 
               
               
                 (0-5 mm) ≅  
                 Development 
                 Pathways 
                 protein activity 
               
               
                 (&gt;10 mm) 
                 Lipid Deposition 
                 Auxin Perception, 
                 modulating cell 
               
               
                   
                   
                 Response and Signaling 
                 strucure 
               
               
                   
                   
                 Protein Remodeling 
                 Stability of 
               
               
                   
                   
                 Lipid Biosynthesis and 
                 factors for 
               
               
                   
                   
                 Storage 
                 protein 
               
               
                   
                   
                   
                 translation 
               
               
                   
                   
                   
                 Changes in cell 
               
               
                   
                   
                   
                 wall/membrane 
               
               
                   
                   
                   
                 structure 
               
               
                   
                   
                   
                 Chromatin 
               
               
                   
                   
                   
                 structure and/or 
               
               
                   
                   
                   
                 DNA topology 
               
               
                   
                   
                   
                 Biosynthetic 
               
               
                   
                   
                   
                 enzymes 
               
               
                 (&gt;10 mm) &gt;  
                 Cotyledon Elongation 
                 Cell Elongation 
                 Transcription 
               
               
                 (0-5 mm) ≅  
                 (expansion) 
                 Specific Gene Transcription 
                 Factors 
               
               
                 (5-10 mm) 
                 Lipid Deposition 
                 Initiation 
                 Transporters 
               
               
                   
                 Protein Deposition 
                 Sucrose Mobilization and 
                 Kinases 
               
               
                   
                 Desiccation 
                 Partitioning 
                 Chaperones 
               
               
                   
                   
                 Sucrose Signaling 
                 for protein 
               
               
                   
                   
                 Lipoxygenase 
                 translation 
               
               
                   
                   
                 Localization 
                 Changes in cell 
               
               
                   
                   
                 Repressors of metabolic 
                 wall/membrane 
               
               
                   
                   
                 pathways 
                 structure 
               
               
                   
                   
                 Hormone Perception, 
                 Chromatin 
               
               
                   
                   
                 Response and Signaling (e.g. 
                 structure and/or 
               
               
                   
                   
                 abscissic acid) 
                 DNA topology 
               
               
                   
                   
                 Protein Remodeling 
                 Biosynthetic 
               
               
                   
                   
                 Protein synthesis and Storage 
                 enzymes 
               
               
                   
                   
                 Lipid Synthesis and Storage 
                 Metabolic 
               
               
                   
                   
                 Acquisition of Dessication 
                 enzymes 
               
               
                   
                   
                 Tolerance 
                   
               
               
                   
                   
                 Senescence 
                   
               
               
                 (0-5 mm) &lt;  
                 Ovule Elongation 
                 Cell elongation 
                 Transcription 
               
               
                 (5-10 mm) ≅  
                 Repressors of 
                 Negative regulation of  
                 Factors 
               
               
                 (&gt;10 mm) 
                 Ethylene 
                 ethylene pathways 
                 Transporters 
               
               
                 (0-5 mm) &lt;&lt;  
                 production 
                 Maintenance of Ethylene  
                 Kinases 
               
               
                 (5-10 mm) ≅  
                 Tissue 
                 response 
                 Chaperones 
               
               
                 (&gt;10 mm) 
                 specialization 
                 Changes in pathways and 
                 Stability of 
               
               
                 (0-5 mm) &lt;&lt;  
                 Vascular System 
                 processes operation in cells  
                 factors 
               
               
                 (5-10 mm) &lt;  
                 Meristem 
                   
                 Biosynthetic 
               
               
                 (&gt;10 mm) 
                 Cotyledon 
                   
                 enzymes 
               
               
                 (0-5 mm) &lt;&lt;  
                 Seed Coat 
                   
                 Metabolic 
               
               
                 (&gt;10 mm) &lt;  
                   
                   
                 enzymes 
               
               
                 (5-10 mm) 
                   
                   
                   
               
               
                 (5-10 mm) &lt;  
                 Organelle 
                 Negative regulation of 
                 Transcription 
               
               
                 (0-5 mm) ≅  
                 differentiation 
                 hormone pathways 
                 Factors 
               
               
                 (&gt;10 mm) 
                 Cotyledon elongation 
                 Maintenance of hormone 
                 Transporters 
               
               
                   
                 (division) 
                 response 
                 -Kinases 
               
               
                   
                 Vacuome 
                 Changes in pathways and 
                 Chaperones 
               
               
                   
                 development 
                 processes operation in cells 
                   
               
               
                   
                 Lipid development 
                 Dehydration and acquisition of 
                   
               
               
                   
                 Desiccation 
                 desiccation tolerance 
                   
               
               
                   
                   
                 Senescence 
                   
               
               
                 (&gt;10 mm) &lt;  
                 Cotyledon Elongation 
                 Cell elongation 
                 Transcription 
               
               
                 (0-5 mm) ≅  
                 (expansion) 
                 Negative regulation of 
                 Factors 
               
               
                 (5-10 mm) 
                 Lipid deposition 
                 hormone pathways 
                 Transporters 
               
               
                   
                 Protein deposition 
                 Maintenance of hormone 
                 Kinases 
               
               
                   
                 Desiccation 
                 response 
                 Chaperones 
               
               
                   
                   
                 Changes in pathways and 
                 Metabolic 
               
               
                   
                   
                 processes operation in cells 
                 enzymes 
               
               
                   
                   
                 Dehydration and acquisition of 
                 Biosynthetic 
               
               
                   
                   
                 desiccation tolerance 
                 enzymes 
               
               
                   
                   
                 Senescence 
                   
               
               
                 (0-5 mm) ≅  
                 All stages 
                 Ribosome/polysome 
                 Transcription 
               
               
                 (5-10 mm) ≅  
                   
                 production and maintenance 
                 Factors 
               
               
                 (&gt;10 mm) 
                   
                 Housekeeping genes 
                 Transporters 
               
               
                   
                   
                   
                 Kinases 
               
               
                   
                   
                   
                 Chaperones 
               
               
                   
               
            
           
         
       
     
     III.B. Development Genes, Gene Components and Products 
     III.B.1. Imbibition and Germination Responsive Genes, Gene Components and Products 
     Seeds are a vital component of the world&#39;s diet. Cereal grains alone, which comprise ˜90% of all cultivated seeds, contribute up to half of the global per capita energy intake. The primary organ system for seed production in flowering plants is the ovule. At maturity, the ovule consists of a haploid female gametophyte or embryo sac surrounded by several layers of maternal tissue including the nucleus and the integuments. The embryo sac typically contains seven cells including the egg cell, two synergids, a large central cell containing two polar nuclei, and three antipodal cells. That pollination results in the fertilization of both egg and central cell. The fertilized egg develops into the embryo. The fertilized central cell develops into the endosperm. And the integuments mature into the seed coat. As the ovule develops into the seed, the ovary matures into the fruit or silique. Late in development, the developing seed ends a period of extensive biosynthetic and cellular activity and begins to desiccate to complete its development and enter a dormant, metabolically quiescent state. Seed dormancy is generally an undesirable characteristic in agricultural crops, where rapid germination and growth are required. However, some degree of dormancy is advantageous, at least during seed development. This is particularly true for cereal crops because it prevents germination of grains while still on the ear of the parent plant (preharvest sprouting), a phenomenon that results in major losses to the agricultural industry. Extensive domestication and breeding of crop species have ostensibly reduced the level of dormancy mechanisms present in the seeds of their wild ancestors, although under some adverse environmental conditions, dormancy may reappear. By contrast, weed seeds frequently mature with inherent dormancy mechanisms that allow some seeds to persist in the soil for many years before completing germination. 
     Germination commences with imbibition, the uptake of water by the dry seed, and the activation of the quiescent embryo and endosperm. The result is a burst of intense metabolic activity. At the cellular level, the genome is transformed from an inactive state to one of intense transcriptional activity. Stored lipids, carbohydrates and proteins are catabolized fueling seedling growth and development. DNA and organelles are repaired, replicated and begin functioning. Cell expansion and cell division are triggered. The shoot and root apical meristem are activated and begin growth and organogenesis. Schematic 4 summarizes some of the metabolic and cellular processes that occur during imbibition. Germination is complete when a part of the embryo, the radicle, extends to penetrate the structures that surround it. In  Arabidopsis , seed germination takes place within twenty-four (24) hours after imbibition. As such, germination requires the rapid and orchestrated transcription of numerous polynucleotides. Germination is followed by expansion of the hypocotyl and opening of the cotyledons. Meristem development continues to promote root growth and shoot growth, which is followed by early leaf formation. 
     Genes with activities relevant to imbibition-germination and early seedling growth are described in the two sections A and B below. 
     III.B.1.a. Identification of Imbibition and Germination Genes 
     Imbibition and germination includes those events that commence with the uptake of water by the quiescent dry seed and terminate with the expansion and elongation of the shoots and roots. The germination period exists from imbibition to when part of the embryo, usually the radicle, extends to penetrate the seed coat that surrounds it. Imbibition and germination genes identified herein are defined as genes, gene components and products capable of modulating one or more processes of imbibition and germination described above. They are useful to modulate many plant traits from early vigor to yield to stress tolerance. Examples of such germination genes and gene products are shown in the Reference and Sequence Tables. The functions of many of the genes were deduced from comparisons with known proteins and are also given in the REF Tables. 
     Imbibition and Germination Genes Identified by Phenotypic Observations 
     Imbibition and germination genes are active, potentially active or more active during growth and development of a dry seed into a seedling. These genes herein were discovered and characterized from a much larger set of genes in experiments designed to find genes that cause poor germination. 
     In these experiments, imbibition and germination genes were identified by either 1) ectopic expression of a cDNA in a plant or (2) mutagenesis of the plant genome. The seeds were then imbibed and cultivated under standardized conditions and any phenotypic differences in the modified plants compared with the parental “wild-type” seedlings were recorded. The genes causing the changes were deduced from the cDNA inserted or gene mutated. The phenotypic differences observed were poor germination and aberrant seedlings. 
     Imbibition and Germination Genes Identified by Differential Expression 
     Germination genes were also identified by measuring the relative levels of mRNA products of genes in different stages of germination of a seed versus the plant as a whole. Specifically, mRNA was isolated from whole imbibed seeds of  Arabidopsis  plants 1, 2, 3 or 4 days after imbibition and compared to mRNA isolated from dry seed-utilizing microarray procedures. The MA_diff Table reports the transcript levels of the experiment. For transcript levels that were higher in the imbibed seed than in dry seed a “+” is shown. A “−” is shown when the transcript levels in dry seed were greater than those in imbibed seed. For more experimental detail, see the examples below: 
     Germination associated genes can be identified by comparing expression profiles of imbibed gibberellin treated and untreated gal mutant seed. Germination associated genes can also be identified by comparing expression profiles in late maturation seed from wild-type and mutants that are defective for the establishment of dormancy and can germinate precociously (e.g. aba1, aba2, abi4 in  arabidopsis  and vp1, vp5 in maize) or are defective for the specification of cotyledon identity and dessication tolerance (e.g. lec1, lec2, and fus3). 
     The MA_diff Table(s) reports the transcript levels of the experiment (see EXPT ID: 108461, 108462, 108463, 108464, 108528, 108529, 108530, 108531, 108545, 108546, 108547, 108518, 108529, 108543, 108544). For transcripts that had higher levels in the samples than the control, a “+” is shown. A “−” is shown for when transcript levels were reduced in root tips as compared to the control. For more experimental detail see the Example section below. 
     Imbibed &amp; Germinating Seeds genes are those sequences that showed differential expression as compared to controls, namely those sequences identified in the MA_diff tables with a “+” or “−” indication. 
     Imbibed &amp; Germinating Seeds Genes Identified by Cluster Analyses of Differential Expression 
     Imbibed &amp; Germinating Seeds Genes Identified by Correlation to Genes that are Differentially Expressed 
     As described above, the transcription profiles of genes that act together are well correlated. Applicants not only have identified the genes that are differentially expressed in the microarray experiments, but also have identified the genes that act in concert with them. The MA_clust table indicates groups of genes that have well correlated transcription profiles and therefore participate in the same pathway or network. 
     A pathway or network of Imbibed &amp; Germinating Seeds genes is any group in the MA_clust that comprises a cDNA ID that also appears in Expt ID 108461, 108462, 108463, 108464, 108528, 108529, 108530, 108531, 108545, 108546, 108547, 108518, 108529, 108543, 108544 of the MA_diff table(s). 
     Imbibed &amp; Germinating Seeds Genes Identified by Correlation to Genes that Cause Physiological Consequences 
     Additionally, the differential expression data and the phenotypic observations can be merged to identify pathways or networks of Imbibed &amp; Germinating Seeds genes. A group in the MA_clust is considered a Imbibed &amp; Germinating Seeds pathway or network if the group comprises a cDNA ID that also appears in Knock-in or Knock-out tables that causes one or more of the phenotypes described in section above. 
     Imbibed &amp; Germinating Seeds Genes Identified by Amino Acid Sequence Similarity 
     Imbibed &amp; Germinating Seeds genes from other plant species typically encode polypeptides that share amino acid similarity to the sequences encoded by corn and  Arabidopsis  Imbibed &amp; Germinating Seeds genes. Groups of Imbibed &amp; Germinating Seeds genes are identified in the Protein Group table. In this table, any protein group that comprises a peptide ID that corresponds to a cDNA ID member of a Imbibed &amp; Germinating Seeds pathway or network is a group of proteins that also exhibits Imbibed &amp; Germinating Seeds functions/utilities. 
     III.B.1.b. Use of Imbibition and Germination Genes, Gene Components and Products to Modulate Phenotypes 
     Imbibition and germination genes and gene products can be divided into those that act during primary events, secondary events, and/or termination. The genes and gene products of the instant invention are useful to modulate any one or more of the phenotypes described below: 
     I. Primary events 
     A. Dormancy 
     Imbibition and germination genes and gene products of the invention can act to modulate different types of dormancy including:
         1. Primary dormancy—dormancy is established during seed development   2. Seed coat-imposed dormancy—dormancy is imposed by blocking water uptake, mechanical restraint of embryo, blocking the exit of inhibitors   3. Embryo dormancy—cotyledon mediated inhibition of embryonic axis growth   4. Secondary dormancy—dormancy is induced when dispersed, mature seeds are exposed to unfavorable conditions for germination (e.g. anoxia, unsuiTable temperature or illumination).   5. Hormone-induced       

     B. Dormancy-Breaking Signal Perception and Transduction 
     Germination genes and gene products include those that are able to modulate the response to dormancy releasing signals such as fruit ripening and seed development; imbibition; temperature (low and high, range 0-23°); light, particularly for coat imposed dormancy (white light, intermittent illumination, orange and red region of the spectrum (longer than 700 or 730 nm), and phytochrome); coat softening; chemicals (respiratory inhibitors, sulfhydryl compounds, oxidants, nitrogenous compounds, growth regulators—ga, ba, ethylene, and various, ethanol, methylene blue, ethyl ether, fusicoccin); oxygen and carbon dioxide; and stress. 
     II. Secondary Events 
     During the secondary events of germination, dormancy-maintaining metabolism is repressed, dormancy-breaking metabolism is induced and structures surrounding the embryo weaken (where present). Germination genes and gene products are useful to modulate processes of the secondary events including water uptake, such as cell expansion and change in osmotic state (ion exchange); and respiration—(oxygen consumption). The genes and genes products of the invention can regulate the following pathways which resume during the first respiratory burst of germination including glycolysis, pentose phosphate, citric acid, and tricarboxylic acid cycle. 
     A. Mitochondrial Development 
     Tissues of the mature dry seed contain mitochondria, and although these organelles are poorly differentiated as a consequence of the drying, they contain sufficient Kreb&#39;s cycle enzymes and terminal oxidases to provide adequate amount of ATP to support metabolism for several hours after imbibition. During germination of embryos, there appears to be two distinct patterns of mitochondrial development. In starch-storing seeds, repair and activation of preexisting organelles predominate, whereas oil-storing seeds typically produce new mitochondria. Germination genes and gene products of the invention are useful to modulate the repair, activation and biogenesis pathways of mitochondria, including membrane formation and repair, DNA repair and synthesis, protein synthesis, and coordinated regulation of mitochondrial and nuclear genomes 
     B. Metabolism 
     In addition to respiration and organelle activity, enzyme activity, DNA repair, RNA synthesis and protein synthesis are fundamental cellular activities intimately involved in the completion of germination and the preparation for subsequent growth. Imbibition and germination genes and gene products of the invention can participate in or modulate these activities, including ABA response, GA response, ATP synthesis and adenylate energy charge during germination, and the synthesis and utilization of reducing power: pyridine nucleotides (NADH and NADPH) 
     III. Termination 
     The last stage of seed germination is characterized by the emergence of the radicle or root apex through the seed coat. Typically, the cell walls loosen and the radicle extends from the embryo during late germination. Germination genes and gene products are useful to modulate the mobilization of stored reserves, DNA synthesis and cell division that are typical of this stage of germination. 
     To regulate any of the phenotype(s) above, activities of one or more of the late germination genes or gene products can be modulated and tested by screening for the desired trait. Specifically, the gene, mRNA levels, or protein levels can be altered in a plant utilizing the procedures described herein and the phenotypes can be assayed. As an example, a plant can be transformed according to Bechtold and Pelletier (1998, Methods. Mol. Biol. 82:259-266) and/or screened for variants as in Winkler et al. (1998) Plant Physiol 118: 743-50 and visually inspected for the desired phenotype or metabolically and/or functionally assayed according to Dolan et al. (1993, Development 119: 71-84), Dolan et al. (1997, Development 124: 1789-98), Crawford and Glass (1998, Trends Plant Science 3: 389-95), Wang et al. (1998, PNAS USA 95: 15134-39), Gaxiola et al. (1998, PNAS USA 95: 4046-50), Apse et al. (1999, Science 285: 1256-58), Fisher and Long (1992, Nature 357: 655-60), Schneider et al. (1998, Genes Devel 12: 2013-21) and Hirsch (1999, Curr Opin Plant Biol. 2: 320-326). 
     III.B.1.c. Use of Imbibition and Germination Genes, Gene Components and Product to Modulate Biochemical Activities 
     The roles of the biochemical changes associated with imbibition and germination can be appreciated from a summary of the processes occurring. 
     Physiology 
     Water plays an important role throughout the plant life cycle. The most dramatic example of this is in seed germination. Although germination is triggered by water, the germination response is also positively regulated by the plant growth regulators the gibberellins and negatively affected by the growth regulator abscisic acid. Genes that are activated by water and genes that are activated by gibberellins can be identified through expression profiling experiments using  arabidopsis  mutants defective for gibberellin biosynthesis or perception (gal, gai), abscisic acid biosynthesis or perception (aba1, abi3, and abi4) in the presence or absence of exogenous gibberellins. These genes can be used to promote seedling growth and development and other phases of plant development. 
     Transcriptional Control of Gene Activity 
     At the end of seed development, dessication and dormancy have imposed a global state of repression on gene activity throughout the seed. Reactivation of the genome requires water and gibberellins. One function of the genes that are activated early by imbibition is the rapid and dramatic reversal of gene repression. For example, expression-profiling experiments revealed that several thousand genes are hyperactivated in  arabidopsis  upon imbibition. These include genes involved in metabolic pathways, genes that promote cell growth and division, and transcriptional control genes. Thus one class of genes expressed early in imbibition includes those that promote high levels of gene expression. Other early genes are responsible for regulating specific metabolic, cell, and developmental processes. The strategy for distinguishing these functions was outlined in the Introduction. 
     Mobilization of Storage Reserves 
     In contrast to the synthesis and accumulation of reserves during seed development an important function of genes expressed during imbibition and germination is the control of the mobilization and catabolism of seed storage reserves in the endosperm (in grasses and cereals) and the embryo. The mobilization of seed storage reserves is triggered by imbibition and may occur over several days. There are three classes of high molecular weight seed storage reserves: carbohydrates, triacylglycerols, and storage proteins. Upon imbibition seed storage reserves are converted into forms that can be transported and metabolized. Genes encoding enzymes for storage reserve catabolism are expressed shortly after imbibition. Starch for example is converted to sucrose. Triacylglycerols are converted into acetyl-CoA. Storage proteins are converted into amino acids or deaminated to provide carbon skeletons for oxidation. 
     Carbohydrate Catabolism 
     Starch is the most common storage carbohydrate in seeds. The primary components of starch are amylose and amylopectin. 
     Mobilization 
     There are two pathways for starch catabolism—hydrolytic and phosphorolytic. The product of these pathways is the monosaccharide glucose. Examples of the enzymes responsible for hydrolytic catabolism of starch are: amylase, glucosidase, amylase, dextrinase, isoamylase. The enzyme responsible for phosphorolytic activity is starch phosphorylase. 
     Transport 
     The mobilization of starch involves the synthesis of sucrose from glucose, which can then be transported to sites for growth in the root and shoot. In some seeds, maltose may be a major form of transported carbohydrate. The production of sucrose-6-P from glucose involves the following enzymes: UDP-glucose pyrophosphorylase, sucrose-6-P synthetase, and sucrose phosphatase. 
     Sucrose Catabolism 
     In target tissues sucrose is hydrolyzed by fructofuransidase (invertase) and/or sucrose synthetase. The synthesis of glucose from glucose-1-P involves sucrose synthetase. 
     Cell Biology 
     The lumen of the endoplasmic reticulum (ER) is target for other hydrolase activities including mannosidase, glucosaminidase, acid phosphatase, phosphodiesterase, and phospholipase D. 
     Triacylglycerol (TAG) Catabolism 
     Triacylglycerols are the major storage lipids of seeds. The products of TAG catabolism in imbibed and germinating seed are glycerol and free fatty acids. Most of the glycerol is converted to sucrose for export. Free fatty acids are catabolized through oxidation through the glyoxylate cycle and gluconeogenesis. 
     Mobilization 
     Hydrolysis of triacylglycerols is by lipases yielding glycerol and free fatty acids. Free fatty acids are oxidized to acetyl-CoA and propionyl-CoA via oxidation requiring ATP and coenzyme A. Catabolism of unsaturated fatty acids also requires cis, trans-isomerases, epimerases, and hydratases. Acetyl-CoA is oxidized through the citric acid cycle to CO2 and H2O. More importantly, acetyl-CoA can be utilized via the glyoxylate cycle and gluconeogenesis for glucose synthesis. Free fatty acids are also broken down via oxidation. Glycerol is converted via phosphorylation and oxidation to DHAP and G3P, which are used to synthesize glucose or oxidized via the citric acid cycle. Examples of other induced enzymes include isocitrate lyase and malate synthetase 
     Transport 
     Most of the glycerol, acetyl-CoA, and propionyl-CoA are converted to sucrose for transport. This requires the enzymes glycerol kinase and glycerol phosphate oxidoreductase. 
     Cell Biology 
     Glyoxysome biogenesis is required to support fatty acid catabolism and gluconeogenesis. Upon exposure to light there is a loss of glyoxysomes due to their conversion to peroxisomes. 
     Storage Protein Catabolism 
     Mobilization 
     The hydrolysis of storage proteins to amino acids is performed by a diverse group of proteinases and peptidases. The peptidases include endopeptidases, aminopeptidases, and carboxypeptidases. They include the A and B class proteinases. The liberated amino acids are available for protein synthesis, for deamination and reutilization of ammonia via glutamine and asparagine synthesis, and to provide carbon skeletons for respiration. Several enzymes including, deaminase, asparagine synthetase, glutamine synthetase and glutamate dehydrogenase are important players in the mobilization and utilization of stored nitrogen in imbibed seed. 
     Transport 
     The major transported form of amino acid in germinated seeds is asparagine. In some species glutamine and/or homoserine are the major form of transported amino acid. Aspartate, glutamate, alanine, glycine, and serine can be converted to sucrose and transported as sucrose. Other amino acids are transported unchanged. 
     Cell Biology 
     Proteinases are sequestered in lumen of endoplasmic reticulum (ER) which then fuses with protein bodies. 
     While catabolism is high in the storage tissues of imbibed seed the products of catabolism are transported to sites of growth including the shoot and root apices fueling respiration, biosynthesis, cell division and differentiation. 
     Development 
     Imbibition triggers several key processes for seedling development. One is the activation of the shoot and root apical meristems. The shoot apical meristem is responsible for two primary growth activities. One is the production of the protoderm, procambium and ground meristem. The protoderm gives rise to the epidermal system of the plant, the procambium to the primary vascular tissues, and the ground meristem to the ground tissues including the cortex and pith. The second is the production of leaf primordia, which arise on the flanks of the apex. Thus, activation of the shoot apical meristem results in shoot growth and organogenesis. 
     The root apical meristem, by contrast is responsible for vegetative root development. The first primary growth activity of the root apical meristem is the production of the protoderm, procambium and ground meristem. The second primary growth activity is the production of the cells that give rise to the root cap. 
     Genes that govern shoot apical meristem activation and development can be identified in  arabidopsis  by gene profiling experiments comparing gene expression in wild-type imbibed seed and partial loss-of-function stm (shootmeristemless) mutants (see SAM). Genes governing root meristem activity can be identified by gene profiling experiments comparing gene expression in wild-type imbibed seed and rml (rootmeristemless) mutants. 
     Genes identified in this way are useful to promote or retard meristem growth, modify and strengthen shoot and root development, promote leaf development as described below. 
     Changes in the concentration of imbibition-germination activated polynucleotides result in the modulation of many other polynucleotides and polynucleotide products. Examples of such activated responsive polynucleotides and polynucleotide products relative to leaves and floral stem and to fruits at different development stages are shown in the Reference and Sequence Tables. These polynucleotides and/or products are responsible fore effects on traits such as seedling growth, seedling viability, and seedling vigor. The polynucleotides were discovered by isolating seeds from  Arabidopsis  wild-type ecotype “Wassilewskija” imbibed for 24 hours, and measuring the mRNAs expressed in them relative to those in a leaf and floral stem sample and to those in fruits at different developmental stages. 
     While imbibition-germination activated polynucleotides and polynucleotide products can act alone, combinations of these polynucleotides also affect germination. Useful combinations include different polynucleotides and/or polynucleotide products that have similar transcription profiles or similar biological activities, and members of the same or functionally similar biochemical pathways. In addition, the combination of imbibition germination activated polynucleotides and/or polynucleotide products with environmentally responsive polynucleotides is also useful because of the interactions that exist between development, hormone-regulated pathways, stress and pathogen induced pathways and nutritional pathways. Here, useful combinations include polynucleotides that may have different transcription profiles, and participate in common or overlapping pathways but combine to produce a specific, phenotypic change. 
     Such imbibition and germination activated polynucleotides and polynucleotide products can function to either increase or dampen the above phenotypes or activities either in response to transcript changes in fruit development or in the absence of fruit-specific polynucleotide fluctuations. 
     
       
         
           
               
               
               
             
               
                   
               
               
                   
                 BIOCHEMICAL  
                   
               
               
                   
                 OR METABOLIC  
                   
               
               
                   
                 ACTIVITIES 
                 CITATIONS  
               
               
                   
                 AND/OR PATHWAYS 
                 INCLUDING 
               
               
                 PROCESS 
                 ALTERED 
                 ASSAYS 
               
               
                   
               
             
            
               
                 Growth,  
                 Farnesylation Mediated  
                 Pei et al (1998) Science 282: 
               
               
                 Differentiation 
                 Seed Dormancy 
                 287-290; Cutler et al. (1996) 
               
               
                 and Development 
                   
                 Science 273: 1239 
               
               
                 Metabolic activity 
                 Nitrogen metabolism 
                 Goupil et al (1998) J Exptl 
               
               
                   
                   
                 Botany 49: 1855-62 
               
               
                 Metabolic activity 
                 -H+ export  
                 Cerana et al. (1983) 
               
               
                   
                 and membrane 
                   
               
               
                   
                 hyperpolarization 
                   
               
               
                 Metabolic activity 
                 Chloroplast functioning 
                 Benkova et al (1999) Plant 
               
               
                   
                   
                 Physil 121: 245-252 
               
               
                 Growth,  
                 Regulation of  
                 Riou-Khamlichi et al. (1999) 
               
               
                 Differentiation 
                 Morphogenesis 
                 Science 283: 1541-44 
               
               
                 and development 
                   
                   
               
               
                 Metabolic activity 
                 Cell Death 
                 Lohman et al. (1994) Physiol 
               
               
                   
                   
                 Plant 92: 322-328 
               
               
                 Growth and  
                 Promotion of  
                 Kakimoto (1996) Science 
               
               
                 development 
                 cell division 
                 274: 982-985 
               
               
                   
                 Shoot formation  
                   
               
               
                   
                 in absence of 
                   
               
               
                   
                 exogenous cytokinin 
                   
               
               
                 Metabolic activity 
                 Membrane repair 
                 Heath et al. (1986) Planta  
               
               
                   
                   
                 169: 304-12 
               
               
                   
                   
                 Browse et al. (1986) Anal 
               
               
                   
                   
                 Biochem 152: 141-5 
               
               
                   
                   
                 D&#39;Aoust et al (1999) Plant 
               
               
                   
                   
                 Cell 11: 2407-18 
               
               
                 Metabolism 
                 Organic molecule  
                 Moody et al. (1988) 
               
               
                   
                 export 
                 Phytochemistry 27: 2857-61 
               
               
                 Metabolic activity 
                 Nutrient Uptake 
                 Uozumio et al. (2000) Plant 
               
               
                   
                   
                 Physiol 122: 1249-59 
               
               
                 Metabolic activity 
                 Ion export 
                 Uozumi et al. (2000) Plant 
               
               
                   
                   
                 Physiol 122: 1249-59 
               
               
                   
                   
                 Frachisse et al. (2000) Plant J 
               
               
                   
                   
                 21: 361-71 
               
               
                 Growth,  
                 Division and/or  
                 Zhang and Forde (1998) 
               
               
                 Differentiation 
                 elongation 
                 Science 279: 407-409. 
               
               
                 and development 
                   
                 Coruzzi et al. U.S. Pat. No. 
               
               
                   
                   
                 5,955,651 
               
               
                 Metabolic activity 
                 Regulation of Molecular 
                 Wisniewski et al. (1999) 
               
               
                   
                 chaperones 
                 Physiolgia Plantarum 105: 
               
               
                   
                   
                 600-608 
               
               
                 Metabolic activity 
                 Reactivation of  
                 Lee and Vierling (2000) Plant 
               
               
                   
                 Aggregation and 
                 Physiol. 122: 189-197 
               
               
                   
                 Protein Folding 
                   
               
               
                 Metabolic activity 
                 Maintenance of  
                 Queitsch et al. (2000) The 
               
               
                   
                 Native Conformation  
                 Plant Cell 12: 479-92 
               
               
                   
                 (cytosolic proteins) 
                   
               
               
                 Metabolic activity 
                 Regulation of  
                 Wells et al. (1998) Genes and 
               
               
                   
                 Translational 
                 Development 12: 3236-51 
               
               
                   
                 Efficiency 
                   
               
               
                 Metabolic activity 
                 DNA Repair 
                 Bewley (1997) Plant Cell  
               
               
                   
                   
                 9: 1055-66 
               
               
                 Metabolic activity 
                 Protein Synthesis using  
                 Heath et al. (1986) Planta  
               
               
                   
                 stored or newly  
                 169: 304-12 
               
               
                   
                 synthesized mRNAs 
                   
               
               
                 Metabolic activity 
                 Mitochondrial repair  
                 MacKenzie and McIntosh 
               
               
                   
                 and synthesis 
                 (1999) Plant Cell 11: 571-86 
               
               
                 Metabolic activity 
                 Commencement of  
                 Debeaujon et al. (2000) Plant 
               
               
                   
                 respiration 
                 Physiol 122: 403-4132 
               
               
                   
                 Water Uptake 
                 Debeaujon et al. (2000) Plant 
               
               
                   
                   
                 Physiol 122: 403-4132 
               
               
                   
               
            
           
         
       
     
     Other biological activities that are modulated by the imbibition-activated polynucleotides and polynucleotide products are listed in the Reference Tables. Assays for detecting such biological activities are described in the Table below as well as in the Domain section of the Reference Table. 
     III.B.1.d. Use of Imbibition and Germination Genes to Modulate the Transcription Levels of Other Genes 
     The expression of many genes is “upregulated” or “downregulated” during imbibition and germination because some imbibition and germination genes are integrated into complex networks that regulate transcription of many other genes. Some imbibition and germination genes are therefore useful for regulating other genes and hence complex phenotypes. 
     Imbibition-activated polynucleotides may also be differentially transcribed in response to fluctuating developmental-specific polynucleotide levels or concentrations, whether internal or external to a cell, at different times during the plant life cycle to promote associated biological activities. These activities are, by necessity, a small subset of the genes involved in the development process. Furthermore, because development is a continuous process with few clear demarcations between stages, the associated metabolic and biochemical pathways overlap. Some of the changes in gene transcription are summarized in the Table below: 
     
       
         
           
               
               
               
             
               
                   
               
               
                   
                   
                 EXAMPLES OF 
               
               
                   
                   
                 BIOCHEMICAL 
               
               
                   
                   
                 REGULATORY 
               
               
                 DEVELOPMENTAL 
                   
                 ACTIVITIES 
               
               
                 PROCESS REGULATED 
                 PHYSIOLOGICAL/METABOLIC  
                 ASSOCIATED WITH 
               
               
                 BY IMBIBITION- 
                 CONSEQUENCES OF MODIFYING 
                 IMBIBITION AND 
               
               
                 GERMINATION GENES 
                 GENE PRODUCT LEVELS 
                 GERMINATION 
               
               
                   
               
             
            
               
                 Tissue Specialization 
                 Lipid Catabolism 
                 Transcription Factors 
               
               
                 Cotyledon Expansion 
                 Lipoxygenase 
                 Transporters 
               
               
                 Endosperm (???) 
                 Localization 
                 Kinases 
               
               
                 Activation of the Shoot 
                 Starch Catabolism 
                 Changes in cytoskeletal 
               
               
                 Apical Meristem 
                 Seed Protein Catabolism 
                 protein activity 
               
               
                 Activation of the Root 
                 Growth Regulator Production, 
                 modulating cell structure 
               
               
                 Apical Meristem 
                 Transport, Perception, 
                 Stability of factors for 
               
               
                 Radicle Growth 
                 Signaling, Response (e.g., 
                 protein translation 
               
               
                 Vascular System 
                 Gibberellins, Ethylene, 
                 Changes in cell 
               
               
                 Development 
                 Auxin) 
                 wall/membrane structure 
               
               
                   
                 Global Gene Activation 
                 Chromatin structure 
               
               
                   
                 Transcription Initiation 
                 and/or DNA topology 
               
               
                   
                 Sucrose Synthesis and 
                 Biosynthetic enzymes 
               
               
                   
                 Partitioning 
                 Metabolic enzymes 
               
               
                   
                 Sucrose catabolism 
                   
               
               
                   
                 Sucrose Signaling 
                   
               
               
                   
                 Cell Wall Biosynthesis 
                   
               
               
                   
                 Activators of Metabolic 
                   
               
               
                   
                 Pathways 
                   
               
               
                   
                 Protein Remodeling 
                   
               
               
                 Organelle  
                 Cell Wall Biosynthesis 
                 Transcription Factors 
               
               
                 Differentiation  
                 Membrane Repair and 
                 Transporters 
               
               
                 and Development 
                 Synthesis 
                 Kinases 
               
               
                   
                 Specific Gene Transcription 
                 Chaperones 
               
               
                   
                 Initiation 
                 Changes in cytoskeletal 
               
               
                   
                 Sucrose Mobilization and 
                 protein activity 
               
               
                   
                 Partitioning 
                 modulating cell structure 
               
               
                   
                 Sucrose Signaling 
                 Stability of factors for 
               
               
                   
                 Activators of Metabolic 
                 protein translation 
               
               
                   
                 Pathways 
                 Changes in cell 
               
               
                   
                 Auxin Perception, 
                 wall/membrane structure 
               
               
                   
                 Response and Signaling 
                 Chromatin structure 
               
               
                   
                 Protein Remodeling 
                 and/or DNA topology 
               
               
                   
                 Lipid Mobilization, 
                 Biosynthetic enzymes 
               
               
                   
                 Metabolism and Biosynthesis 
                 Metabolic enzymes 
               
               
                   
                 Protein Transport, 
                   
               
               
                   
                 Metabolism, and Biosynthesis 
                   
               
               
                 DNA Repair 
                 Cell Division 
                 Transcription Factors 
               
               
                   
                 Cell Cycle Control 
                 Transporters 
               
               
                   
                 DNA Replication 
                 Kinases 
               
               
                   
                 Specific Gene Transcription 
                 Chaperones 
               
               
                   
                 Initiation 
                 for protein translation 
               
               
                   
                 Protein Remodeling 
                 Changes in cell 
               
               
                   
                 Protein Synthesis 
                 wall/membrane structure 
               
               
                   
                 Repressors of Senescence 
                 Chromatin structure 
               
               
                   
                   
                 and/or DNA topology 
               
               
                   
                   
                 Biosynthetic enzymes 
               
               
                 Cellular Metabolism 
                 Lipid Catabolism 
                 Transcription Factors 
               
               
                   
                 oxidation 
                 Transporters 
               
               
                   
                 Glyoxylate cycle 
                 Kinases 
               
               
                   
                 Citric acid cycle 
                 Chaperones 
               
               
                   
                 Gluconeogenesis 
                 Translation Initiation 
               
               
                   
                 Sucrose Synthesis and 
                 Factors 
               
               
                   
                 Partitioning 
                 Biosynthetic Enzymes 
               
               
                   
                 Starch Catabolism 
                 Metabolic Enzymes 
               
               
                   
                 Seed Protein Catabolism 
                   
               
               
                   
                 Asparagine Synthesis and 
                   
               
               
                   
                 Transport 
                   
               
               
                   
                 Sucrose catabolism 
                   
               
               
                   
                 Sucrose Signaling 
                   
               
               
                   
                 Ribosome/polysome 
                   
               
               
                   
                 production and maintenance 
                   
               
               
                   
                 Housekeeping genes 
                   
               
               
                   
                 Respiration 
                   
               
               
                   
                 Photosynthesis 
               
               
                   
               
            
           
         
       
     
     Changes in the processes of germination are the result of modulation of the activities of one or more of these many germination genes and gene products. These genes and/or products are responsible for effects on traits such as fast germination, plant vigor and seed yield, especially when plants are growing in the presence of biotic or abiotic stresses or when they are growing in barren conditions or soils depleted of certain minerals. 
     Germination genes and gene products can act alone or in combination as described in the introduction. Of particular interest are combination of these genes and gene products with those that modulate stress tolerance and/or metabolism. Stress tolerance and metabolism genes and gene products are described in more detail in the sections below. 
     Use of Promoters of Imbibition and Germination Genes 
     These promoters can be used to control expression of any polynucleotide, plant or non-plant, in a plant host. Selected promoters when operably linked to a coding sequence can direct synthesis of the protein in specific cell types or to loss of a protein product, for example when the coding sequence is in the antisense configuration. They are thus useful in controlling changes in imbibition and germination phenotypes or enabling novel proteins to be made in germinating seeds. 
     III.B.2. Early Seedling-Phase Specific Responsive Genes, Gene Components and Products 
     One of the more active stages of the plant life cycle is a few days after germination is complete, also referred to as the early seedling phase. During this period the plant begins development and growth of the first leaves, roots, and other organs not found in the embryo. Generally this stage begins when germination ends. The first sign that germination has been completed is usually that there is an increase in length and fresh weight of the radicle. 
     III.B.2.a. Identification of Early Seedling Phase Genes, Gene Components and Products 
     These genes defined and identified herein are capable of modulating one or more processes of development and growth of many plant organs as described below. These genes and gene products can regulate a number of plant traits to modulate yield. Examples of such early seedling phase genes and gene products are shown in the Reference and Sequence, Knock-in, Knock-out and MA-diff Tables. The functions of the protein of some of these genes are also given in these Tables. 
     Early Seedling Genes Identified by Phenotypic Observations 
     Some early seedling genes were discovered and characterized from a much larger set of genes by experiments designed to find genes that cause phenotypic changes in germinating seeds as the transitioned into seedlings. 
     In these experiments, leaf genes were identified by either (1) ectopic expression of a cDNA in a plant or (2) mutagenesis of the plant genome. The plants were then cultivated and one or more of the following leaf phenotypes, which varied from the parental “wild-type”, were observed:
         Abnormal growth   Abnormal cotyledons or root growth
           Reduced growth   Abnormal first leaf   Abnormal hypocotyl   Abnormal pigmentation
 
The genes identified by these phenotypes are given in the Knock-in and Knock-out Tables.
   
               

     Early Seedling Phase Genes Identified by Differential Expression 
     Such genes are active or potentially active to a greater extent in developing and rapidly growing cells, tissues and organs, as exemplified by development and growth of a seedling 3 or 4 days after planting a seed. These genes herein were also discovered and characterized from a much larger set of genes in experiments designed to find genes. Early seedling phase genes were identified by measuring the relative levels of mRNA products in a seedling 3 or 4 days after planting a seed versus a sterilized seed. Specifically, mRNA was isolated from aerial portion of a seedling 3 or 4 days after planting a seed and compared to mRNA isolated from a sterilized seed utilizing microarray procedures. The MA_diff Table(s) reports the transcript levels of the experiment (see EXPT ID: Sqn (relating to SMD 7133, SMD 7137)). For transcripts that had higher levels in the samples than the control, a “+” is shown. A “−” is shown for when transcript levels were reduced in root tips as compared to the control. For more experimental detail see the Example section below. 
     Early Seedling Phase genes are those sequences that showed differential expression as compared to controls, namely those sequences identified in the MA_diff tables with a “+” or “−” indication. 
     Early Seedling Phase Genes Identified by Cluster Analyses of Differential Expression 
     Early Seedling Phase Genes Identified by Correlation to Genes that are Differentially Expressed 
     As described above, the transcription profiles of genes that act together are well correlated. Applicants not only have identified the genes that are differentially expressed in the microarray experiments, but also have identified the genes that act in concert with them. The MA_clust table indicates groups of genes that have well correlated transcription profiles and therefore participate in the same pathway or network. 
     A pathway or network of Early Seedling Phase genes is any group in the MA_clust that comprises a cDNA ID that also appears in Expt ID Sqn (relating to SMD 7133, SMD 7137) of the MA_diff table(s). 
     Early Seedling Phase Genes Identified by Correlation to Genes that Cause Physiological Consequences 
     Additionally, the differential expression data and the phenotypic observations can be merged to identify pathways or networks of Early Seedling Phase genes. A group in the MA_clust is considered a Early Seedling Phase pathway or network if the group comprises a cDNA ID that also appears in Knock-in or Knock-out tables that causes one or more of the phenotypes described in section above. 
     Early Seedling Phase Genes Identified by Amino Acid Sequence Similarity 
     Early Seedling Phase genes from other plant species typically encode polypeptides that share amino acid similarity to the sequences encoded by corn and  Arabidopsis  Early Seedling Phase genes. Groups of Early Seedling Phase genes are identified in the Protein Group table. In this table, any protein group that comprises a peptide ID that corresponds to a cDNA ID member of a Early Seedling Phase pathway or network is a group of proteins that also exhibits Early Seedling Phase functions/utilities. 
     Of particular interest are early seedling phase genes that are differentially expressed 3 or 4 days after planting a seed but not differentially expressed germinating seeds and/or mature leaves. 
     Examples of phenotypes, biochemical activities, and transcription profiles that can be modulated by these genes and gene products are described above and below. 
     III.B.2.b. Use of Early Seedling Genes, Gene Components and Products to Modulate Phenotypes 
     Rapid, efficient establishment of a seedling is very important in commercial agriculture and horticulture. It is also vital that resources are approximately partitioned between shoot and root to facilitate adaptive growth. Phototropism and geotropism need to be established. All these require post-germination process to be sustained to ensure that vigorous seedlings are produced. Early seedling phase genes, gene components and products are useful to manipulate these and other processes. 
     I. Development 
     The early seedling phase genes, gene components and products of the instant invention are useful to modulate one or more processes of the stages of leaf morphogenesis including: stage 1—organogenesis that gives rise to the leaf primordium; stage 2—delimiting basic morphological domains; and stage 3—a coordinated processes of cell division, expansion, and differentiation. Early seedling phase genes include those genes that terminate as well as initiate leaf development. Modulating any or all of the processes leads to beneficial effects at specific locations. 
     Gene Sequences Affecting Types of Leaves—Applicants provide with these genes, gene components and gene products the means to modulate one or more of the types of leaves, and stem, including cotyledons and major leaves. 
     Gene sequences affecting cell properties—These genes, gene components and gene products are useful to modulate changes in cell size, cell division, rate and direction, cell elongation, cell differentiation, xylem and phloem cell numbers, cell wall composition, and all cell types. 
     Gene Sequences Affecting Leaf Architecture—Modifying leaf architecture is useful to modulate change in overall leaf architectur including veination, such as improvements in photosynthetic efficiency, stress tolerance efficiency of solute and nutrient movement to and from the leaf which are accomplished by increases or decreases in vein placement and number of cells in the vein and shape, such as elongated versus rounded and symmetry (around either abaxial-adaxial (dorsiventral) axis or apical-basal (proximodistal) axis, margin-blade-midrib (lateral) axis). 
     Genes Sequences Influencing Leaf Responses—Shoot apical meristem cells differentiate to become leaf primordia that eventually develop into leaves. The genes, gene components and gene products of this invention are useful to modulate any one or all of these growth and development processes, by affecting timing and rate or planes of cell divisions for example, in response to the internal plant stimuli and/or programs such as embryogenesis, germination, hormones (like Auxin), phototropism, coordination of leaf growth and development with that of other organs (like roots and stems), and stress-related program. 
     II. Interaction with the Environment 
     Successful seedling establishment demands successful interaction with the environment in the soil. Early vegetation genes orchestrate and respond to interactions with the environment. Thus early seedling phase genes are useful for improving interactions between a plant and the environment including pigment accumulation, oxygen gain/loss control, carbon dioxide gain/loss control, water gain/loss control, nutrient transport, light harvesting, chloroplast biogenesis, circadian rhythm control, light/dark adaptation, defense systems against biotic and abiotic stresses, metabolite accumulation, and secondary metabolite production 
     III. Organizing Tissues for Photosynthesis and Metabolism 
     Following germination and utilization of seed reserves, plant tissues prepare for photosynthesis and seedling metabolism. Leaf meristems, and root meristems participate in these changes before cell differentiation. Many of the uses for plants depend on the success of leaves as the powerhouses for plant growth, their ability to withstand stresses and their chemical composition. Leaves are organs with many different cell types and structures. Most genes of a plant are active in leaves and therefore leaves have very diverse of pathways and physiological processes. Examples of such pathways and processes that are modulated by early seedling phase genes, gene components and products include photosynthesis, sugar metabolism, starch synthesis, starch degradation, nitrate and ammonia metabolism, amino acid biosynthesis, transport, protein biosynthesis, DNA replication, repair, lipid biosynthesis and breakdown, protein biosynthesis, storage and breakdown, nucleotide transport and metabolism, cell envelope biogenesis, membrane formation, mitochondrial and chloroplast biogenesis, transcription and rna metabolism, vitamin biosynthesis, steroid and terpenoid biosynthesis, devise secondary metabolite synthesis, co-enzyme metabolism, flavonoid biosynthesis and degradation, synthesis of waxes, glyoxylate metabolism, and hormone perception and response pathways. 
     Use of Plants that are Modified as Described Above 
     Altering leaf genes or gene products in a plant modifies one or more the following plant traits, to make the plants more useful for specific purposes in agriculture, horticulture and for the production of valuable molecules. The useful plants have at least one of the following characteristics: more seedling vigor; a higher yield of early leaves and their molecular constituents due to different number, size, weight, harvest index, composition including and amounts and types of carbohydrates, proteins, oils, waxes, etc., photosynthetic efficiency, e.g. reduced photorespiration, absorption of water and nutrients to enhance yields, including under stresses such as high light, herbicides, and heat, pathways to accumulate new valuable molecules; more optimal leaf shape and architecture in early seedling—enhancing photosynthesis and enhancing appeal in ornamental species including size, number, or pigment; a better overall plant architecture—enhancing photosynthesis and enhancing appeal in ornamental species; reduced negative effects of high planting density, by altering leaf placement to be more vertical instead of parallel to the ground; for instance better stress tolerance, including drought resistance, by decreasing water loss, and pathogen resistance; better overall yield and vigor—Plant yield of biomass and of constituent molecules and plant vigor are modulated to create benefits by genetically changing the growth rate of seedling, coleoptile elongation, and young leaves. 
     To change any of the phenotype(s) above, activities of one or more of the early seedling phase genes or gene products are modulated in an organism and the consequence evaluated by screening for the desired trait. Specifically, the gene, mRNA levels, or protein levels are altered in a plant utilizing the procedures described herein and the phenotypes can be assayed. As an example, a plant can be transformed according to Bechtold and Pelletier ( Methods. Mol. Biol.  82:259-266 (1998)) with leaf gene constructs and/or screened for variants as in Winkler et al.,  Plant Physiol.  118: 743-50 (1998) and visually inspected for the desired phenotype and metabolically and/or functionally assayed for altered levels of relevant molecules. 
     III.B.2.c. Use of Early Seedling Phase Genes, Gene Components and Products to Modulate Biochemical Activities 
     Seedlings are complex and their structure, function and properties result from the integration of many processes and biochemical activities. Some of these are known from the published literature and some can be deduced from the genes and their products described in this application. Early seedling phase genes, and gene components are used singly or in combination to modify these processes and biochemical activities and hence modify the phenotypic and trait characteristics described above. Examples of the processes and metabolic activities are given in the Table below. The resulting changes are measured according to the citations included in the Table. 
     
       
         
           
               
               
               
             
               
                   
               
               
                   
                 BIOCHEMICAL OR 
                   
               
               
                   
                 METABOLIC ACTIVITIES 
                 CITATIONS INCLUDING 
               
               
                 PROCESS 
                 AND/OR PATHWAYS 
                 ASSAYS 
               
               
                   
               
             
            
               
                 Metabolism - anabolic 
                 G. Farnesylation 
                 Pei et al.,  Science 282 : 287-290 
               
               
                 and catabolic 
                 H. Cell Wall Biosynthesis 
                 (1998); Cutler et al.,  Science 273 : 
               
               
                   
                 I. Nitrogen Metabolism 
                 1239 (1996) 
               
               
                   
                 J. Secondary Metabolite 
                 Goupil et al.,  J Exptl. Botany   
               
               
                   
                 Biosynthesis and 
                   49 : 1855-62 (1998) 
               
               
                   
                 Degradation 
                 Walch-Liu et al.,  J Exppt. Botany   
               
               
                   
                   
                   51 , 227-237 (2000) 
               
               
                 Water Conservation And 
                 A. Production of polyols 
                 Allen et al.,  Plant Cell 11 : 1785-1798 
               
               
                 Resistance To Drought 
                 B. Regulation of salt 
                 (1999) 
               
               
                 And Other Related 
                 concentration 
                 Li et al.,  Science 287 : 300-303 
               
               
                 Stresses 
                 C. ABA response(s) 
                 (2000) 
               
               
                   
                   
                 Burnett et al.,  J Exptl. Botany 51 : 
               
               
                   
                   
                 197-205 (2000) 
               
               
                   
                   
                 Raschke, In:  Stomatal Function , 
               
               
                   
                   
                 Zeiger et al. Eds., 253-279 (1987) 
               
               
                 Transport Anion and 
                 (i) Ca2+ Accumulation 
                 Lacombe et al.,  Plant Cell 12 : 837-51 
               
               
                 Cation Fluxes 
                 (a) K+ Fluxes 
                 (2000); 
               
               
                   
                 (b) Na+ Fluxes 
                 Wang et al.,  Plant Physiol.   
               
               
                   
                 1. Receptor - ligand 
                   118 : 1421-1429 (1998); 
               
               
                   
                 binding 
                 Shi et al.,  Plant Cell 11 : 2393-2406 
               
               
                   
                 2. Anion and Cation fluxes 
                 (1999) 
               
               
                   
                   
                 Gaymard et al.,  Cell 94 : 647-655 
               
               
                   
                   
                 (1998) 
               
               
                   
                   
                 Jonak et al.,  Proc. Natl. Acad. Sci.   
               
               
                   
                   
                   93 : 11274-79 (1996); 
               
               
                   
                   
                 Sheen,  Proc. Natl. Acad. Sci. 95 : 
               
               
                   
                   
                 975-80 (1998); 
               
               
                   
                   
                 Allen et al.,  Plant Cell 11 : 1785-98 
               
               
                   
                   
                 (1999) 
               
               
                 Carbon Fixation 
                 3. Calvin Cycle 
                 Wingler et al.,  Philo Trans R Soe   
               
               
                   
                 5. Photorespiration 
                   Lond B Biol Sci 355 , 1517-1529 
               
               
                   
                 6. Oxygen evolution 
                 (2000); 
               
               
                   
                 7. RuBisCO 
                 Palecanda et al.,  Plant Mol Biol   
               
               
                   
                 4. Chlorophyll metabolism 
                   46 , 89-97 (2001); 
               
               
                   
                 (ii) Chloroplast Biogenesis 
                 Baker et al.,  J Exp Bot 52 , 615-621 
               
               
                   
                 and Metabolism 
                 (2001) 
               
               
                   
                 5. Fatty Acid and Lipid 
                 Chen et al.,  Acta Biochim Pol 41 , 
               
               
                   
                 Biosynthesis 
                 447-457 (1999) 
               
               
                   
                 (iii) Glyoxylate metabolism 
                 Imlau et al.,  PlantCell II , 309-322 
               
               
                   
                 (iv) Sugar Transport 
                 (1999) 
               
               
                   
                 (v) Starch Biosynthesis and 
               
               
                   
                 Degradation 
               
               
                 Hormone Perception and 
                 (vi) Hormone Receptors and 
                 Tieman et al.,  Plant J 26 , 47-58 
               
               
                 Growth 
                 Downstream Pathways 
                 (2001) 
               
               
                   
                 for 
                 Hilpert et al.,  Plant J 26 , 435-446 
               
               
                   
                 (a) ethylene 
                 (2001) 
               
               
                   
                 (b) jasmonic acid 
                 Wenzel et al.,  Plant Phys 124 , 
               
               
                   
                 (c) brassinosteroid 
                 813-822 (2000) 
               
               
                   
                 (d) gibberellin 
                 Dengler and Kang,  Curr Opin   
               
               
                   
                 (e) Auxin 
                   Plant Biol 4 , 50-56 (2001) 
               
               
                   
                 (f) cytokinin 
                 Tantikanjana et al.,  Genes Dev 15 , 
               
               
                   
                 Activation Of Specific 
                 1577-1580 (2001) 
               
               
                   
                 Kinases And 
               
               
                   
                 Phosphatases 
               
               
                   
               
               
                 See Imbibition, Shoot Apical Meristem, Root and Leaf sections for more details 
               
            
           
         
       
     
     Other biological activities that are modulated by the leaf genes and gene products are listed in the Reference tables. Assays for detecting such biological activities are described in the Protein Domain table, for example. 
     III.B.2.d. Use of Early Seedling Phase Genes, Gene Components and Products to Modulate Transcription Levels 
     The expression of many genes is “up regulated” or down regulated” in plants because some genes and their products are integrated into complex networks that regulate transcription of many other genes. Some early seedling phase genes, gene components and products are therefore useful for modifying the transcription of other genes and hence complex phenotypes, as described above. Profiles of leaf gene activities are described in the Table below with associated biological activities. “Up-regulated” profiles are those where the mRNA transcript levels are higher in young seedlings as compared to the sterilized seeds. “Down-regulated” profiles represent higher transcript levels in the plantlet as compared to sterilized seed only. 
     III.B.3. Size and Stature Genes, Gene Components and Products 
     Great agronomic value can result from modulating the size of a plant as a whole or of any of its organs. For example, the green revolution came about as a result of creating dwarf wheat plants, which produced a higher seed yield than taller plants because they could withstand higher levels and inputs of fertilizer and water. Size and stature genes elucidated here are capable of modifying the growth of either an organism as a whole or of localized organs or cells. Manipulation of such genes, gene components and products can enhance many traits of economic interest from increased seed and fruit size to increased lodging resistance. Many kinds of genes control the height attained by a plant and the size of the organs. For genes additional to the ones in this section other sections of the Application should be consulted. 
     III.B.3.a. Identification of Size and Stature Genes, Gene Components and Products 
     Size and stature genes identified herein are defined as genes, gene components and products capable of modulating one or more processes in growth and development, to produce changes in size of one or more organs. Examples of such stature genes and gene products are shown in the Reference, Sequence, Protein Group, Protein Group Matrix, Knock-in, Knock-out, MA-diff and MA-clust. The biochemical functions of the protein products of many of these genes determined from comparisons with known proteins are also given in the Reference tables. 
     Size and Stature Genes, Gene Components and Products Identified by Phenotypic Observations 
     Mutant plants exhibiting increased or decreased stature in comparison to parental wild-type plants were used to identify size and stature genes. In these experiments, size and stature genes were identified by either (1) the ectopic expression of a cDNA in a plant or (2) mutagenesis of the plant genome. The plants were then cultivated and stature genes were identified from plants that were smaller than the parental “wild-type”. The phenotypes and gene mutations associated with them are given in Tables 
     Examples of phenotypes, biochemical activities, or transcript profiles that are modulated using these genes are described above and below. 
     Use of Size and Stature Genes, Gene Components and Products to Modulate Phenotypes 
     Typically, these genes can cause or regulate cell division, rate and time; and also cell size and shape. Many produce their effects via meristems. These genes can be divided into three classes. One class of genes acts during cytokinesis and/or karyokinesis, such as mitosis and/or meiosis. A second class is involved in cell growth; examples include genes regulating metabolism and nutrient uptake pathways. Another class includes genes that control pathways that regulate or constrain cell division and growth. Examples of these pathways include those specifying hormone biosynthesis, hormone sensing and pathways activated by hormones. 
     Size and stature genes and gene components are useful to selectively alter the size of organs and stems and so make plants specifically improved for agriculture, horticulture and other industries. There are a huge number of utilities. For example, reductions in height of specific ornamentals, crops and tree species can be beneficial, while increasing height of others may be beneficial. 
     Increasing the length of the floral stems of cut flowers in some species would be useful, while increasing leaf size in others would be economically attractive. Enhancing the size of specific plant parts, such as seeds, to enhance yields by stimulating hormone (Brassinolide) synthesis specifically in these cells would be beneficial. Another application would be to stimulate early flowering by altering levels of gibberellic acid in specific cells. Changes in organ size and biomass also results in changes in the mass of constituent molecules. This makes the utilities of size and stature genes useful for the production of valuable molecules in parts of plants, for extraction by the chemical and pharmaceutical industries. 
     Examples of phenotypes that can be modulated by the genes and gene components include cell size, cell shape, cell division, rate and direction, cell elongation, cell differentiation, stomata number, and trichome number. The genes of the invention are useful to regulate the development and growth of roots (primary, lateral, root hairs, root cap, apical meristem, epidermis, cortex, and stele); stem (pholem, xylem, nodes, internodes, and shoot apical meristem); leaves (cauline, rosette, and petioles); flowers (receptacle, sepals, petals, and tepals, including color, shape, size, number, and petal drop, androecium, stamen, anther, pollen, sterility, size, shape, weight, color, filament, gynoecium, carpel, ovary, style, stigma, ovule, size, shape, and number, pedicel and peduncle, flowering time, and fertilization); seeds (placenta, embryo, cotyledon, endosperm, suspensor, and seed coat (testa)); and fruits (pericarp—thickness, texture, exocarp, mesocarp, and endocarp. Traits can be modulated with the genes and gene products of this invention to affect the traits of a plant as a whole include architecture (such as branching, ornamental architecture, shade avoidance, planting density effects, and wind resistance) and vigor (such as increased biomass and drought tolerance). 
     To regulate any of the phenotype(s) above, activities of one or more of the sizing genes or gene products are modulated in an organism and tested by screening for the desired trait. Specifically, the gene, mRNA levels, or protein levels can be altered in a plant utilizing the procedures described herein and the phenotypes can be assayed. As an example, a plant can be transformed according to Bechtold and Pelletier ( Methods. Mol. Biol.  82:259-266 (1998)) and/or screened for variants as in Winkler et al., ( Plant Physiol.  118: 743-50 1998) and visually inspected for the desired phenotype or metabolically and/or functionally assayed. 
     III.B.3.b. Use of Size and Stature Genes, Gene Components and Products to Modulate Biochemical Activities 
     Many metabolic and developmental processes can be modulated by size and stature genes and gene components to achieve the phenotypic characteristics exemplified above. Some of these are listed below. Such biological activities can be measured according to the citations included in the Table below: 
     
       
         
           
               
               
               
             
               
                   
               
               
                   
                 BIOCHEMICAL OR 
                   
               
               
                   
                 METABOLIC ACTIVITIES 
                 CITATIONS INCLUDING 
               
               
                 PROCESS 
                 AND/OR PATHWAYS 
                 ASSAYS 
               
               
                   
               
             
            
               
                 Growth and Development 
                 Gibberellic Acid Biosynthesis 
                 Swain SM, Tseng Ts, 
               
               
                   
                 Gibberellic Acid Receptor and 
                 Olszewski NE. Altered 
               
               
                   
                 Downstream Pathways 
                 expression of spindly affects 
               
               
                   
                   
                 gibberellin response and plant 
               
               
                   
                   
                 development. Plant Physiol 
               
               
                   
                   
                 2001 Jul; 126(3): 1174-85 
               
               
                   
                   
                 Hooley, R. Gibberellins: 
               
               
                   
                   
                 perception, transduction, and 
               
               
                   
                   
                 responses. Plant Mol. Biol. 
               
               
                   
                   
                 1994 26: 1529-1555. 
               
               
                   
                   
                 Hooley, R. Gibberellins: 
               
               
                   
                   
                 perception, transduction, and 
               
               
                   
                   
                 responses. Plant Mol. Biol. 
               
               
                   
                   
                 1994 26: 1529-1555. 
               
               
                   
                   
                 Perata, P, Matsukura, C, 
               
               
                   
                   
                 Vernieri, P, Yamaguchi, J, 
               
               
                   
                   
                 Sugar repression of a 
               
               
                   
                   
                 gibberellin-dependent 
               
               
                   
                   
                 signaling pathway in barley 
               
               
                   
                   
                 embryos. Plant Cell 1997 
               
               
                   
                   
                 9: 2197-2208. 
               
               
                   
                 Brassinolide Biosynthesis 
                 Noguchi T, Fujioka S, Choe S, 
               
               
                   
                 Brassinolide Receptors, 
                 Takatsuto S, Tax FE, Yoshida S, 
               
               
                   
                 Degradation of Brassinolide 
                 Feldmann KA. Biosynthetic 
               
               
                   
                 Pathways affected by 
                 pathways of brassinolide in 
               
               
                   
                 Brassinolide 
                 Arabidopsis. Plant Physiol 
               
               
                   
                   
                 2000 Sep; 124(1): 201-9 
               
               
                   
                   
                 Wang ZY, Seto H, Fujioka S, 
               
               
                   
                   
                 Yoshida S, Chory J. BRI1 is a 
               
               
                   
                   
                 critical component of a 
               
               
                   
                   
                 plasma-membrane receptor for 
               
               
                   
                   
                 plant steroids. Nature 2001 
               
               
                   
                   
                 Mar 15; 410(6826): 380-3 
               
               
                   
                   
                 Neff MM, Nguyen SM, 
               
               
                   
                   
                 Malancharuvil EJ, Fujioka S, 
               
               
                   
                   
                 Noguchi T, Seto H, Tsubuki M, 
               
               
                   
                   
                 Honda T, Takatsuto S, 
               
               
                   
                   
                 Yoshida S, Chory J. BAS1: A 
               
               
                   
                   
                 gene regulating brassinosteroid 
               
               
                   
                   
                 levels and light responsiveness 
               
               
                   
                   
                 in Arabidopsis. Proc Natl Acad 
               
               
                   
                   
                 Sci USA 1999 Dec 
               
               
                   
                   
                 21; 96(26): 15316-23 
               
               
                   
                   
                 Kang JG, Yun J, Kim DH, 
               
               
                   
                   
                 Chung KS, Fujioka S, Kim JI, 
               
               
                   
                   
                 Dae HW, Yoshida S, 
               
               
                   
                   
                 Takatsuto S, Song PS, Park CM. 
               
               
                   
                   
                 Light and brassinosteroid 
               
               
                   
                   
                 signals are integrated via a 
               
               
                   
                   
                 dark-induced small G protein 
               
               
                   
                   
                 in etiolated seedling growth. 
               
               
                   
                   
                 Cell 2001 Jun 1; 105(5): 625-36 
               
               
                   
                 Cytokinin biosynthesis 
                 Mok DW, Mok MC. Cytokinin 
               
               
                   
                 Cytokinin receptor 
                 metabolism and action. Annu 
               
               
                   
                 Degradation of Cytokinin 
                 Rev Plant Physiol Plant Mol 
               
               
                   
                 Pathways affected by Cytokinin 
                 Biol 2001; 52: 89-118 
               
               
                   
                   
                 Schmulling T. CREam of 
               
               
                   
                   
                 cytokinin signalling: receptor 
               
               
                   
                   
                 identified. Trends Plant Sci 
               
               
                   
                   
                 2001 Jul; 6(7): 281-4 
               
               
                   
                   
                 Mok DW, Mok MC. Cytokinin 
               
               
                   
                   
                 metabolism and action. Annu 
               
               
                   
                   
                 Rev Plant Physiol Plant Mol 
               
               
                   
                   
                 Biol 2001; 52: 89-118 
               
               
                   
                   
                 Seyedi M, Selstam E, Timko MP, 
               
               
                   
                   
                 Sundqvist C. The 
               
               
                   
                   
                 cytokinin 2-isopentenyladenine 
               
               
                   
                   
                 causes partial reversion to 
               
               
                   
                   
                 skotomorphogenesis and 
               
               
                   
                   
                 induces formation of 
               
               
                   
                   
                 prolamellar bodies and 
               
               
                   
                   
                 protochlorophyllide657 in the 
               
               
                   
                   
                 lip1 mutant of pea. Physiol 
               
               
                   
                   
                 Plant 2001 Jun; 112(2): 261-272 
               
               
                   
                 Auxin Biosynthesis 
                 Zhao Y, Christensen SK, 
               
               
                   
                 Auxin Receptor 
                 Fankhauser C, Cashman JR, 
               
               
                   
                 Auxin Degradation 
                 Cohen JD, Weigel D, Chory J. 
               
               
                   
                 Pathways affected by Auxins 
                 A role for flavin 
               
               
                   
                 Auxin transport 
                 monooxygenase-like enzymes 
               
               
                   
                   
                 in Auxin biosynthesis. Science 
               
               
                   
                   
                 2001 Jan 12; 291(5502): 306-9 
               
               
                   
                   
                 Abel S, Ballas N, Wong LM, 
               
               
                   
                   
                 Theologis A. DNA elements 
               
               
                   
                   
                 responsive to Auxin. Bioessays 
               
               
                   
                   
                 1996 Aug; 18(8): 647-54 
               
               
                   
                   
                 del Pozo JC, Estelle M. 
               
               
                   
                   
                 Function of the ubiquitin- 
               
               
                   
                   
                 proteosome pathway in Auxin 
               
               
                   
                   
                 response. Trends Plant Sci 
               
               
                   
                   
                 1999 Mar; 4(3): 107-112. 
               
               
                   
                   
                 Rahman A, Amakawa T, Goto N, 
               
               
                   
                   
                 Tsurumi S. Auxin is a 
               
               
                   
                   
                 positive regulator for ethylene- 
               
               
                   
                   
                 mediated response in the 
               
               
                   
                   
                 growth of Arabidopsis roots. 
               
               
                   
                   
                 Plant Cell Physiol 2001 Mar; 
               
               
                   
                   
                 42(3): 301-7 
               
               
                   
                   
                 Zhao Y, Christensen SK, 
               
               
                   
                   
                 Fankhauser C, Cashman JR, 
               
               
                   
                   
                 Cohen JD, Weigel D, Chory J. 
               
               
                   
                   
                 A role for flavin 
               
               
                   
                   
                 monooxygenase-like enzymes 
               
               
                   
                   
                 in Auxin biosynthesis. Science 
               
               
                   
                   
                 2001 Jan 12; 291(5502): 306-9 
               
               
                   
                   
                 Abel S, Ballas N, Wong LM, 
               
               
                   
                   
                 Theologis A. DNA elements 
               
               
                   
                   
                 responsive to Auxin. Bioessays 
               
               
                   
                   
                 1996 Aug; 18(8): 647-54 
               
               
                   
                   
                 del Pozo JC, Estelle M. 
               
               
                   
                   
                 Function of the ubiquitin- 
               
               
                   
                   
                 proteosome pathway in Auxin 
               
               
                   
                   
                 response. Trends Plant Sci 
               
               
                   
                   
                 1999 Mar; 4(3): 107-112. 
               
               
                   
                   
                 Rahman A, Amakawa T, Goto N, 
               
               
                   
                   
                 Tsurumi S. Auxin is a 
               
               
                   
                   
                 positive regulator for ethylene- 
               
               
                   
                   
                 mediated response in the 
               
               
                   
                   
                 growth of Arabidopsis roots. 
               
               
                   
                   
                 Plant Cell Physiol 2001 Mar; 
               
               
                   
                   
                 42(3): 301-7 
               
               
                   
                   
                 Gil P, Dewey E, Friml J, Zhao Y, 
               
               
                   
                   
                 Snowden KC, Putterill J, 
               
               
                   
                   
                 Palme K, Estelle M, Chory J. 
               
               
                   
                   
                 BIG: a calossin-like protein 
               
               
                   
                   
                 required for polar Auxin 
               
               
                   
                   
                 transport in Arabidopsis. 
               
               
                   
                   
                 Genes Dev. 2001 Aug 
               
               
                   
                   
                 1; 15(15): 1985-97 
               
               
                   
                   
                 Estelle M., Polar Auxin 
               
               
                   
                   
                 transport. New support for an 
               
               
                   
                   
                 old model. Plant Cell 1998 
               
               
                   
                   
                 Nov; 10(11): 1775-8 
               
               
                   
                 Cell wall growth 
                 Cosgrove DJ., Loosening of 
               
               
                   
                   
                 plant cell walls by expansins. 
               
               
                   
                   
                 Nature 2000 Sep 
               
               
                   
                   
                 21; 407(6802): 321-6 
               
               
                   
               
            
           
         
       
     
     Other biological activities that are modulated by the stature genes and gene products are listed in the Reference tables. Assays for detecting such biological activities are described in the Protein Domain table, for example. 
     Changes in the size, vigor, or yield of a plant are the result of modulation of the activities of one or more of these many size and stature genes and gene products. While size and stature polynucleotides and gene products can act alone, combinations of these polynucleotides and also with others that also affect growth and development are especially useful. 
     Use of Promoters of “Size and Stature” Genes 
     Promoters of “size and stature” genes are useful for controlling the transcription of any desired polynucleotides, both plant and non-plant. They can be discovered from the “size and stature” genes in the Reference Tables, and their patterns of activity from the MA Tables. When operably linked to any polynucleotide encoding a protein, and inserted into a plant, the protein will be synthesized in those cells in which the promoter is active. Many “size and stature” genes will function in meristems, so the promoters will be useful for expressing proteins in meristems. The promoters can be used to cause loss of, as well as synthesis of, specific proteins via antisense and sense suppression approaches. 
     III.B.4. Shoot-Apical Meristem Genes, Gene Components and Products 
     New organs, stems, leaves, branches and inflorescences develop from the stem apical meristem (SAM). The growth structure and architecture of the plant therefore depends on the behavior of SAMs. Shoot apical meristems (SAMs) are comprised of a number of morphologically undifferentiated, dividing cells located at the tips of shoots. SAM genes elucidated here are capable of modifying the activity of SAMs and thereby many traits of economic interest from ornamental leaf shape to organ number to responses to plant density. 
     III.B.4.a. Identification of Sam Genes, Gene Components and Products 
     SAM genes identified herein are defined as genes, gene components and products capable of modulating one or more processes or functions of SAMs as described below. Regulation of SAM genes and gene products are useful to control many plant traits including architecture, yield and vigor. Examples of such SAM genes and gene products are shown in the Reference, Sequence, Protein Group, Protein Group Matrix, phenotype and MA-diff Tables. The functions of many of the protein products of these genes are also given in the Reference tables. 
     Sam Genes, Gene Components and Products Identified by Phenotypic Observations 
     SAM genes were discovered and characterized from a much larger set of genes by experiments designed to find genes that cause phenotypic changes in leaf morphology, such as cotyledon or leaf fusion. In these experiments, SAM genes were identified by either (1) ectopic expression of a cDNA in a plant or (2) mutagenesis of the plant genome. The plants were then cultivated and one or more of the following phenotypes, which varied from the parental “wild-type”, was observed:
         I. Cotyledon
           Fused   
           II. Leaves
           Fused   Leaf placement on stems   
           III. Branching
           Number   
           IV. Flowers
           Petals fused   Altered bolting   Early bolting   Late bolting   Strong bolting   Weak bolting   Abnormal branching   
               

     For more experimental detail see the Example section below. The genes identified by these results of the phenotypes that are shown in Knock-in and Knock-out Tables. 
     Sam Genes, Gene Components and Products Identified by Differential Expression 
     SAM genes were also identified in experiments designed to find genes whose mRNA products are associated specifically or preferentially with SAMs. The concentration of mRNA products in the  arabidopsis  plant with the SHOOTMERISTEMLESS (STM) gene knocked-out was measured relative to the concentration in the parental, non-mutant plant. The  Arabidopsis  STM gene is required for embryonic SAM formation. The STM gene encodes a Knottedl (Kn1) type of homeodomain protein. Homeodomain proteins regulate transcription of many genes in many species and have been shown to play a role in the regulation of translation as well. Seedlings homozygous for recessive loss-of-function alleles germinate with roots, a hypocotyl, and cotyledons, but no SAM is formed. The MA_diff Table(s) reports the transcript levels of the experiment (see EXPT ID: 108478, 108479, 108480, 108481, 108598, 108535, 108536, 108435). For transcripts that had higher levels in the samples than the control, a “+” is shown. A “−” is shown for when transcript levels were reduced in root tips as compared to the control. For more experimental detail see the Example section below. 
     Meristem genes are those sequences that showed differential expression as compared to controls, namely those sequences identified in the MA_diff tables with a “+” or “−” indication. 
     Meristem Genes Identified by Cluster Analyses of Differential Expression 
     Meristem Genes Identified by Correlation to Genes that are Differentially Expressed 
     As described above, the transcription profiles of genes that act together are well correlated. Applicants not only have identified the genes that are differentially expressed in the microarray experiments, but also have identified the genes that act in concert with them. The MA_clust table indicates groups of genes that have well correlated transcription profiles and therefore participate in the same pathway or network. 
     A pathway or network of Meristem genes is any group in the MA_clust that comprises a cDNA ID that also appears in Expt ID 108478, 108479, 108480, 108481, 108598, 108535, 108536, 108435 of the MA_diff table(s). 
     Meristem Genes Identified by Correlation to Genes that Cause Physiological Consequences 
     Additionally, the differential expression data and the phenotypic observations can be merged to identify pathways or networks of Meristem genes. A group in the MA_clust is considered a Meristem pathway or network if the group comprises a cDNA ID that also appears in Knock-in or Knock-out tables that causes one or more of the phenotypes described in section above. 
     Meristem Genes Identified by Amino Acid Sequence Similarity 
     Meristem genes from other plant species typically encode polypeptides that share amino acid similarity to the sequences encoded by corn and  Arabidopsis  Meristem genes. Groups of Meristem genes are identified in the Protein Group table. In this table, any protein group that comprises a peptide ID that corresponds to a cDNA ID member of a Meristem pathway or network is a group of proteins that also exhibits Meristem functions/utilities. 
     Examples of phenotypes, biochemical activities, and transcription profiles that can be modulated by SAM genes and gene products are described above and below. 
     III.B.4.b. Use of Sam Genes, Gene Components and Products to Modulate Phenotypes 
     With the SAM genes and gene products of the invention, Applicants provide the means to modulate one or more of the following types of SAMs:
         1. Embryonic meristem   2. Vegetative lateral SAMs   3. Inflorescence lateral SAMs   4. Floral meristems   5. Adventitious SAM       

     The SAM genes of the instant invention are useful for modulating one or more processes of SAM structure and/or function including (I) cell size and division; (II) cell differentiation and organ primordia. 
     I. Cell Size and Division 
     A. Cell Properties 
     SAM genes and gene products can be used to modulate changes in cell size, cell division, rate and direction, and cell division symmetry. 
     A key attribute of the SAM is its capacity for self-renewal. The self-renewing initial cell population resides in the central zone of the SAM. A small number of slowly dividing initial cells (typically 2 to 4 per layer) act as a self-replenishing population, whereas some of their descendants, pushed out onto the flanks of the SAM, differentiate into leaves. Other descendants, displaced below the SAM, differentiate into stem. The immediate descendants of the initial cells divide further, amplifying the cell population before being incorporated into leaf or stem primordia. 
     The genes and gene components of this invention are useful for modulating any one or all of these cell division processes generally, as in timing and rate, for example. In addition, the polynucleotides and polypeptides of the invention can control the response of these processes to the internal plant programs associated with embryogenesis, hormone responses like cytokinin (inhibitory for root development, see section on cytokinin-responsive genes), coordination of growth and development with that of other plant organs (such as leaves, flowers, seeds, and fruits. 
     SAM genes can also be used to control the response of these processes to changes in the environment, including heat, cold, drought, high light and nutrition. 
     B. Sam Cell Patterns and Organization 
     Although SAMs appear as small regions of morphological undifferentiated dividing cells, a group of morphologically undifferentiated dividing cells does not necessarily constitute a SAM. Rather, evidence indicates that SAMs are highly organized or patterned regions of the plant in which many important events in early organogenesis occur. Thus, the term “SAM” is used to denote a highly organized structure and site of pattern formation. The invention also permits engineering of specific as well as overall features of SAM architecture including zones (central, peripheral, and rib), layers (11, 12, and 13) and symmetry. 
     II Cell Differentiation and Organ Primordia 
     The apical meristem in many species first undergoes a vegetative phase whereby cells set aside from the apex become leaf primordia with an axillary vegetative meristem. Upon floral induction, the apical meristem is converted to an inflorescence meristem. The inflorescence meristem arises in the axils of modified leaves and is indeterminate, producing whorls or rings of floral organ primordia. In species which produce terminal flowers, the apical meristem is determinate and eventually adopts a third identity, that of a floral meristem. Examples of the plant properties that the genes and gene products of the invention can be used to modulate include indeterminancy (inhibiting or increasing differentiation and enhancing plant growth and yield), symmetry (symmetry of organs developed, and symmetry of arrangement of organs, such as leaves, petals, flowers, etc.), leaf fate and timing internode length modulation, such as longer internodes to increase shade avoidance and shorter internodes to favor leaf development), and floral fate and timing of flowering. 
     Uses of Plants Modified as Described Above Using Sam Genes, Gene Components and Products 
     Because SAMs determine the architecture of the plant, modified plants will be useful in many agricultural, horticultural, forestry and other industrial sectors. Plants with a different shape, numbers of flowers and seed and fruits will have altered yields of plant parts. For example, plants with more branches can produce more flowers, seed or fruits. Trees without lateral branches will produce long lengths of clean timber. Plants with greater yields of specific plant parts will be useful sources of constituent chemicals. Such plants will have, for example, more prolific leaf development, better optimized stem and shoot development, adventitious shoots, more flowers, seeds, and fruits, enhanced vigor (including growth rate of whole plant, including height, flowering time, etc., seedling, coleoptile elongation, young leaves, flowers, seeds, and fruit. Higher yields based on biomass (fresh and dry weight during any time in plant life, including maturation and senescence), number of flowers, seed yield (number, size, weight, harvest index, content and composition, e.g. amino acid, jasmonate, oil, protein and starch) and fruit yield (number, size, weight, harvest index, content and composition, e.g. amino acid, jasmonate, oil, protein and starch). 
     To regulate any of the phenotype(s) above, activities of one or more of the SAM genes or gene products can be modulated and tested by screening for the desired trait. Specifically, the gene, mRNA levels, or protein levels can be altered in a plant utilizing the procedures described herein and the phenotypes can be assayed. As an example, a plant can be transformed according to Bechtold and Pelletier (1998, Methods. Mol. Biol. 82:259-266) and/or screened for variants as in Winkler et al. (1998) Plant Physiol 118: 743-50 and visually inspected for the desired phenotype or metabolically and/or functionally assayed according to Dolan et al. (1993, Development 119: 71-84), Dolan et al. (1997, Development 124: 1789-98), Crawford and Glass (1998, Trends Plant Science 3: 389-95), Wang et al. (1998, PNAS USA 95: 15134-39), Gaxiola et al. (1998, PNAS USA 95: 4046-50), Apse et al. (1999, Science 285: 1256-58), Fisher and Long (1992, Nature 357: 655-60), Schneider et al. (1998, Genes Devel 12: 2013-21) and Hirsch (1999, Curr Opin Plant Biol. 2: 320-326). 
     III.B.4.c. Use of Sam Genes and Gene Components to Modulate Biochemical Activities 
     SAM genes and gene components are useful for modulating biochemical or metabolic activities and/or pathways such as those noted below. Such biological activities can be measured according to the citations included in the Table below: 
     
       
         
           
               
               
               
             
               
                   
               
               
                   
                 BIOCHEMICAL OR 
                   
               
               
                   
                 METABOLIC ACTIVITIES 
                 CITATIONS INCLUDING 
               
               
                 PROCESS 
                 AND/OR PATHWAYS 
                 ASSAYS 
               
               
                   
               
             
            
               
                 Growth, Differentiation 
                 Leaf shape and inflorescence and 
                 Chuck, G. et al., 1996 Plant Cell 
               
               
                 And Development 
                 flower morphology systems 
                 8: 1227-1289. 
               
               
                   
                 Activities of SAM 
                 Schneeberger et al., 1998 
               
               
                   
                 transcriptional regulatory 
                 Development 125: 2857-2865. 
               
               
                   
                 proteins. 
               
               
                   
                 Meristem size and organ number 
                 Kayes, J. M. and Clark, S. E. 
               
               
                   
                 determinants 
                 1998 Development 125: 3843-3851. 
               
               
                   
                 Regulated by Receptor Kinases 
                 Jeong, S. et al., 1999 Plant 
               
               
                   
                 Receptor kinase location and 
                 Cell 11: 1925-1934. 
               
               
                   
                 activity. 
               
               
                   
                 Meristem proliferation activities 
                 Tantikanjana, T. Genes and 
               
               
                   
                   
                 Development. Jun. 15, 2001. 
               
               
                   
                   
                 15(12): 1577-1588. 
               
               
                 Internode elongation 
                 Hormone signaling pathways 
                 Yamamuro, C. et al., 2000 Plant 
               
               
                   
                   
                 Cell. 12: 1591-1605. 
               
               
                 Hormone Perception 
                 Levels of growth hormones 
                 Kusaba, S. et al; 1998 Plant 
               
               
                   
                 including gibberellic acid, Auxin 
                 Physiology 116(2): 471-476. 
               
               
                   
                 and cytokinin. 
               
               
                   
                 Gibberellic acid biosynthesis 
                 Modulation of GA perception 
               
               
                   
                 GA biosynthetic enzyme GA-20 
                 and function can be assayed as 
               
               
                   
                 oxidase is a required step in GA 
                 described in Sakamoto, T. et al. 
               
               
                   
                 biosynthesis. GA-20 oxidase is 
                 2001 Genes and Development 
               
               
                   
                 Regulated by some SAM gene 
                 15: 581-590. 
               
               
                   
                 products. 
               
               
                   
                 Over expression of SAM genes 
                 Sakamoto, T. et al. 2001. 
               
               
                   
                 can lead to reduced internode 
                 Genes and Development 15: 
               
               
                   
                 elongation, reduced cell 
                 581-590. 
               
               
                   
                 elongation and reduced cell 
               
               
                   
                 expansion. 
               
               
                   
                 Cytokinin Receptor activity 
                 Inoue, T. et al., Nature 
               
               
                   
                   
                 409: 1060-1063. 
               
               
                   
                 SAM gene products can affect 
                 Sieberer, T. et al., 2000 Current 
               
               
                   
                 the activity of Auxin dependent 
                 Biology 10: 1595-1598. 
               
               
                   
                 postranscriptional gene protein 
                 del Pozo, J. C.; Estelle, M. 
               
               
                   
                 expression. 
                 PNAS (USA) 1999. 
               
               
                   
                   
                 96(26): 15342-15347. 
               
               
                   
                 SAM gene products can affect 
                 Tantikanjana, T. Genes and 
               
               
                   
                 Auxin Perception/metabolism in 
                 Development. Jun. 15, 2001. 
               
               
                   
                 the meristem to produce useful 
                 15(12): 1577-1588. 
               
               
                   
                 changes in plant architecture. 
               
               
                 Leaf senescence 
                 SAM gene products can increase 
                 Ori, N. et al; Plant Cell. June, 
               
               
                   
                 and decrease leaf senescence 
                 1999. 11(6): 1073-1080. 
               
               
                   
                 rate. This can be done by 
               
               
                   
                 modulating cytokinin hormone 
               
               
                   
                 levels. 
               
               
                   
                 Cytokinin effect on cell division 
                 Beemster, Gerrit T. S.; Baskin, 
               
               
                   
                 and expansion. 
                 Tobias I. 2000 Plant Physiology 
               
               
                   
                   
                 124: 1718-1727. 
               
               
                 Adventitious shoot 
                 Alter growth hormone status. 
                 Kusaba, S. et al; 1998 Plant 
               
               
                 formation 
                   
                 Physiology 116(2): 471-476 
               
               
                   
                 Ectopic expression of SAM 
                 Chuck, G. 1996 Plant Cell 8: 
               
               
                   
                 genes in leaf or other non SAM 
                 1227-1289. 
               
               
                   
                 organs or tissue can produce 
               
               
                   
                 shoots 
               
               
                   
                 Pathways comprising 
               
               
                   
                 isopentenyl transferase (ipt) 
               
               
                   
               
            
           
         
       
     
     Other biological activities that can be modulated by the SAM genes and gene products are listed in the Reference tables. Assays for detecting such biological activities are described in the Protein Domain table. 
     III.B.4.d. Use of Sam Genes, Gene Components and Products to Modulate Transcription Levels of Other Genes 
     The expression of many genes is “upregulated” or “downregulated” in the SAM mutants because some of the SAM genes are integrated into complex networks that regulate the transcription of many other genes. Some SAM genes and gene components are therefore useful for modifying the transcription of other genes and hence complex phenotypes as described above. Profiles of genes altered by SAM mutations and genes are described in the Table below with associated biological activities. “Up-regulated” profiles are for genes whose mRNA levels are higher in the stm plants as compared to parental wild-type plants; and vice-versa for “down-regulated” profiles. 
     
       
         
           
               
               
               
               
             
               
                   
               
               
                   
                   
                 PHYSIOLOGICAL 
                 EXAMPLES OF 
               
               
                   
                 TYPE OF GENES 
                 CONSEQUENCES 
                 BIOCHEMICAL 
               
               
                   
                 WHOSE 
                 OF MODIFYING 
                 ACTIVITIES WHOSE 
               
               
                 TRANSCRIPT 
                 TRANSCRIPTS ARE 
                 SAM GENE 
                 TRANSCRIPTS ARE 
               
               
                 LEVELS 
                 CHANGED 
                 PRODUCT LEVELS 
                 CHANGED 
               
               
                   
               
             
            
               
                 Up Regulated 
                 Genes repressed by 
                 Altered 
                 Transporters 
               
               
                 Transcripts 
                 SAMs directly or 
                 Auxin/cytokinin 
                 Metabolic Enzymes 
               
               
                   
                 indirectly 
                 hormone ratio and 
                 Cell Membrane 
               
               
                   
                   
                 perception. 
                 Structure 
               
               
                   
                   
                 Increased/decreased 
                 Kinases, Phosphatases, 
               
               
                   
                   
                 cell expansion - 
                 G-Proteins 
               
               
                   
                   
                 promoting effects of 
                 Transcription 
               
               
                   
                   
                 brassinosteroids and 
                 Activators/Repressors 
               
               
                   
                   
                 gibberellic acids, due 
                 Transcription 
               
               
                   
                   
                 to altered levels of 
                 coactivators/corepressors 
               
               
                   
                   
                 biosynthetic pathway 
                 Chromatin Structure 
               
               
                   
                   
                 enzymes and or the 
                 And/Or Localized DNA 
               
               
                   
                   
                 amount of functional 
                 Topology Proteins 
               
               
                   
                   
                 hormone receptor. 
                 Cell Wall Proteins 
               
               
                   
                   
                 Increased or 
                 Translational 
               
               
                   
                   
                 decreased rate of cell 
                 activators/repressors 
               
               
                   
                   
                 division. 
                 Cell wall proteins 
               
               
                   
                   
                 Altered planes of cell 
                 involved in cell rigidity 
               
               
                   
                   
                 division 
                 e.g. extensin, glycine 
               
               
                   
                   
                 Increased or 
                 rich proteins. 
               
               
                   
                   
                 decreased rate and 
                 Cell cycle regulatory 
               
               
                   
                   
                 extent of cell 
                 proteins such as cyclins 
               
               
                   
                   
                 expansion. 
                 and cyclin dependent 
               
               
                   
                   
                 Increased or 
                 protein kinases (CDKs). 
               
               
                   
                   
                 decreased rigidity of 
               
               
                   
                   
                 cell ways. 
               
               
                 Down-Regulated 
                 Genes involved in SAM 
                 Altered pattern of 
                 Auxin transporter 
               
               
                 Transcripts 
                 cells and genes whose 
                 organs immerging 
                 proteins 
               
               
                   
                 expression is induced by 
                 from the meristem 
                 Auxin receptor proteins 
               
               
                   
                 SAMs 
                 Increased or 
                 Cytokinin receptor 
               
               
                   
                   
                 decreased the number 
                 proteins 
               
               
                   
                   
                 of cells partitioned 
                 Gibberellic acid receptor 
               
               
                   
                   
                 into a lateral organ. 
                 proteins 
               
               
                   
                   
                 Altered apical 
                 Brassinolide receptor 
               
               
                   
                   
                 dominance due to 
                 proteins 
               
               
                   
                   
                 suppression of lateral 
                 Hormone biosynthesis 
               
               
                   
                   
                 bud growth. 
                 proteins 
               
               
                   
                   
                 Altered apical 
                 Hormone degradation 
               
               
                   
                   
                 dominance due to 
                 proteins 
               
               
                   
                   
                 releasing of axillary 
                 Hormone conjugation 
               
               
                   
                   
                 meristems from 
                 proteins 
               
               
                   
                   
                 repression. 
                 Ubiquitin conjugating 
               
               
                   
                   
                 Increased/or 
                 enzymes. 
               
               
                   
                   
                 decreased production 
                 Receptor kinase signal 
               
               
                   
                   
                 of adventitious 
                 transduction 
               
               
                   
                   
                 meristems. 
               
               
                   
                   
                 Increased potential to 
               
               
                   
                   
                 form somatic 
               
               
                   
                   
                 embryos. 
               
               
                   
                   
                 Altered cell signaling 
               
               
                   
                   
                 pathways 
               
               
                   
                   
                 Altered hormone 
               
               
                   
                   
                 levels 
               
               
                   
               
            
           
         
       
     
     SAM genes and gene products can be modulated alone or in combination as described in the introduction. Of particular interest are combination of these genes and gene products with those that modulate hormone responsive pathways. Hormone responsive genes and gene products are described in more detail in the sections below. 
     Use of Sam Gene Promoters to Modify SAMs 
     Promoters of SAM genes, as described in the Reference tables, for example, can be used to modulate transcription of coding sequences in SAM cells to influence growth, differentiation or patterning of development or any of the phenotypes or biological activities above. For example, any desired sequence can be transcribed in similar temporal, tissue, or environmentally specific patterns as a SAM gene when the desired sequence is operably linked to the promoter of the SAM gene. 
     A specific instance is linking of a SAM gene promoter normally active in floral meristem primordia, to a phytotoxic protein coding sequence to inhibit apical meristem switching into an inflorescence and/or floral meristem, thereby preventing flowering. 
     SAM gene promoters can also be used to induce transcription of antisense RNA copies of a gene or an RNA variant to achieve reduced synthesis of a specific protein in specific SAM cells. This provides an alternative way to the example above, to prevent flowering. 
     
       
         
           
               
               
               
               
             
               
                   
               
               
                   
                   
                   
                 EXAMPLES OF 
               
               
                   
                   
                 PHYSIOLOGICAL 
                 BIOCHEMICAL 
               
               
                   
                 TYPE OF GENES 
                 CONSEQUENCES 
                 ACTIVITIES OF 
               
               
                   
                 WHOSE 
                 OF MODIFYING 
                 GENE PRODUCTS 
               
               
                 TRANSCRIPT 
                 TRANSCRIPTS 
                 GENE PRODUCT 
                 WITH MODIFIED 
               
               
                 LEVELS 
                 ARE CHANGED 
                 LEVELS 
                 LEVELS 
               
               
                   
               
             
            
               
                 Up regulated Transcripts 
                 Genes involved in 
                 Leaf cells 
                 Transcription 
               
               
                   
                 leaf, stem and root 
                 proliferate and 
                 factors, signal 
               
               
                   
                 cell differentiation, 
                 differentiate; 
                 transduction 
               
               
                   
                 cell division, cell 
                 Leaf structures 
                 proteins, kinase 
               
               
                   
                 expansion 
                 form and expand 
                 and phosphatases 
               
               
                   
                 Genes involved in 
                   
                 Chromatin 
               
               
                   
                 positive regulation of 
                   
                 remodeling 
               
               
                   
                 root, stem and leaf 
                   
                 Hormone 
               
               
                   
                 genes 
                   
                 biosynthesis 
               
               
                   
                 Repressors of root 
                   
                 enzymes 
               
               
                   
                 and other organ cell 
                   
                 Receptors 
               
               
                   
                 types e.g. flowers 
               
               
                   
                 Genes involved in 
                 Photosynthesis 
                 Light harvesting 
               
               
                   
                 photosynthesis 
                 and plastid 
                 coupled to ATP 
               
               
                   
                   
                 differentiation 
                 production 
               
               
                   
                   
                 Calvin cycle 
                 Chlorophyll 
               
               
                   
                   
                 activated 
                 biosynthesis 
               
               
                   
                   
                 Chloroplast 
                 Ribulose 
               
               
                   
                   
                 biogenesis and 
                 Bisphosphate 
               
               
                   
                   
                 plastid 
                 carboxylase 
               
               
                   
                   
                 differentiation 
                 Chloroplast 
               
               
                   
                   
                 activated 
                 membranes 
               
               
                   
                   
                   
                 synthesis 
               
               
                   
                   
                   
                 Chloroplast 
               
               
                   
                   
                   
                 ribosome 
               
               
                   
                   
                   
                 biogenesis 
               
               
                   
                 Other genes involved 
                 Starch 
                 Starch synthase 
               
               
                   
                 in metabolism 
                 biosynthesis 
                 Nitrate reductase 
               
               
                   
                   
                 Lipid 
                 Terpenoid 
               
               
                   
                   
                 biosynthesis 
                 biosynthesis 
               
               
                   
                   
                 Nitrogen 
                 Transcription 
               
               
                   
                   
                 metabolism - 
                 factors 
               
               
                   
                   
                 NO3 reduced and 
                 Transporters 
               
               
                   
                   
                 amino acids made 
                 Kinases 
               
               
                   
                   
                 Secondary 
                 Phosphatases and 
               
               
                   
                   
                 metabolites 
                 signal 
               
               
                   
                   
                 produced 
                 transduction 
               
               
                   
                   
                   
                 protein 
               
               
                   
                   
                   
                 Chromatin 
               
               
                   
                   
                   
                 structure 
               
               
                   
                   
                   
                 modulators 
               
               
                 Down regulated genes 
                 Genes involved in 
                 Leaf genes 
                 Transcription 
               
               
                   
                 negative regulation 
                 activated and leaf 
                 factors 
               
               
                   
                 of root, stem and leaf 
                 functions induced 
                 Signal 
               
               
                   
                 genes 
                 Other organs not 
                 transduction 
               
               
                   
                 Genes involved in 
                 induced 
                 proteins - kinases 
               
               
                   
                 other organs e.g. 
                 Leaf, stem and 
                 and phosphatases 
               
               
                   
                 flowers 
                 root metabolic 
                 Metabolic 
               
               
                   
                   
                 pathways induced 
                 enzymes 
               
               
                   
                   
                   
                 Chromatin 
               
               
                   
                   
                   
                 remodeling 
               
               
                   
                   
                   
                 proteins 
               
               
                   
               
            
           
         
       
     
     While early seedling phase polynucleotides and gene products are used singly, combinations of these polynucleotides are often better to optimize new growth and development patterns. Useful combinations include different leaf polynucleotides and/or gene products with a hormone responsive polynucleotide. These combinations are useful because of the interactions that exist between hormone-regulated pathways, nutritional pathways and development. 
     Use of Early Seedling Phase Gene Promoters 
     Promoters of early seedling phase genes are useful for transcription of desired polynucleotides, both plant and non-plant. If the gene is expressed only in the post-germination seedling, or in certain kinds of leaf cells, the promoter is used to drive the synthesis of proteins specifically in those cells. For example, extra copies of carbohydrate transporter cDNAs operably linked to a early seedling phase gene promoter and inserted into a plant increase the “sink” strength of leaves. Similarly, early seedling phase promoters are used to drive transcription of metabolic enzymes that alter the oil, starch, protein, or fiber contents of the seedling. Alternatively, the promoters direct expression of non-plant genes that can, for instance, confer resistance to specific pathogen. Additionally the promoters are used to synthesize an antisense mRNA copy of a gene to inactivate the normal gene expression into protein. The promoters are used to drive synthesis of sense RNAs to inactivate protein production via RNA interference. 
     III.B.5. Vegetative-Phase Specific Responsive Genes, Gene Components and Products 
     Often growth and yield are limited by the ability of a plant to tolerate stress conditions, including water loss. To combat such conditions, plant cells deploy a battery of responses that are controlled by a phase shift, from so called juvenile to adult. These changes at distinct times involve, for example, cotyledons and leaves, guard cells in stomata, and biochemical activities involved with sugar and nitrogen metabolism. These responses depend on the functioning of an internal clock, that becomes entrained to plant development, and a series of downstream signaling events leading to transcription-independent and transcription-dependent stress responses. These responses involve changes in gene expression. 
     Manipulation of the activation of one or more genes controlling the phase changes is useful to modulate the biological processes and/or phenotypes listed below. Phase responsive genes and gene products can act alone or in combination. Useful combinations include phase responsive genes and/or gene products with similar transcription profiles, similar biological activities, or members of the same or functionally related biochemical pathways. Whole pathways or segments of pathways are controlled by transcription factor proteins and proteins controlling the activity of signal transduction pathways. Therefore, manipulation of such protein levels is especially useful for altering phenotypes and biochemical activities of plants. 
     Phase responsive genes and gene products can function to either increase or dampen the above phenotypes or activities. Characterization of phase responsive genes was carried out using microarray technology. Microarray technology allows monitoring of gene expression levels for thousands of genes in a single experiment. This is achieved by hybridizing labeled fluorescent cDNA pools to glass slides that contain spots of DNA (Schena et al. (1995) Science 270: 467-70). The US  Arabidopsis  Functional Genomics Consortium (AFGC) has recently made public the results from such microarray experiments conducted with AFGC chips containing about 10,000 non-redundant ESTs, selected from about 37,000 randomly sequenced ESTs generated from mRNA of different tissues and developmental stages. 
     The sequences of the ESTs showing at least two-fold increases or decreases in a mutant of  Arabidopsis thaliana , squint, that appears not to undergo phase changes and appears adult-like throughout its growth cycle, compared with wild type were identified, compared to the Ceres full length cDNA and genomic sequence databanks, and equivalent Ceres clones identified. The MA_diff tables reports the results of this analysis, indicating those Ceres clones which are up or down regulated over controls, thereby indicating the Ceres clones which represent phase responsive genes. The MA_diff Table(s) reports the transcript levels of the experiment (see EXPT ID: Sqn (relating to SMD 7133, SMD 7137)). For transcripts that had higher levels in the samples than the control, a “+” is shown. A “−” is shown for when transcript levels were reduced in root tips as compared to the control. For more experimental detail see the Example section below. 
     Phase responsive genes are those sequences that showed differential expression as compared to controls, namely those sequences identified in the MA_diff tables with a “+” or “−” indication. 
     Phase Responsive Genes Identified by Cluster Analyses of Differential Expression 
     Phase Responsive Genes Identified by Correlation to Genes that are Differentially Expressed 
     As described above, the transcription profiles of genes that act together are well correlated. Applicants not only have identified the genes that are differentially expressed in the microarray experiments, but also have identified the genes that act in concert with them. The MA_clust table indicates groups of genes that have well correlated transcription profiles and therefore participate in the same pathway or network. 
     A pathway or network of phase responsive genes is any group in the MA_clust that comprises a cDNA ID that also appears in Expt ID Sqn (relating to SMD 7133, SMD 7137) of the MA_diff table(s). 
     Phase Responsive Genes Identified by Correlation to Genes that Cause Physiological Consequences 
     Additionally, the differential expression data and the phenotypic observations can be merged to identify pathways or networks of phase responsive genes. A group in the MA_clust is considered a phase responsive pathway or network if the group comprises a cDNA ID that also appears in Knock-in or Knock-out tables that causes one or more of the phenotypes described in section above. 
     Phase Responsive Genes Identified by Amino Acid Sequence Similarity 
     Phase responsive genes from other plant species typically encode polypeptides that share amino acid similarity to the sequences encoded by corn and  Arabidopsis  phase responsive genes. Groups of phase responsive genes are identified in the Protein Grouping table. In this table, any protein group that comprises a peptide ID that corresponds to a cDNA ID member of a phase responsive pathway or network is a group of proteins that also exhibits Phase responsive functions/utilities. 
     Further, promoters of phase responsive genes, as described in Reference tables, for example, are useful to modulate transcription that is induced by phase or any of the following phenotypes or biological activities below. Further, any desired sequence can be transcribed in similar temporal, tissue, or environmentally specific patterns as the phase responsive genes when the desired sequence is operably linked to a promoter of a phase responsive gene. 
     III.B.5.a. Use of Phase Responsive Genes to Modulate 
     PhenotypesPhase responsive genes and gene products are useful to or modulate one or more phenotype including timing phenotypes, dormancy, germination, cotyledon opening, first leaves, juvenile to adult transition, bolting, flowering, pollination, fertilization, seed development, seed set, fruit drop, senescence, epinasty, biomass, fresh and dry weight during any time in plant life, such as maturation, number of flowers, seeds, branches, and/or leaves, seed yield, including number, size, weight, and/or harvest index, fruit yield, including number, size, weight, and/or harvest index, plant development, time to fruit maturity, cell wall strengthening and reinforcement, stress tolerance, drought tolerance, flooding tolerance, and UV tolerance. 
     To regulate any of the phenotype(s) above, activities of one or more of the phase responsive genes or gene products can be modulated and the plants can be tested by screening for the desired trait. Specifically, the gene, mRNA levels, or protein levels can be altered in a plant utilizing the procedures described herein and the phenotypes can be screened for variants as in Anderson et al. (1997)  Plant Cell  9: 1727-1743; Heintzen et al. (1997)  Proc. Natl. Acad. Sci. USA  94: 8515-20; Schaffer et al. (1998)  Cell  93:1219-1229; Somers et al. (1998)  Development  125: 485-494; Somers et al. (1998)  Science  282: 1488-1490; Wang and Tobin (1998)  Cell  93: 1207-1217; Zhong et al. (1998)  Plant Cell  10: 2005-2017; Sugano et al. (1998)  Proc. Natl. Acad. Sci. USA  95: 11020-11025; Dowson-Day and Millar (1999)  Plant J  17: 63-71; Green and Tobin (1999)  Proc. Natl. Acad. Sci. USA  96: 4176-419; Staiger and Apel (1999)  Mol. Gen. Genet.  261: 811-819; Strayer and Kay (1999)  Curr. Opin. Plant Biol.  2:114-120; Strayer et. al. (2000)  Science  289:768-771; Kreps et al. (2000)  J Biol Rhythms  (2000) 15:208-217; Nelson et al. (2000)  Cell  101:331-340; Somers et al. (2000)  Cell  101:319-329. 
     III.B.5.b. Use of Phase Responsive Genes to Modulate Biochemical Activities 
     The activities of one or more of the phase responsive genes can be modulated to change biochemical or metabolic activities and/or pathways such as those noted below. Such biological activities are documented and can be measured according to the citations above and included in the table below: 
     
       
         
           
               
               
               
             
               
                   
               
               
                   
                 Biochemical Or Metabolic 
                   
               
               
                 Process 
                 Activities And/Or Pathways 
                 Citations including assays 
               
               
                   
               
             
            
               
                 Germination And 
                 Cold, Light And Water 
                 Bognar et al. (1999)  Proc. Natl. Acad.   
               
               
                 Seedling 
                 Modulated Signal Transduction 
                   Sci. USA  96: 14652-14657; Sugano et 
               
               
                 Development 
                 Pathways, Receptors, Kinases, 
                 al (1999)  Proc. Natl. Acad. Sci. USA   
               
               
                   
                 PAS Domain Proteins 
                 96: 12362-12366; Dowson-Day and 
               
               
                   
                   
                 Millar (1999)  Plant J  17: 63-71; 
               
               
                   
                   
                 Somers et al. (2000)  Cell  101: 319-329; 
               
               
                   
                   
                 Zhong et al. (1998)  Plant Cell   
               
               
                   
                   
                 10: 2005-2017 
               
               
                 Growth 
                 Cold And Light Modulated 
                 Nelson et al. (2000)  Cell  101: 331-340; 
               
               
                 Transitions And 
                 Signal Transduction Pathways, 
                 Fowler et al. (1999)  EMBO J.   
               
               
                 Flowering 
                 Receptors, Kinases, PAS 
                 18: 4679-4688 
               
               
                   
                 Domain Protiens 
               
               
                 Tuber Formation 
                 Cold And Light Modulated 
                 Yanovsky et al. (2000)  Plant J . 23: 
               
               
                   
                 Signal Transduction Pathways 
                 223-232 
               
               
                 METABOLISM 
               
               
                 Lipid Metabolism 
                 Membrane Lipid Synthesis 
                 Bradley and Reddy (1997)  J.   
               
               
                   
                 Including Omega-3 Fatty Acid 
                   Bacteriol . 179: 4407-4410; Martin, M 
               
               
                   
                 Desaturase, Lipases, Lipid 
                 et al. 1999 Europe J. Biochem 262: 
               
               
                   
                 Transfer Proteins 
                 283-290 
               
               
                 Sugar 
                 Glycosylhydrolases, 
                 Liu et al. (1996)  Plant Physiol . 
               
               
                 Metabolism 
                 Glycosyltransferases, 
                 112: 43-51; Millar and Kay (1996) 
               
               
                   
                 Amylases, Sucrose Synthase, 
                   Proc Natl Acad Sci USA  93: 15491-15496; 
               
               
                   
                 CAB, Rubisco, Light Signal 
                 Wang et al. (1997)  Plant Cell   
               
               
                   
                 Transduction 
                 9: 491-507; Shinohara et al (1999)  J.   
               
               
                   
                   
                   Biol. Chem.  273: 446-452 
               
               
                 Nitrogen 
                 Aminotransferases, Arginase, 
                 Bradley and Reddy (1997)  J.   
               
               
                 Metabolism 
                 Proteases And Vegetative 
                   Bacteriol . 179: 4407-4410 
               
               
                   
                 Storage Proteins, Aromatic 
               
               
                   
                 Amino Acid Synthesis 
               
               
                 Photorespiration 
                 Mitochondrial, Chloroplast And 
                 Zhong and McClung (1996)  Mol. Gen.   
               
               
                   
                 Peroxisomal Photorespiratory 
                   Genet . 251: 196-203; McClung (1997) 
               
               
                   
                 Enzymes, Serine 
                   Free. Radic. Biol. Med.  23: 489-496; 
               
               
                   
                 Hydroxymethyl Transferases, 
                 McClung et al. (2000) Plant Physiol. 
               
               
                   
                 Catalase 
                 123: 381-392 
               
               
                 Responses To 
                 Expression Of Genes Involved 
                 McClung (1997)  Free Radic Biol Med   
               
               
                 Environmental 
                 In Responses To Drought, Salt, 
                 23: 489-496; Shi et al. (2000)  Proc.   
               
               
                 Stress 
                 UV 
                   Natl. Acad. Sci. USA  97: 6896-6901 
               
               
                   
               
            
           
         
       
     
     Other biological activities that can be modulated by the phase responsive genes and their products are listed in the Reference tables. Assays for detecting such biological activities are described in the Protein Domain table. 
     Phase responsive genes are characteristically differentially transcribed in response to maturity of the cell, organ or tissue which depends on a timing mechanism, which is internal to an organism or cell. The Intensity Table reports the changes in transcript levels of various phase responsive genes in a plant. 
     The data from this experiment reveal a number of types of phase responsive genes and gene products. Profiles of some classes of phase responsive genes are shown in the table below with examples of which associated biological activities are modulated when the activities of one or more such genes vary in plants. 
     
       
         
           
               
               
               
               
             
               
                   
               
               
                 Transcript 
                   
                 Physiological 
                 Examples Of 
               
               
                 Levels 
                 Type Of Genes 
                 Consequences 
                 Biochemical Activity 
               
               
                   
               
             
            
               
                 Up Regulated Transcripts 
                 Responders To 
                 Adult phase 
                 Metabolic Enzymes 
               
               
                   
                 mutation that confers 
                 adoption 
                 Change In Cell 
               
               
                   
                 adult like phase 
                 Metabolisms 
                 Membrane Structure 
               
               
                   
                 Genes induced in 
                 Affected By phase 
                 And Potential 
               
               
                   
                 adult-like phase 
                 change 
                 Kinases And 
               
               
                   
                   
                 Synthesis Of 
                 Phosphatases 
               
               
                   
                   
                 Secondary 
                 Transcription 
               
               
                   
                   
                 Metabolites 
                 Activators 
               
               
                   
                   
                 And/Or Proteins 
                 Change In Chromatin 
               
               
                   
                   
                 Modulation Of 
                 Structure And/Or 
               
               
                   
                   
                 Phase Response 
                 Localized DNA 
               
               
                   
                   
                 Transduction 
                 Topology 
               
               
                   
                   
                 Pathways 
               
               
                   
                   
                 Specific Gene 
               
               
                   
                   
                 Transcription 
               
               
                   
                   
                 Initiation 
               
               
                 Down-Regulated Transcripts 
                 Responders To 
                 Negative 
                 Transcription Factors 
               
               
                   
                 mutation that confers 
                 Regulation of 
                 Change In Protein 
               
               
                   
                 adult phase 
                 adult phase 
                 Structure By 
               
               
                   
                 Genes repressed in 
                 pathways 
                 Phosphorylation 
               
               
                   
                 adult-like phase 
                 Changes In 
                 (Kinases) Or 
               
               
                   
                 Genes With 
                 Pathways And 
                 Dephosphoryaltion 
               
               
                   
                 Discontinued 
                 Processes 
                 (Phosphatases) 
               
               
                   
                 Expression Or 
                 Operating In Cells 
                 Change In Chromatin 
               
               
                   
                 Unstable mRNA in 
                 Changes In 
                 Structure And/Or 
               
               
                   
                 adult-like phase 
                 Metabolic 
                 DNA Topology 
               
               
                   
                   
                 pathways other 
                 Stability Factors For 
               
               
                   
                   
                 than phase 
                 Protein Synthesis And 
               
               
                   
                   
                 specific pathways 
                 Degradation 
               
               
                   
                   
                   
                 Metabolic Enzymes 
               
               
                   
               
            
           
         
       
     
     Use of Promoters of Phase Responsive Genes 
     Promoters of phase responsive genes are useful for transcription of any desired polynucleotide or plant or non-plant origin. Further, any desired sequence can be transcribed in a similar temporal, tissue, or environmentally specific patterns as the phase responsive genes where the desired sequence is operably linked to a promoter of a phase responsive gene. The protein product of such a polynucleotide is usually synthesized in the same cells, in response to the same stimuli as the protein product of the gene from which the promoter was derived. Such promoter are also useful to produce antisense mRNAs to down-regulate the product of proteins, or to produce sense mRNAs to down-regulate mRNAs via sense suppression. 
     III.C. Hormone Responsive Genes, Gene Components and Products 
     III.C.1. Abscissic Acid Responsive Genes, Gene Components and Products 
     Plant hormones are naturally occurring substances, effective in very small amounts, which act as signals to stimulate or inhibit growth or regulate developmental processes in plants. Abscisic acid (ABA) is a ubiquitous hormone in vascular plants that has been detected in every major organ or living tissue from the root to the apical bud. The major physiological responses affected by ABA are dormancy, stress stomatal closure, water uptake, abscission and senescence. In contrast to Auxins, cytokinins and gibberellins, which are principally growth promoters, ABA primarily acts as an inhibitor of growth and metabolic processes. 
     Changes in ABA concentration internally or in the surrounding environment in contact with a plant results in modulation of many genes and gene products. Examples of such ABA responsive genes and gene products are shown in the Reference, Sequence, Protein Group, Protein Group Matrix tables, MA_diff, and MA_clust tables. These genes and/or products are responsible for effects on traits such as plant vigor and seed yield. They were discovered and characterized from a much larger set of genes by experiments designed to find genes whose mRNA products changed in concentration in response to application of ABA to plants. 
     While ABA responsive polynucleotides and gene products can act alone, combinations of these polynucleotides also affect growth and development. Useful combinations include different ABA responsive polynucleotides and/or gene products that have similar transcription profiles or similar biological activities, and members of the same or similar biochemical pathways. Whole pathways or segments of pathways are controlled by transcription factor proteins and proteins controlling the activity of signal transduction pathways. Therefore, manipulation of such protein levels is especially useful for altering phenotypes and biochemical activities of plants. In addition, the combination of an ABA responsive polynucleotide and/or gene product with another environmentally responsive polynucleotide is also useful because of the interactions that exist between hormone-regulated pathways, stress and defence induced pathways, nutritional pathways and development. Here, in addition to polynucleotides having similar transcription profiles and/or biological activities, useful combinations include polynucleotides that may have different transcription profiles but which participate in common or overlapping pathways. 
     Such ABA responsive genes and gene products can function to either increase or dampen the above phenotypes or activities either in response to changes in ABA concentration or in the absence of ABA fluctuations. The MA_diff Table(s) reports the transcript levels of the experiment (see EXPT ID: 108560, 108561, 108513, 108597). For transcripts that had higher levels in the samples than the control, a “+” is shown. A “−” is shown for when transcript levels were reduced in root tips as compared to the control. For more experimental detail see the Example section below. 
     ABA genes are those sequences that showed differential expression as compared to controls, namely those sequences identified in the MA_diff tables with a “+” or “−” indication. 
     ABA Genes Identified by Cluster Analyses of Differential Expression 
     ABA Genes Identified by Correlation to Genes that are Differentially Expressed 
     As described above, the transcription profiles of genes that act together are well correlated. Applicants not only have identified the genes that are differentially expressed in the microarray experiments, but also have identified the genes that act in concert with them. The MA_clust table indicates groups of genes that have well correlated transcription profiles and therefore participate in the same pathway or network. 
     A pathway or network of ABA genes is any group in the MA_clust that comprises a cDNA ID that also appears in Expt ID 108560, 108561, 108513, 108597 of the MA_diff table(s). 
     ABA Genes Identified by Correlation to Genes that Cause Physiological Consequences 
     Additionally, the differential expression data and the phenotypic observations can be merged to identify pathways or networks of ABA genes. A group in the MA_clust is considered a ABA pathway or network if the group comprises a cDNA ID that also appears in Knock-in or Knock-out tables that causes one or more of the phenotypes described in section above. 
     ABA Genes Identified by Amino Acid Sequence Similarity 
     ABA genes from other plant species typically encode polypeptides that share amino acid similarity to the sequences encoded by corn and  Arabidopsis  ABA genes. Groups of ABA genes are identified in the Protein Group table. In this table, any protein group that comprises a peptide ID that corresponds to a cDNA ID member of a ABA pathway or network is a group of proteins that also exhibits ABA functions/utilities. 
     Further, promoters of ABA responsive genes, as described in the Reference tables, for example, are useful to modulate transcription that is induced by ABA or any of the following phenotypes or biological activities below. 
     III.C.1.a. Use of Abscissic Acid Responsive Genes to Modulate Phenotypes 
     ABA responsive genes and gene products are useful to or modulate one or more of the following phenotypes including development such as cell growth (promotion of leaf cell elongation), fruit development (fruit drop and inhibition of parthenocarpy and ovary growth), seed development (maturation of zygotic and somatic embryos, embryo development, seed development and maturation, acquisition of desiccation tolerance, dormancy including control rate and timing of germination, prolongation of seed storage and viability, and inhibition of hydrolytic enzyme synthesis); growth of roots such as inhibition of root elongation under low water potential), stems, buds (such as promotion of dormancy and lateral/axillary bud formation), leaves, and inhibition of aba-induced growth and elongation; biomass (such as fresh and dry weight during any time in plant life, such as maturation), number, size, and weight of flowers and seeds); senescence (including abscission, leaf fall, and flower longevity); differentiation (including plastid/chloroplast differentiation and regulation of sterility); and stress responses (such as mediation of response to desiccation, drought, salt and cold). 
     To regulate any of the phenotype(s) above, activities of one or more of the ABA responsive genes or gene products can be modulated in an organism and tested by screening for the desired trait. Specifically, the gene, mRNA levels, or protein levels can be altered in a plant utilizing the procedures described herein and the phenotypes can be assayed. As an example, a plant can be transformed according to Bechtold and Pelletier (1998, Methods. Mol. Biol. 82:259-266) and/or screened for variants as in Winkler et al. (1998) Plant Physiol 118: 743-50 and visually inspected for the desired phenotype or metabolically and/or functionally assayed according to Koorneef and Karssen (1994, Seed dormancy and germination, In:  Arabidopsis , Cold Spring Harbor Lab. Press, pp 314-334), Cramer et al (1998, J. Exptl. Botany 49:191-198), and White and Rivin (2000, Plant Physiol 122: 1089-97). Phillips et al. (1997) EMBO J 16: 4489-96; Nambara et al (1995) Development 121: 629-636; Hays et al (1999) Plant Physiol. 119: 1065-72; Filonova et al (2000) J Exptl Botany 51: 249-64; White et al (2000) Plant Physiol. 122: 1081-88; and Visser et al. (1998) Plant Mol Biol 37: 131-40; Rohde et al. (2000) Plant Cell 12:35-52; and Cramer et al. (1998) J. experimental Botany. 49: 191-198. 
     III.C.1.b. Use of Abscissic Acid Responsive Genes to Modulate Biochemical Activities 
     The activities of one or more of the ABA responsive genes can be modulated to change biochemical or metabolic activities and/or pathways such as those noted below. Such biological activities can be measured according to the citations included in the Table below: 
     
       
         
           
               
               
               
             
               
                   
               
               
                   
                 BIOCHEMICAL OR 
                   
               
               
                   
                 METABOLIC 
               
               
                   
                 ACTIVITIES AND/OR 
                 CITATIONS INCLUDING 
               
               
                 PROCESS 
                 PATHWAYS 
                 ASSAYS 
               
               
                   
               
             
            
               
                 Growth, 
                 Farnesylation 
                 Pei Et Al (1998) Science 282: 287-290; 
               
               
                 Differentiation And 
                   
                 Cutler Et Al. (1996) Science 
               
               
                 Development 
                   
                 273: 1239 
               
               
                   
                 Nitrogen Metabolism 
                 Goupil Et Al (1998) J Exptl Botany 
               
               
                   
                   
                 49: 1855-62 
               
               
                 Water Conservation 
                 Stomatal Development 
                 Allen Et Al. (1999) Plant Cell 11: 
               
               
                 And Resistance To 
                 And Physiology 
                 1785-1798 
               
               
                 Drought And Other 
                   
                 Li Et Al. 2000 Science 287: 300-303 
               
               
                 Related Stresses 
                   
                 Burnett Et Al 2000. J. Exptl Botany 
               
               
                   
                   
                 51: 197-205 
               
               
                   
                   
                 Raschke (1987) In: Stomatal 
               
               
                   
                   
                 Function Zeiger Et Al. Eds., 253-279 
               
               
                   
                 Stress Response Pathways 
                 Bush And Pages (1998) Plant Mol. 
               
               
                   
                   
                 Biol. 37: 425-35 
               
               
                   
                 Inhibition Of Ethylene 
                 Spollen Et Al (2000) Plant Physiol. 
               
               
                   
                 Production Under Low 
                 122: 967-976 
               
               
                   
                 Water Potential 
               
               
                   
                 Proline And Other 
                 Hare Et Al. (1998) Plant, Cell And 
               
               
                   
                 Osmolite Synthesis And 
                 Environment 21: 535-553; Hare Et Al. 
               
               
                   
                 Degradation 
                 (1999) J. Exptl. Botany 50: 413-434 
               
               
                   
                 Plasmalemma And 
                 Macrobbie (1998) Philos Trans R Soc 
               
               
                   
                 Tonoplast Ion Channel 
                 Lond B Biol Sci 353: 1475-88; Li Et 
               
               
                   
                 Changes 
                 Al (2000) Science 287: 300-303; 
               
               
                   
                   
                 Barkla Et Al. (1999) Plant Physiol. 
               
               
                   
                   
                 120: 811-819 
               
               
                   
                 Ca2+ Accumulation 
                 Lacombe Et Al. (2000) Plant Cell 12: 
               
               
                   
                   
                 837-51; Wang Et Al. (1998) Plant 
               
               
                   
                   
                 Physiol 118: 1421-1429; Shi Et Al. 
               
               
                   
                   
                 (1999) Plant Cell 11: 2393-2406 
               
               
                   
                 K+ Efflux 
                 Gaymard Et Al. (1998) Cell 94: 647-655 
               
               
                   
                 Activation Of Kinases 
                 Jonak Et Al. (1996) Proc. Natl. Acad. 
               
               
                   
                 And Phosphatases 
                 Sci 93: 11274-79; Sheen (1998) Proc. 
               
               
                   
                   
                 Natl. Acad. Sci. 95: 975-80; Allen Et 
               
               
                   
                   
                 Al. (1999) Plant Cell 11: 1785-98 
               
               
                   
               
            
           
         
       
     
     Other biological activities that can be modulated by the ABA responsive genes and gene products are listed in the Reference tables. Assays for detecting such biological activities are described in the Protein Domain table. 
     ABA responsive genes are characteristically differentially transcribed in response to fluctuating ABA levels or concentrations, whether internal or external to an organism or cell. The MA_diff reports the changes in transcript levels of various ABA responsive genes in entire seedlings at 1 and 6 hours after a plant was sprayed with a Hoagland&#39;s solution enriched with ABA as compared to seedlings sprayed with Hoagland&#39;s solution only. 
     The data from this time course can be used to identify a number of types of ABA responsive genes and gene products, including “early responders,” and “delayed ABA responders”, “early responder repressors” and “delayed repressors”. Profiles of these different ABA responsive genes are shown in the Table below together with examples of the kinds of associated biological activities. 
                                                     EXAMPLES OF       TRANSCRIPT   TYPE OF   PHYSIOLOGICAL   BIOCHEMICAL       LEVELS   GENES   CONSEQUENCES   ACTIVITY                  Up Regulated   Early Responders   ABA Perception   Transcription Factors       Transcripts   To ABA   ABA Uptake   Transporters       (Level At 1 Hr ≅ 6 Hr)       Modulation Of ABA   Change In Cell Membrane       or       Response   Structure       (Level At 1 Hr &gt; 6 Hr)       Transduction   Kinases And Phosphatases               Pathways   Transcription Activators               Specific Gene   Change In Chromatin               Transcription   Structure And/Or               Initiation   Localized DNA Topology       Up Regulated   Delayed   Maintenance Of   Transcription Factors       Transcripts   Responders   Response To ABA   Specific Factors (Initiation       (Level At 1 Hr &lt; 6 Hr)       Maintenance Of Seed   And Elongation) For               Dormancy, Stress   Protein Synthesis               Stomatal Closure,   Maintenance Of Mrna               Water Uptake   Stability               Control, Abscission   Maintenance Of Protein               And Senescence   Stability               Control Pathways   Maintenance Of Protein-                   Protein Interaction       Down-Regulated   Early Responder   Negative Regulation   Transcription Factors       Transcripts   Repressors Of   Of ABA Pathways   Change In Protein       (Level At 1 Hr ≅ 6 Hr)   ABA State Of   Released   Structure By       or   Metabolism   Changes In Pathways   Phosphorylation (Kinases)       (Level At 6 Hr &gt; 1 Hr)   Genes With   And Processes   Or Dephosphoryaltion           Discontinued   Operating In Cells   (Phosphatases)           Expression Or       Change In Chromatin           UnsTable mRNA       Structure And/Or DNA           In Presence Of       Topology           ABA       Down-Regulated   Delayed   Negative Regulation   Transcription Factors       Transcripts   Repressors Of   Of ABA Pathways   Kinases And Phosphatases       (Level At 1 Hr &gt; 6 Hr)   ABA State Of   Released   Stability Of Factors For           Metabolism   Maintenance Of   Protein Synthesis And           Genes With   Pathways Released   Degradation           Discontinued   From Repression           Expression Or   Changes In Pathways           UnsTable mRNA   And Processes           In Presence Of   Operating In Cells           ABA                    
Use of Promoters of ABA Responsive Genes
 
     Promoters of ABA responsive genes are useful for transcription of any desired polynucleotide or plant or non-plant origin. Further, any desired sequence can be transcribed in a similar temporal, tissue, or environmentally specific patterns as the ABA responsive genes where the desired sequence is operably linked to a promoter of a ABA responsive gene. The protein product of such a polynucleotide is usually synthesized in the same cells, in response to the same stimuli as the protein product of the gene from which the promoter was derived. Such promoter are also useful to produce antisense mRNAs to down-regulate the product of proteins, or to produce sense mRNAs to down-regulate mRNAs via sense suppression. 
     III.C.2. Auxin Responsive Genes, Gene Components and Products 
     Plant hormones are naturally occurring substances, effective in very small amounts that stimulate or inhibit growth or regulate developmental processes in plants. One of the plant hormones is indole-3-acetic acid (IAA), often referred to as Auxin. 
     Changes in Auxin concentration in the surrounding environment in contact with a plant or in a plant results in modulation of the activities of many genes and hence levels of gene products. Examples of such Auxin responsive genes and their products are shown in the Reference and Sequence Tables. These genes and/or products are responsible for effects on traits such as plant vigor and seed yield. The genes were discovered and characterized from a much larger set by experiments designed to find genes whose mRNA products changed in response to application of Auxin to plants. 
     Manipulation of one or more Auxin responsive gene activities are useful to modulate the biological activities and/or phenotypes listed below. Auxin response genes and gene products can act alone or in combination. Useful combinations include Auxin response genes and/or gene products with similar transcription profiles, similar biological activities, or members of the same or functionally related biochemical pathways. Whole pathways or segments of pathways are controlled by transcription factor proteins and proteins controlling the activity of signal transduction pathways. Therefore, manipulation of the levels of such proteins is especially useful for altering phenotypes and biochemical activities of plants. The MA_diff Table(s) reports the transcript levels of the experiment (see EXPT ID: 108564, 108565, 108516, 108554, 108466, 107886, 107891, SMD 3743, and NAA (relating to SMD 3749, SMD 6338, SMD 6339)). For transcripts that had higher levels in the samples than the control, a “+” is shown. A “−” is shown for when transcript levels were reduced in root tips as compared to the control. For more experimental detail see the Example section below. 
     NAA genes are those sequences that showed differential expression as compared to controls, namely those sequences identified in the MA_diff tables with a “+” or “−” indication. 
     NAA Genes Identified by Cluster Analyses of Differential Expression 
     NAA Genes Identified by Correlation to Genes that are Differentially Expressed 
     As described above, the transcription profiles of genes that act together are well correlated. Applicants not only have identified the genes that are differentially expressed in the microarray experiments, but also have identified the genes that act in concert with them. The MA_clust table indicates groups of genes that have well correlated transcription profiles and therefore participate in the same pathway or network. 
     A pathway or network of NAA genes is any group in the MA_clust that comprises a cDNA ID that also appears in Expt ID 108564, 108565, 108516, 108554, 108466, 107886, 107891, SMD 3743, and NAA (relating to SMD 3749, SMD 6338, SMD 6339) of the MA_diff table(s). 
     NAA Genes Identified by Correlation to Genes that Cause Physiological Consequences 
     Additionally, the differential expression data and the phenotypic observations can be merged to identify pathways or networks of NAA genes. A group in the MA_clust is considered a NAA pathway or network if the group comprises a cDNA ID that also appears in Knock-in or Knock-out tables that causes one or more of the phenotypes described in section above. 
     NAA Genes Identified by Amino Acid Sequence Similarity 
     NAA genes from other plant species typically encode polypeptides that share amino acid similarity to the sequences encoded by corn and  Arabidopsis  NAA genes. Groups of NAA genes are identified in the Protein Group table. In this table, any protein group that comprises a peptide ID that corresponds to a cDNA ID member of a NAA pathway or network is a group of proteins that also exhibits NAA functions/utilities. 
     Such Auxin responsive genes and gene products can function to either increase or dampen the above phenotypes or activities either in response to changes in Auxin concentration or in the absence of Auxin fluctuations. Further, promoters of Auxin responsive genes, as described in the Reference tables, for example, are useful to modulate transcription that is induced by Auxin or any of the following phenotypes or biological activities below. 
     III.C.2.a. Use of Auxin Responsive Genes, Gene Components and Products to Modulate Phenotypes 
     Auxin responsive genes and gene products are useful to or modulate one or more phenotypes including growth, apical dominance, vascular growth, roots, inhibition of primary root elongation, increased lateral root formation, stems, lateral buds, lateral branching, reduction of branching, for high density growth per acre, for increased wood production, lateral organ initiation and/or positioning in apical meristem, organ formation, for example, fruit number in tomatoes, leaves, height/stature, e.g., taller crops or increase wood production, regeneration and differentiation of cultured cells or plantlets, biomass, fresh and dry weight during any time in plant life, such as maturation; number of flowers; number of seeds; number of branches; number of leaves; starch content, seed yield, including number, size, weight, harvest index, starch content, fruit yield, number, size, weight, harvest index, starch content, development, orienting cell growth, establishment and maintenance of plant axis, apical dominance, cell plate placement, polarised growth, initiation and/or development, of embryos morphogenic progression, e.g., from early radial to late axialized torpedo stages, differentiation of cells into morphologically different cell layers, cotyledon separation, fruit development, abscission, leading to modulation of fruit drop, parthenocarpy, seedless crops resulting from lack of seed set, vascularization, e.g. hypocotyl and cotyledon tissues, genetic control of vascular patterning and influences its maturation; specification of the sites where vascular differentiation will occur; determination of the direction and extent of vascular tissue formation, maintenance of the continuity of vascular development with plant growth, tropic responses, gravitropic responses, e.g. affecting roots and shoots, and modulation of phototropic sensitivity, e.g. increase growth under a reduced light spectrum. 
     Further, any desired sequence can be transcribed in similar temporal, tissue, or environmentally specific patterns as the Auxin responsive genes when the desired sequence is operably linked to a promoter of an Auxin responsive gene. 
     To modulate any of the phenotype(s) above, activities of one or more of the Auxin response genes or gene products can be modulated and the plants can be tested by screening for the desired trait. Specifically, the gene, mRNA levels, or protein levels can be altered in a plant utilizing the procedures described herein and the phenotypes can be screened for variants as in Winkler et al. (1998) Plant Physiol 118: 743-50 and assayed, for example, in accordance with Bechtold and Pelletier (1998). Methods Mol. Biol. 82: 259-266; Clough and Bent (1998). 16: 735-743; Krysan et al. (1999). Plant Cell 11:2283-2290. 
     III.C.2.b. Use of Auxin Responsive Genes, Gene Components and Products to Biochemical Activities: 
     The activities of one or more of the Auxin responsive genes can be modulated to change biochemical or metabolic activities and/or pathways such as those noted below. Such biological activities are documented and can be measured according to the citations included in the Table below: 
     
       
         
           
               
               
               
             
               
                   
               
               
                   
                 BIOCHEMICAL OR 
                   
               
               
                   
                 METABOLIC 
               
               
                   
                 ACTIVITIES AND/OR 
                 CITATIONS INCLUDING 
               
               
                 PROCESS 
                 PATHWAYS 
                 ASSAYS 
               
               
                   
               
             
            
               
                 Cell Growth and 
                 Protein Ubiquitination 
                 Gray et al. (1999) Genes and 
               
               
                 Differentiation 
                   
                 Develop, 13: 1678-1691 
               
               
                   
                   
                 Bechtold and Pelletier (1998). 
               
               
                   
                   
                 Methods. Mol. Biol. 82: 259-266 
               
               
                   
                 Cell Wall loosening and 
                 Catala et al. (2000). Plant Physiol. 
               
               
                   
                 Expansion 
                 122: 527-534. 
               
               
                   
                   
                 Cosgrove, D. (1993). New Phytol. 
               
               
                   
                   
                 124: 1-23. 
               
               
                 Auxin/Cytokinin Ratio 
                 Changing Auxin and/or 
                 Chen et al. (1988). Plant Physiol. 
               
               
                   
                 cytokinin synthesis and/or 
                 86: 822-825 
               
               
                   
                 turnover 
                 Tam et al. (2000). Plant Physiol. 
               
               
                   
                   
                 123: 589-595 
               
               
                   
                   
                 Bartel and Fink. (1995). Science 
               
               
                   
                   
                 268: 1745-1748. 
               
               
                   
                   
                 Prinsen et al. (1995). Quantifying 
               
               
                   
                   
                 phytohormones in transformed 
               
               
                   
                   
                 plants. In: Methods in Molecular 
               
               
                   
                   
                 Biology. 44: 245-262. 
               
               
                 Auxin Transport 
                 Channeling of polar Auxin 
                 Reed et al. (1998). Plant Physiol. 
               
               
                   
                 Transport 
                 118: 1369-1378. 
               
               
                   
                   
                 Estelle, M. (1998). Plant Cell 
               
               
                   
                   
                 10: 1775-1778 
               
               
                   
                 Auxin Efflux Between Cells 
                 Reed et al. (1998). Plant Physiol. 
               
               
                   
                   
                 118: 1369-1378. 
               
               
                   
                   
                 Marchant et al. (1999). EMBO J. 
               
               
                   
                   
                 18: 2066-2073. 
               
               
                   
                 Auxin Influx In and Out of a 
                 Reed et al. (1998). Plant Physiol. 
               
               
                   
                 Cell 
                 118: 1369-1378. 
               
               
                   
                   
                 Marchant et al. (1999). EMBO J. 
               
               
                   
                   
                 18: 2066-2073. 
               
               
                   
                 Electogenic Proton Symport 
                 Young et al. (1999). Biochim 
               
               
                   
                 of Auxin 
                 Biophys Acta. 1415(2): 306-22 
               
               
                 Signal Transduction 
                 K+ Accumulation 
                 Philippar et al. (1999). Proc. Natl. 
               
               
                   
                   
                 Acad. Sci. 96: 12186-12191 
               
               
                   
                 Permeability of Cell 
                 Marchant et al. (1999). EMBO J. 
               
               
                   
                 Membranes 
                 18: 2066-2073. 
               
               
                   
                 Guanine-Nucleotide 
                 Steinmann et al. (1999). Science 
               
               
                   
                 Exchange 
                 286: 316-318. 
               
               
                   
                   
                 Peyroche et al. (1996). Nature 
               
               
                   
                   
                 384: 479-481. 
               
               
                   
                 Protein Phosphorylation 
                 Christensen et al. (2000). Cell 
               
               
                   
                   
                 100: 469-478. 
               
               
                   
                   
                 Hirt (2000). Proc. Natl. Acad Sci. 
               
               
                   
                   
                 97: 2405-2407. 
               
               
                   
                 Interaction with Ethylene 
                 Madlung et al. (1999). Plant 
               
               
                   
                 mode of action 
                 Physiol. 120: 897-906. 
               
               
                   
                   
                 Xu et al. (1998). Plant Physiol. 
               
               
                   
                   
                 118: 867-874. 
               
               
                 Protein Turnover 
                 Localization of Polypeptides 
                 Grebe et al. (2000). Plant Cell. 
               
               
                   
                 with the basal End of Cells 
                 12: 343-356 
               
               
                   
               
            
           
         
       
     
     Other biological activities that can be modulated to by the Auxin responsive genes and their products are listed in the Reference Tables. Assays for detecting such biological activities are described in the Domain section of the Reference Tables. 
     Auxin responsive genes are characteristically differentially transcribed in response to fluctuating Auxin levels or concentrations, whether internal or external to an organism or cell. The MA_diff(s) report(s) the changes in transcript levels of various Auxin responsive genes in the aerial parts of a seedling at 1 and 6 hours after the seedling was sprayed with a solution enriched with Auxin as compared to aerial parts of a seedling sprayed with water. 
     The data from this time course can be used to identify a number of types of Auxin responsive genes and gene products, including “early responders,” and “delayed responders.” Profiles of these different classes of Auxin responsive genes are shown in the Table below together with examples of the kinds of associated biological activities. 
                                                     EXAMPLES OF                   BIOCHEMICAL       TRANSCRIPT   TYPE OF   PHYSIOLOGICAL   ACTIVITY OF GENE       LEVEL   GENES   CONSEQUENCES   PRODUCTS                  Upregulated   Early   Auxin perception   Transcription factors       transcripts   responders to   Auxin   Transporters; channeling       (level at 1 hr ≅6    Auxin   Uptake/transport   of polar Auxin transport       hours) (level       Modulation of   Kinases and       at 1 hr &gt; 6 hours)       Auxin response   phosphatases; protein               transduction   ubiqutination; guanine               pathways   nucelotide exchange;                   changing Auxin and/or                   cytokininin synthesis                   and/or turnover;                   interaction with ethylene                   mode of action               Initiating   Auxin metabolic               transcription of   pathways               specific gene(s)   Change in chromatin                   structure and/or DNA                   topology                   Transcriptional activators                   Change in activity of                   protein-protein                   interactions               Modification of cell   Cell wall and cell growth               walls   promoting pathways               Modification of cell   Change in activity of               structures   cytoskeletal proteins                   modulating cell structure               Modification of   Metabolic enzymes               metabolism   Coordination and control                   of central carbon and                   Auxin metabolism       Upregulated   “Delayed”   Completion and/or   Transcription factors       transcripts (level   Responders   Maintenance of   Changes in membrane       at 1 hr &lt; 6 hr)       Auxin response   protein, membrane channel                   and/or transporter protein                   activity               Initiating   Change in chromatin               transcription of   structure and/or DNA               specific gene(s)   topology                   Transcriptional activators                   Change in activity of                   protein-protein interactions               Modification of cell   Cell wall proteins               walls               Modification of cell   Change(s) in activity of               structures   cytoskeletal proteins                   modulating cell structure               Modification of   Coordination and control of               metabolism   central carbon and Auxin                   metabolism                   metabolic enzymes       Downregulated   Early repressor   Repression of   Transcription factors       transcripts   responders to   Auxin induced   Changes in activity of       (level at 1 hour ≅   Auxin   proteins released   cytoskeletal proteins       6 hours)   Genes for   Reorientation of   modulating cell structure       (level at 1 hour &gt;   pathways   metabolism in   Changes in chromatin       6 hours)   diminished in   certain cells   structure and/or DNA           presence of       topology           Auxin       Changes in protein                   structure and/or function                   by phosphorylation                   (kinases) and/or                   dephosphorylation                   (phosphatases)                   Stability of factors for                   protein translation                   Changes in cell                   membrane structure                   Changes in chromatin                   and/or localized DNA                   topology                   Changes in protein-                   protein interaction                   Metabolic enzymes       Down-regulated   “Delayed”   Maintenance of   Transcription factors       transcripts   repressor   Auxin stimulated   Change in activity of       (level at 1 hour &lt;   responders to   state(s) in certain cells   cytoskeletal proteins       6 hours)   Auxin       modulating cell structure           Genes for   Reorientation of   Changes in chromatin           pathways   metabolism in   structure and/or DNA           diminished in   certain cells   topology           presence of       Changes in protein           Auxin       structure and/or function                   by phosphorylation                   (kinases) and/or                   dephosphorylation                   (phosphatases)                   Stability of factors for                   protein translation                   Changes in cell                   membrane structure                   Changes in chromatin                   and/or localized DNA                   topology                   Changes in protein-                   protein interaction                   Metabolic enzymes                    
Use of Promoters of NAA Responsive Genes
 
     Promoters of NAA responsive genes are useful for transcription of any desired polynucleotide or plant or non-plant origin. Further, any desired sequence can be transcribed in a similar temporal, tissue, or environmentally specific patterns as the NAA responsive genes where the desired sequence is operably linked to a promoter of a NAA responsive gene. The protein product of such a polynucleotide is usually synthesized in the same cells, in response to the same stimuli as the protein product of the gene from which the promoter was derived. Such promoter are also useful to produce antisense mRNAs to down-regulate the product of proteins, or to produce sense mRNAs to down-regulate mRNAs via sense suppression. 
     III.C.3. Brassinosteroid Responsive Genes, Gene Components and Products: 
     Plant hormones are naturally occurring substances, effective in very small amounts, which act as signals to stimulate or inhibit growth or regulate developmental processes in plants. Brassinosteroids (BRs) are the most recently discovered, and least studied, class of plant hormones. The major physiological response affected by BRs is the longitudinal growth of young tissue via cell elongation and possibly cell division. Consequently, disruptions in BR metabolism, perception and activity frequently result in a dwarf phenotype. In addition, because BRs are derived from the sterol metabolic pathway, any perturbations to the sterol pathway can affect the BR pathway. In the same way, perturbations in the BR pathway can have effects on the later part of the sterol pathway and thus the sterol composition of membranes. 
     Changes in BR concentration in the surrounding environment or in contact with a plant result in modulation of many genes and gene products. Examples of such BR responsive genes and gene products are shown in the Reference and Sequence Tables. These genes and/or products are responsible for effects on traits such as plant biomass and seed yield. These genes were discovered and characterized from a much larger set of genes by experiments designed to find genes whose mRNA abundance changed in response to application of BRs to plants. 
     While BR responsive polynucleotides and gene products can act alone, combinations of these polynucleotides also affect growth and development. Useful combinations include different BR responsive polynucleotides and/or gene products that have similar transcription profiles or similar biological activities, and members of the same or functionally related biochemical pathways. Whole pathways or segments of pathways are controlled by transcription factors and proteins controlling the activity of signal transduction pathways. Therefore, manipulation of such protein levels is especially useful for altering phenotypes and biochemical activities of plants. In addition, the combination of a BR responsive polynucleotide and/or gene product with another environmentally responsive polynucleotide is useful because of the interactions that exist between hormone-regulated pathways, stress pathways, nutritional pathways and development. Here, in addition to polynucleotides having similar transcription profiles and/or biological activities, useful combinations include polynucleotides that may have different transcription profiles but which participate in common or overlapping pathways. The MA_diff Table(s) reports the transcript levels of the experiment (see EXPT ID: 108580, 108581, 108557, 108478, 108479, 108480, 108481). For transcripts that had higher levels in the samples than the control, a “+” is shown. A “−” is shown for when transcript levels were reduced in root tips as compared to the control. For more experimental detail see the Example section below. 
     BR genes are those sequences that showed differential expression as compared to controls, namely those sequences identified in the MA_diff tables with a “+” or “−” indication. 
     BR Genes Identified by Cluster Analyses of Differential Expression 
     BR Genes Identified by Correlation to Genes that are Differentially Expressed 
     As described above, the transcription profiles of genes that act together are well correlated. Applicants not only have identified the genes that are differentially expressed in the microarray experiments, but also have identified the genes that act in concert with them. The MA_clust table indicates groups of genes that have well correlated transcription profiles and therefore participate in the same pathway or network. 
     A pathway or network of BR genes is any group in the MA_clust that comprises a cDNA ID that also appears in Expt ID 108580, 108581, 108557, 108478, 108479, 108480, 108481 of the MA_diff table(s). 
     BR Genes Identified by Correlation to Genes that Cause Physiological Consequences 
     Additionally, the differential expression data and the phenotypic observations can be merged to identify pathways or networks of BR genes. A group in the MA_clust is considered a BR pathway or network if the group comprises a cDNA ID that also appears in Knock-in or Knock-out tables that causes one or more of the phenotypes described in section above. 
     BR Genes Identified by Amino Acid Sequence Similarity 
     BR genes from other plant species typically encode polypeptides that share amino acid similarity to the sequences encoded by corn and  Arabidopsis  BR genes. Groups of BR genes are identified in the Protein Group table. In this table, any protein group that comprises a peptide ID that corresponds to a cDNA ID member of a BR pathway or network is a group of proteins that also exhibits BR functions/utilities. 
     Such BR responsive genes and gene products can function to either increase or dampen the above phenotypes or activities either in response to changes in BR concentration or in the absence of BR fluctuations. Further, promoters of BR responsive genes, as described in the Reference tables, for example, are useful to modulate transcription that is induced by BR or any of the following phenotypes or biological activities below. 
     III.C.3.a. Use of Brassinosteroid Responsive Genes to Modulate Phenotypes 
     Brassinosteroid responsive genes and gene products are useful to modulate one or more phenotypes including growth (promotes cell elongation, elongation accelerated at low temperatures for increased plant growth in marginal lands, acts in concert with other hormones to promote cell division); roots (inhibitory to root growth, and expression in roots would inhibit bud breaking due to higher auxin:cytokinin ratio in epicotyl); stems (inhibits radial growth while causing stem elongation, in low concentrations, promotes radial expansion, and increases biomass); height; seeds; promotes cell expansion in embryo and thus enhances germination; leaves; increase biomass; flowers, increase reproduction; biomass; fresh and dry weight during any time in plant life, such as maturation; number of flowers; number of seeds; number of branches; number of leaves; starch content; seed yield (including number, size, weight, harvest index, starch content; fruit yield, number, size, weight, harvest index, and starch content); development; morphogenesis; control of organ size and shape; development of new ornamentals; control of leaf size and shape; promotes leaf unrolling and enlargement; for development of new leafy ornamentals; seed development; inhibition of de-etiolation; dormancy; accelerated germination at low temperatures; root; gravitropism; senescence; promoted in light grown plants; inhibiting synthesis or perception could extend life span of desired tissues/organs; differentiation; vascularization; promotes xylem differentiation; increases xylem fiber length; resistance responses; increases resistance to pathogens; and tropic responses. 
     Gravitropic Responses Affecting Roots 
     Further, any desired sequence can be transcribed in similar temporal, tissue, or environmentally specific patterns as the BR responsive genes when the desired sequence is operably linked to a promoter of a BR responsive gene. 
     To improve any of the desired phenotype(s) above, activities of one or more of the BR response genes or gene products can be modulated and the plants tested by screening for the desired trait. Specifically, the gene, mRNA levels, or protein levels can be altered in a plant utilizing the procedures described herein and the phenotypes can be assayed. As an example, a plant can be transformed according to Bechtold and Pelletier (1998, Methods. Mol. Biol. 82:259-266, and/or screened for variants as in Winkler et al. (1998) Plant Physiol 118: 743-50, visually inspected for the desired phenotype and metabolically and/or functionally assayed according to Choe et al. (1999, Plant Cell 11:207-21 and Plant Physiol 119: 897-907), Yamamoto et al. (1997, Plant Cell Physiol 38:980-3), Asami and Yshida (1999, Trends in Plant Sciences, 4:348-353) and Azpiroz et al. (1998, Plant Cell 10:219-230) 
     III.C.3.b. Use of Brassinosteroid Responsive Genes to Modulate Biochemical Activities 
     The activities of one or more of the BR responsive genes can be modulated to change biochemical or metabolic activities and/or pathways such as those noted below. Such biological activities are documented and can be measured according to the citations included in the Table below: 
     
       
         
           
               
               
               
             
               
                   
               
               
                   
                 BIOCHEMICAL OR 
                   
               
               
                   
                 METABOLIC ACTIVITIES 
                 CITATIONS 
               
               
                 PROCESS 
                 AND/OR PATHWAYS 
                 INCLUDING ASSAYS 
               
               
                   
               
             
            
               
                 BR Transport 
                 BR Efflux Between Cells 
                 B. Schulz and 
               
               
                   
                   
                 K. Feldmann, unpub. 
               
               
                   
                   
                 results 
               
               
                   
                 BR Influx In And Out Of A 
                 B. Schulz and 
               
               
                   
                 Cell 
                 K. Feldmann, unpub. 
               
               
                   
                   
                 results 
               
               
                 Signal 
                 Permeability Of Cell 
               
               
                 Transduction 
                 Membranes 
               
               
                   
                 Protein Phosphorylation 
               
               
                 Metabolism 
                 Major Growth Coordinating 
               
               
                   
                 Pathways 
               
               
                   
               
            
           
         
       
     
     Other biological activities that can be modulated by the BR responsive genes and gene products are listed in the Reference Tables. Assays for detecting such biological activities are described in the Domain section of the Reference Tables. 
     BR responsive genes are differentially transcribed in response to fluctuating BR levels or concentrations, whether internal or external to an organism or cell. The MA_diff table(s) report(s) the changes in transcript levels of various BR responsive genes in the aerial parts of a seedling at 1 and 6 hours after a plant was sprayed with a solution enriched with BR as compared to seedlings sprayed with water. The data from this time course can be used to identify a number of types of BR responsive genes and gene products, including “early responders,” “delayed responders.” Profiles of these different categories of BR responsive genes are shown in the Table below together with examples of the kinds of associated biological activities. 
                                                     EXAMPLES OF       TRANSCRIPT       PHYSIOLOGICAL   BIOCHEMICAL       LEVELS   TYPE OF GENES   CONSEQUENCES   ACTIVITY                  Up Regulated   Early   BR Perception   Transcription       Transcripts   Responders   BR Transport   Factors       (Level At 1 Hr ≈ 6 Hr)   To BR   BR Biosynthesis   Receptors       (Level At 1 Hr &gt; 6 Hr)       Feedback   Transporters               Modulation Of   Change In Cell               BR Response   Membrane Structure               Transduction   Feedback Regulated               Pathways   Biosynthetic Genes               Specific Gene   Kinases And               Transcription   Phosphatases               Initiation   2 nd  Messengers, Eg.,                   Calmodulin                   Transcription                   Activators                   Change In                   Chromatin Structure                   And/Or Localized                   DNA Topology       Up Regulated   Delayed   Maintenance Of   Transcription       Transcripts   Responders   Response To Br   Factors       (Level At 1 Hr &lt; 6 Hr)       Cell And Organ   BR Biosynthetic               Elongation   Genes               Gravitropism   Specific Factors                   (Initiation And                   Elongation) For                   Protein Synthesis                   Maintenance Of                   Mrna Stability                   Maintenance Of                   Protein Stability                   Maintenance Of                   Protein-Protein                   Interaction                   Cell Wall                   Elongation       Down-Regulated   Early Responder   Negative   Transcription       Transcripts   Repressors Of BR   Regulation Of BR   Factors       (Level At 1 Hr ≈ 6 Hr)   State Of   Pathways   Change In Protein       (Level At 6 Hr &gt; 1 Hr)   Metabolism   Released   Structure By           Genes With   Changes In   Phosphorylation           Discontinued   Pathways And   (Kinases) Or           Expression Or   Processes   Dephosphoryaltion           UnsTable Mrna In   Operating In   (Phosphatases)           Presence Of   Cells   Change In           BR       Chromatin Structure                   And/Or DNA                   Topology       Down-Regulated   Delayed   Negative   Transcription       Transcripts   Repressors Of   Regulation Of BR   Factors       (Level At 1 Hr &gt; 6 Hr)   BR State Of   Pathways   Kinases And           Metabolism   Released   Phosphatases           Genes With   Maintenance Of   Stability Of Factors           Discontinued   Pathways   For Protein           Expression Or   Released From   Synthesis And           UnsTable Mrna   Repression   Degradation           In Presence Of   Changes In           BR   Pathways And               Processes               Operating In               Cells                    
Use of Promoters of BR Responsive Genes
 
     Promoters of BR responsive genes are useful for transcription of any desired polynucleotide or plant or non-plant origin. Further, any desired sequence can be transcribed in a similar temporal, tissue, or environmentally specific patterns as the BR responsive genes where the desired sequence is operably linked to a promoter of a BR responsive gene. The protein product of such a polynucleotide is usually synthesized in the same cells, in response to the same stimuli as the protein product of the gene from which the promoter was derived. Such promoter are also useful to produce antisense mRNAs to down-regulate the product of proteins, or to produce sense mRNAs to down-regulate mRNAs via sense suppression. 
     III.C.4. Cytokinin Responsive Genes, Gene Components and Products 
     Plant hormones are naturally occurring substances, effective in very small amounts, which act as signals to stimulate or inhibit growth or regulate developmental processes in plants. Cytokinins (BA) are a group of hormones that are best known for their stimulatory effect on cell division, although they also participate in many other processes and pathways. All naturally occurring BAs are aminopurine derivatives, while nearly all synthetic compounds with BA activity are 6-substituted aminopurine derivatives. One of the most common synthetic BAs used in agriculture is benzylaminopurine (BAP). 
     Changes in BA concentration in the surrounding environment or in contact with a plant results in modulation of many genes and gene products. Examples of such BA responsive genes and gene products are shown in the Reference, Sequence, Protein Group, Protein Group Matrix tables, MA_diff and MA_clust. These genes and/or products are responsible for effects on traits such as plant vigor and seed yield. They were discovered and characterized from a much larger set by experiments designed to find genes whose mRNA products changed in response to application of BA to plants. 
     While cytokinin responsive polynucleotides and gene products can act alone, combinations of these polynucleotides also affect growth and development. Useful combinations include different BA responsive polynucleotides and/or gene products that have similar transcription profiles or similar biological activities, and members of the same or functionally related biochemical pathways. Whole pathways or segments of pathways are controlled by transcription factor proteins and proteins controlling the activity of signal transduction pathways. Therefore, manipulation of such protein levels is especially useful for altering phenotypes and biochemical activities of plants. In addition, the combination of a BA responsive polynucleotide and/or gene product with another environmentally responsive polynucleotide is also useful because of the interactions that exist between hormone-regulated pathways, stress pathways, nutritional pathways and development. Here, in addition to polynucleotides having similar transcription profiles and/or biological activities, useful combinations include polynucleotides that may have different transcription profiles but which participate in common or overlapping pathways. The MA_diff Table(s) reports the transcript levels of the experiment (see EXPT ID: 108566, 108567, 108517). For transcripts that had higher levels in the samples than the control, a “+” is shown. A “−” is shown for when transcript levels were reduced in root tips as compared to the control. For more experimental detail see the Example section below. 
     BA genes are those sequences that showed differential expression as compared to controls, namely those sequences identified in the MA_diff tables with a “+” or “−” indication. 
     BA Genes Identified by Cluster Analyses of Differential Expression 
     BA Genes Identified by Correlation to Genes that are Differentially Expressed 
     As described above, the transcription profiles of genes that act together are well correlated. Applicants not only have identified the genes that are differentially expressed in the microarray experiments, but also have identified the genes that act in concert with them. The MA_clust table indicates groups of genes that have well correlated transcription profiles and therefore participate in the same pathway or network. 
     A pathway or network of BA genes is any group in the MA_clust that comprises a cDNA ID that also appears in Expt ID 108566, 108567, 108517 of the MA_diff table(s). 
     BA Genes Identified by Correlation to Genes that Cause Physiological Consequences 
     Additionally, the differential expression data and the phenotypic observations can be merged to identify pathways or networks of BA genes. A group in the MA_clust is considered a BA pathway or network if the group comprises a cDNA ID that also appears in Knock-in or Knock-out tables that causes one or more of the phenotypes described in section above. 
     BA Genes Identified by Amino Acid Sequence Similarity 
     BA genes from other plant species typically encode polypeptides that share amino acid similarity to the sequences encoded by corn and  Arabidopsis  BA genes. Groups of BA genes are identified in the Protein Group table. In this table, any protein group that comprises a peptide ID that corresponds to a cDNA ID member of a BA pathway or network is a group of proteins that also exhibits BA functions/utilities. 
     Such BA responsive genes and gene products can function to either increase or dampen the above phenotypes or activities either in response to changes in BA concentration or in the absence of BA fluctuations. 
     Further, promoters of BA responsive genes, as described in the Reference tables, for example, are useful to modulate transcription that is induced by BA or any of the following phenotypes or biological activities below. 
     III.C.4.a. Use of Ba-Responsive Genes to Modulate Phenotypes 
     BA responsive genes and gene products are useful to or modulate one or more phenotypes including growth, roots (such as inhibition of elongation of root); stems (such as inhibition of elongation of hypocotyl); lateral buds (such as promotion of outgrowth for rapid production of multiple shoots as a source for grafting); leaves such as development (including cell growth, such as expansion of cotyledon and promotes cell enlargement for increased yield from leaf crops, chloroplast development such as delayed degradation of chloroplasts for increased photosynthesis and crop yield, cell division and senescence such as delays for delayed conversion from photosynthesis to salvage programs in leaves and for increased crop yield); differentiation such as regulation of morphogenesis for manipulating callus growth and shoot/root formation in culture; maintenance of shoot meristem such as for increased usable wood production, and reduced tiller number for denser crop planting regimes; nutrient metabolism for effects on seed size and effects on rate of seed set for increased seed yield; induction of ethylene biosynthesis for control of fruit ripening; and parthenocarpy for control of sexual reproduction and production of seedless fruits. 
     To regulate any of the phenotype(s) above, activities of one or more of the BA responsive genes or gene products can be modulated and the plants tested by screening for the desired trait. Specifically, the gene, mRNA levels, or protein levels can be altered in a plant utilizing the procedures described herein and the phenotypes can be assayed. As an example, a plant can be transformed according to Bechtold and Pelletier (1998, Methods. Mol. Biol. 82:259-266) and/or screened for variants as in Winkler et al. (1998) Plant Physiol 118: 743-50 and visually inspected for the desired phenotype or molecularly or metabolically or functionally assayed according to Lohman et al (1994, Physil. Plant 92:322-328), Woolhouse (1983, In Agricultural Research-Strategies of Plant reproduction, Meudt, ed., 201-236), Medford et al. (1989, Plant Cell 1: 403-13), Vogel et al. (1998, Genetics 149:417-27), Ehnes and Roitsch (1997, Plant J 1: 539-48), Rotino et al. (1997, Nat. Biotchnol. 15: 1398-1401). 
     III.C.4.b. Use of Ba-Responsive Genes to Modulate Biochemical Activities 
     The activities of one or more of the BA responsive genes can be modulated to change biochemical or metabolic activities and/or pathways such as those noted below. Such biological activities can be measured according to the citations included in the Table below: 
     
       
         
           
               
               
               
             
               
                   
               
               
                   
                 BIOCHEMICAL OR 
                   
               
               
                   
                 METABOLIC 
               
               
                   
                 ACTIVITIES AND/OR 
                 CITATIONS 
               
               
                 PROCESS 
                 PATHWAYS 
                 INCLUDING ASSAYS 
               
               
                   
               
             
            
               
                 Chloroplast Functioning 
                 Photosynthesis 
                 Benkova et al (1999) Plant 
               
               
                   
                   
                 Physil 121: 245-252 
               
               
                 Induction And Maintenance 
                 Cell Cycle Phase Transition 
                 Riou-Khamlichi et al. 
               
               
                 Of Cell Division 
                   
                 (1999) Science 283: 1541-44 
               
               
                 Senescence 
                 Cell Death/Apoptosis 
                 Lohman et al. (1994) 
               
               
                   
                   
                 Physiol Plant 92: 322-328 
               
               
                 Signal Transduction 
                 Sensing Endogenous Stimuli 
                 Kakimoto (1996) Science 
               
               
                   
                 To Trigger Growth And 
                 274: 982-985 
               
               
                   
                 Shoot Formation 
               
               
                   
               
            
           
         
       
     
     Other biological activities that can be modulated by the BA responsive genes and gene products are listed in the Reference tables. Assays for detecting such biological activities are described in the Domain section above. 
     BA responsive genes are characteristically differentially transcribed in response to fluctuating BA levels or concentrations, whether internal or external to an organism or cell. The MA_diff table reports the changes in transcript levels of various BA responsive genes in the aerial parts of a seedling at 1 and 6 hours after a plant was sprayed with a Hoagland&#39;s solution enriched with BA as compared to seedlings sprayed with Hoagland&#39;s solution only. 
     The data from this time course can be used to identify a number of types of BA responsive genes and gene products, including “early responders,” and “delayed responders.” Profiles of these different BA responsive genes are shown in the Table below together with examples of the kinds of associated biological activities. 
     
       
         
           
               
               
               
               
             
               
                   
               
               
                 GENE 
                 FUNCTIONAL 
                 TYPE OF 
                 EXAMPLES OF 
               
               
                 EXPRESSION 
                 CATEGORY OF 
                 BIOLOGICAL 
                 BIOCHEMICAL 
               
               
                 LEVELS 
                 GENES 
                 ACTIVITY 
                 ACTIVITY 
               
               
                   
               
             
            
               
                 Up Regulated 
                 Early 
                 BA Perception 
                 Transcription Factors 
               
               
                 Transcripts 
                 Responders To 
                 BA Uptake 
                 Transporters 
               
               
                 (Level At 1 h ≅ 6 h) 
                 BA 
                 Modulation Of BA 
                 Kinase, Receptor-Like 
               
               
                 Or 
                   
                 Response 
                 Protein Kinase 
               
               
                 (Higher At 1 h 
                   
                 Transduction 
               
               
                 Than 6 h) 
                   
                 Pathways 
               
               
                   
                   
                 Specific Gene 
                 Ovule-Specific Homeotic 
               
               
                   
                   
                 Transcription 
                 Protein, Secretory 
               
               
                   
                   
                 Initiation 
                 Pathway 
               
               
                   
                   
                 Initiate And 
                 Cell Division Control 
               
               
                   
                   
                 Coordinate Cell 
                 Protein, Cyclins, Cyclin- 
               
               
                   
                   
                 Division 
                 Dependent Protein 
               
               
                   
                   
                   
                 Kinase (Cdpk), Cell 
               
               
                   
                   
                   
                 Cycle Phosphatases, 
               
               
                   
                   
                   
                 Mitosis-Specific 
               
               
                   
                   
                   
                 Chromosome 
               
               
                   
                   
                   
                 Segregation Protein, 
               
               
                   
                   
                   
                 Mitotic Phosphoprotein, 
               
               
                   
                   
                   
                 Dna Replication Proteins, 
               
               
                   
                   
                   
                 Helicase Telomerase, 
               
               
                   
                   
                   
                 Centromere Protein, 
               
               
                   
                   
                   
                 tRNA Synthase 
               
               
                   
                   
                 Regulation Of 
                 Senescence-Associated 
               
               
                   
                   
                 Pathways To 
                 Protein, Bifunctional 
               
               
                   
                   
                 Senescence 
                 Nuclease, Aba Pathway 
               
               
                   
                   
                   
                 Genes, Ethylene Pathway 
               
               
                   
                   
                   
                 Genes, Proteases, 
               
               
                   
                   
                   
                 Nucleases, Pcd Genes 
               
               
                   
                   
                 Modulation Of 
                 Calvin Cycle, 
               
               
                   
                   
                 Chloroplast Gene 
                 Chlorophyll A/B Binding 
               
               
                   
                   
                 Expression And 
                 Protein (Cab), 
               
               
                   
                   
                 Photosysthesis 
                 Transketolase, 
               
               
                   
                   
                   
                 Lipoxygenase, 
               
               
                   
                   
                   
                 Chloroplast Rna 
               
               
                   
                   
                   
                 Processing Protein, 
               
               
                   
                   
                   
                 Chloroplast Envelope 
               
               
                   
                   
                   
                 Membrane Protein. 
               
               
                   
                   
                 Modulation Of 
                 Glutamate Synthase, 
               
               
                   
                   
                 Photorespiration And 
                 Gogat, Asparagine 
               
               
                   
                   
                 Primary Nitrogen 
                 Synthase, Catalase, 
               
               
                   
                   
                 Assimilation In 
                 Peroxidase 
               
               
                   
                   
                 Leaves 
               
               
                   
                   
                 Expression 
               
               
                   
                   
                 Stress Response 
                 Heat Shock Proteins, 
               
               
                   
                   
                   
                 Gst 
               
               
                   
                   
                 Wax Biosynthesis 
                 Fatty Acid Elongase- 
               
               
                   
                   
                   
                 Like Protein, Very-Long- 
               
               
                   
                   
                   
                 Chain Fatty Acid 
               
               
                   
                   
                   
                 Condensing Enzyme, Coa 
               
               
                   
                   
                   
                 Synthase 
               
               
                   
                   
                 Nutrient Metabolism 
                 Vicilin Storage Protein 
               
               
                   
                   
                 Embryogenesis 
                 Homeobox Domain 
               
               
                   
                   
                   
                 Proteins 
               
               
                   
                   
                 Glycolysis, 
                 Mutase, 
               
               
                   
                   
                 Gluconeogenesis 
                 Phosphoglycerate Mutase 
               
               
                   
                   
                 Ripening 
                 Pectate Lyase, Ethylene 
               
               
                   
                   
                   
                 Pathway Genes 
               
               
                 Upregulated 
                 BA Late 
                 BA Responsive 
                 Transfactors, Kinases, 
               
               
                 Transcripts 
                 Responders 
                 Pathways 
                 Phosphatases, LRR&#39;s, 
               
               
                 (Higher At 6 h 
                   
                   
                 Dna Remodelling 
               
               
                 Than 1 h) 
                   
                   
                 Proteins, Cu-Binding 
               
               
                   
                   
                   
                 Proteins 
               
               
                   
                   
                 Cell Wall Extension 
                 Expansins, Extensins, 
               
               
                   
                   
                   
                 Proline Rich Proteins 
               
               
                   
                   
                 Organogenesis 
                 AP2 Domain Containing 
               
               
                   
                   
                   
                 Proteins 
               
               
                   
                   
                 Modulate Activation 
                 Transfactors Interacting 
               
               
                   
                   
                 Of Disease Defense 
                 With Resistant Genes 
               
               
                   
                   
                 Genes 
               
               
                   
                   
                 Modulate Responses 
                 Glycin-Rich Proteins, 
               
               
                   
                   
                 To External Stimuli 
                 Wall-Associated 
               
               
                   
                   
                   
                 Receptor Kinase (Wak) 
               
               
                   
                   
                 Osmotic Stress 
                 Proline Oxidase 
               
               
                   
                   
                 Tolerance 
               
               
                 Down-Regulated 
                 Repressors Of BA 
                 Regulation Of 
                 Transfactors (Such As 
               
               
                 Transcripts (Low 
                 Pathway 
                 Senescence-Related 
                 Zinc-Finger Type), 
               
               
                 At Both 1 h and 
                   
                 Gene Expression 
                 Kinases, Phosphatases, 
               
               
                 6 h) 
                   
                   
                 G-Proteins, LRR 
               
               
                   
                   
                   
                 Proteins, DNA 
               
               
                   
                   
                   
                 Remodeling Protein 
               
               
                   
                   
                   
                 Carbonyl Reductases 
               
               
                   
                   
                 Regulation Of Genes 
                 Atpases 
               
               
                   
                   
                 Involved In 
                 Oxygenase 
               
               
                   
                   
                 Maintenance Of 
                 Octaprenyltransferase 
               
               
                   
                   
                 Apical Dominance. 
                 Auxin Pathway Genes 
               
               
                   
                   
                   
                 Auxin Binding Proteins 
               
               
                   
               
            
           
         
       
     
     Further, any desired sequence can be transcribed in similar temporal, tissue, or environmentally specific patterns as the BA responsive genes when the desired sequence is operably linked to a promoter of a BA responsive gene. 
     III.C.5. Gibberellic Acid Responsive Genes, Gene Components and Products 
     Plant hormones are naturally occurring substances, effective in very small amounts, which act as signals to stimulate or inhibit growth or regulate developmental processes in plants. Gibberellic acid (GA) is a hormone in vascular plants that is synthesized in proplastids (giving rise to chloroplasts or leucoplasts) and vascular tissues. The major physiological responses affected by GA are seed germination, stem elongation, flower induction, anther development and seed and pericarp growth. GA is similar to Auxins, cytokinins and gibberellins, in that they are principally growth promoters. 
     Changes in GA concentration in the surrounding environment or in contact with a plant result in modulation of many genes and gene products. Examples of such GA responsive genes and gene products are shown in the Reference and Sequence Tables. These genes and/or products are responsible for effects on traits such as plant vigor and biomass and seed yield. They were discovered and characterized from a much larger set of genes by experiments designed to find genes whose mRNA products changed in concentration in response to application of nitrogen to plants. 
     While GA responsive polynucleotides and gene products can act alone, combinations of these polynucleotides also affect growth and development. Useful combinations include different GA responsive polynucleotides and/or gene products that have similar transcription profiles or similar biological activities, and members of the same or similar biochemical pathways. Whole pathways and/or segments of pathways are controlled by transcription factors and proteins that affect the activity of signal transduction pathways. Therefore, manipulation of such protein levels is especially useful for altering phenotypes and biochemical activities of plants. In addition, the combination of a GA responsive polynucleotide and/or gene product with another environmentally responsive polynucleotide is also useful because of the interactions that exist between hormone-regulated pathways, stress pathways, nutritional pathways and development. Here, in addition to polynucleotides having similar transcription profiles and/or biological activities, useful combinations include polynucleotides that may have different transcription profiles but which participate in common overlapping pathways. The MA_diff Table(s) reports the transcript levels of the experiment (see EXPT ID: 108562, 108563, 108519, 108520, 108521, 108484, 108485, 108486). For transcripts that had higher levels in the samples than the control, a “+” is shown. A “−” is shown for when transcript levels were reduced in root tips as compared to the control. For more experimental detail see the Example section below. 
     GA genes are those sequences that showed differential expression as compared to controls, namely those sequences identified in the MA_diff tables with a “+” or “−” indication. 
     GA Genes Identified by Cluster Analyses of Differential Expression 
     GA Genes Identified by Correlation to Genes that are Differentially Expressed 
     As described above, the transcription profiles of genes that act together are well correlated. Applicants not only have identified the genes that are differentially expressed in the microarray experiments, but also have identified the genes that act in concert with them. The MA_clust table indicates groups of genes that have well correlated transcription profiles and therefore participate in the same pathway or network. 
     A pathway or network of GA genes is any group in the MA_clust that comprises a cDNA ID that also appears in Expt ID 108562, 108563, 108519, 108520, 108521, 108484, 108485, 108486 of the MA_diff table(s). 
     GA Genes Identified by Correlation to Genes that Cause Physiological Consequences 
     Additionally, the differential expression data and the phenotypic observations can be merged to identify pathways or networks of GA genes. A group in the MA_clust is considered a GA pathway or network if the group comprises a cDNA ID that also appears in Knock-in or Knock-out tables that causes one or more of the phenotypes described in section above. 
     GA Genes Identified by Amino Acid Sequence Similarity 
     GA genes from other plant species typically encode polypeptides that share amino acid similarity to the sequences encoded by corn and  Arabidopsis  GA genes. Groups of GA genes are identified in the Protein Group table. In this table, any protein group that comprises a peptide ID that corresponds to a cDNA ID member of a GA pathway or network is a group of proteins that also exhibits GA functions/utilities. 
     Such GA responsive genes and gene products can function to either increase or dampen the above phenotypes or activities either in response to changes in GA concentration or in the absence of GA fluctuations. Further, promoters of GA responsive genes, as described in the Reference tables, for example, are useful to modulate transcription that is induced by GA or any of the following phenotypes or biological activities below. 
     III.C.5.a. Use of GA Responsive Genes to Modulate Phenotypes: 
     GA responsive genes and gene products are useful to or modulate one or more phenotypes including growth, promotes root growth, promotes cell division, promotes stem elongation, secondary (woody) growth, promotes growth in leaves, biomass, increase in stem and leaf mass, increase in xylem fiber length and biomass production, development, cell growth, fruit development, seed development, dormancy, breaks dormancy in seeds and buds, promotes trichome formation, decrease senescence, regulation of ferility, stress responses, and flowering time. 
     Further, any desired sequence can be transcribed in similar temporal, tissue, or environmentally specific patterns as the GA responsive genes when the desired sequence is operably linked to a promoter of a GA responsive gene. 
     To regulate any of the phenotype(s) above, activities of one or more of the GA response genes or gene products can be modulated and tested by screening for the desired trait. Specifically, the gene, mRNA levels, or protein levels can be altered in a plant utilizing the procedures described herein and the phenotypes can be assayed. As an example, a plant can be transformed according to Bechtold and Pelletier (1998, Methods. Mol. Biol. 82:259-266) and visually inspected for the desired phenotype or metabolically and/or functionally assayed according to Hedden and Proebsting (1999, Plant Physiol. 119:365-370), Hedden and Phillips (1999, Current Opinion in Plant Biotech. 11:130-137), Perazza et al (1998, Plant Physiol. 117:375-383), Kende and Zeevart (1997, Plant Cell 9:1197-1210) and van der Knaap et al. (2000, Plant Physiol. 122:695-704). 
     III.C.5.b. Use of GA-Responsive Genes to Modulate Biochemical Activities: 
     The activities of one or more of the GA responsive genes can be modulated to change biochemical or metabolic activities and/or pathways such as those noted below. Such biological activities can be measured according to the citations included in the Table below: 
     
       
         
           
               
               
               
             
               
                   
               
               
                   
                 BIOCHEMICAL OR 
                   
               
               
                   
                 METABOLIC ACTIVITIES 
                 CITATIONS 
               
               
                 PROCESS 
                 AND/OR PATHWAYS 
                 INCLUDING ASSAYS 
               
               
                   
               
             
            
               
                 Cell Growth 
                 Biosynthesis of Gas 
                 Hedden and Proebsting 
               
               
                 and 
                   
                 (1999, Plant Physiol. 
               
               
                 Differentiation 
                   
                 119: 365-370) 
               
               
                   
                 Cell wall loosening and cell 
                 Cosgrove (1993, New 
               
               
                   
                 expansion 
                 Phytol. 124: 1-23) 
               
               
                   
                 GA deactivation 
                 Hedden and Proebsting 
               
               
                   
                 Major growth promoting 
                 (1999, Plant Physiol. 
               
               
                   
                 metabolic pathways 
                 119: 365-370) 
               
               
                 Perception 
                 Receptors 
                 Koornneef and van der 
               
               
                 and Signal 
                   
                 Veen (1980, TAG 58: 
               
               
                 Transduction 
                   
                 257-263) 
               
               
                   
                 Synthesis of transcriptional 
                 Bethke and Jones 
               
               
                   
                 regulators 
                 (1998, Curr. Opin. Plant 
               
               
                   
                 Calcium and Calmodulin 
                 Biol. 1: 440-446) 
               
               
                   
               
            
           
         
       
     
     Other biological activities that can be modulated by the GA responsive genes and gene products are listed in the Reference Tables. Assays for detecting such biological activities are described in the Protein Domain table. 
     GA responsive genes are characteristically differentially transcribed in response to fluctuating GA levels or concentrations, whether internal or external to an organism or cell. The MA_diff table(s) report(s) the changes in transcript levels of various GA responsive genes in entire seedlings at 1 and 6 hours after a plant was sprayed with a Hoagland&#39;s solution enriched with GA as compared to seedlings sprayed with Hoagland&#39;s solution only. 
     The data from this time course can be used to identify a number of types of GA responsive genes and gene products, including “early responders,” and “delayed responders.” Profiles of some GA responsive genes are shown in the Table below with examples of associated biological activities. 
                                                     EXAMPLES OF       TRANSCRIPT       PHYSIOLOGICAL   BIOCHEMICAL       LEVELS   TYPE OF GENES   CONSEQUENCES   ACTIVITY                  Up regulated   Early responders to   GA perception   Transcription factors       transcripts   GA   GA transport   Transporters       (level at 1 hr ≈ 6 hr)   Genes induced by   Modulation of GA   Change in cell       (level at 1 hr &gt; 6 hr)   GA   response transduction   membrane structure               pathways   Kinases and               Specific gene   phosphatases               transcription   Transcription activators               initiation   Change in chromatin               Growth stimulating   structure and/or               pathway induction   localized DNA topology                   Cell wall proteins                   Metabolic Enzymes       Up regulated   Maintenance of GA   Maintenance of   Transcription factors       transcripts   response   response to GA   Specific factors       (level at 1 hr &lt; 6 hr)   “Delayed”   Induction of GA   (initiation and           responders   metabolic pathways   elongation) for protein                   synthesis                   Maintenance of mRNA                   stability                   Metabolic enzymes       Down-regulated   Early repressor   Negative regulation   Transcription factors       transcripts   responders to GA   of GA pathways   Calmodulin       (level at 1 hr ≈ 6 hr)   Genes repressed by   released   Change in protein       (level at 6 hr &gt; 1 hr)   GA   Reduced activity of   structure by phosphorylation           Genes whose   repressed pathways   (kinases) or           activities are       dephosphoryaltion           diminished or       (phosphatases)           mRNAs are       Change in chromatin           unsTable in the       structure and/or DNA           presence of GA       topology       Down-regulated   Delayed responders   Maintenance or GA   Transcription factors       transcripts   Genes repressed by   repressed pathways   Kinases and       (level at 1 hr &gt; 6 hr)   GA       phosphatases           Genes whose       Stability factors for           activities are       protein translation           diminished or       Metabolic enzymes           mRNAs are           unsTable in the           presence of GA                    
Use of Promoters of GA Responsive Genes
 
     Promoters of GA responsive genes are useful for transcription of any desired polynucleotide or plant or non-plant origin. Further, any desired sequence can be transcribed in a similar temporal, tissue, or environmentally specific patterns as the GA responsive genes where the desired sequence is operably linked to a promoter of a GA responsive gene. The protein product of such a polynucleotide is usually synthesized in the same cells, in response to the same stimuli as the protein product of the gene from which the promoter was derived. Such promoter are also useful to produce antisense mRNAs to down-regulate the product of proteins, or to produce sense mRNAs to down-regulate mRNAs via sense suppression. 
     III.D. Metabolism Affecting Genes, Gene Components and Products 
     III.D.1. Nitrogen Responsive Genes, Gene Components and Products 
     Nitrogen is often the rate-limiting element in plant growth, and all field crops have a fundamental dependence on exogenous nitrogen sources. Nitrogenous fertilizer which is usually supplied as ammonium nitrate, potassium nitrate, or urea, typically accounts for 40% of the costs associated with crops, such as corn and wheat in intensive agriculture. Increased efficiency of nitrogen use by plants should enable the production of higher yields with existing fertilizer inputs and/or enable existing yields of crops to be obtained with lower fertilizer input, or better yields on soils of poorer quality. Also, higher amounts of proteins in the crops could also be produced more cost-effectively. 
     Changes in nitrogen concentration in the surrounding environment or in contact with a plant results in modulation of the activities of many genes and hence levels of gene products. Examples of such “nitrogen responsive” genes and gene products with these properties are shown in the Reference, Sequence, Protein Group, Protein Group Matrix tables, MA_diff, MA_clust, Knock-in and Knock-out tables. These genes and/or products are responsible for effects on traits such as plant vigor and seed yield. They were discovered and characterized from a much larger set by experiments designed to find genes whose mRNA products changed in response to changing levels of available nitrogen to plants. 
     Manipulation of one or more “nitrogen responsive” gene activities is useful to modulate the biological activities and/or phenotypes listed below. “Nitrogen responsive” genes and gene products can act alone or in combination. Useful combinations include nitrogen responsive genes and/or gene products with similar transcription profiles, similar biological activities, or members of the same or functionally related biochemical pathways. Whole pathways or segments of pathways are controlled by transcription factor proteins and proteins controlling the activity of signal transduction pathways. Therefore, manipulation of the levels of such proteins is especially useful for altering phenotypes and biochemical activities of plants. The MA_diff Table(s) reports the transcript levels of the experiment (see EXPT ID: 108592, 108593, 108588, 108589, 108590, 108591, 108532, 108548, 108549, 108550, 108551, 108454, 108455, 108487, 108488, 108489, and Nitrogen (relating to SMD 3787, SMD 3789)). For transcripts that had higher levels in the samples than the control, a “+” is shown. A “−” is shown for when transcript levels were reduced in root tips as compared to the control. For more experimental detail see the Example section below. 
     Nitrogen genes are those sequences that showed differential expression as compared to controls, namely those sequences identified in the MA_diff tables with a “+” or “−” indication. 
     Nitrogen Genes Identified by Cluster Analyses of Differential Expression 
     Nitrogen Genes Identified by Correlation to Genes that are Differentially Expressed 
     As described above, the transcription profiles of genes that act together are well correlated. Applicants not only have identified the genes that are differentially expressed in the microarray experiments, but also have identified the genes that act in concert with them. The MA_clust table indicates groups of genes that have well correlated transcription profiles and therefore participate in the same pathway or network. 
     A pathway or network of Nitrogen genes is any group in the MA_clust that comprises a cDNA ID that also appears in Expt ID 108592, 108593, 108588, 108589, 108590, 108591, 108532, 108548, 108549, 108550, 108551, 108454, 108455, 108487, 108488, 108489, and Nitrogen (relating to SMD 3787, SMD 3789) of the MA_diff table(s). 
     Nitrogen Genes Identified by Correlation to Genes that Cause Physiological Consequences 
     Additionally, the differential expression data and the phenotypic observations can be merged to identify pathways or networks of Nitrogen genes. A group in the MA_clust is considered a Nitrogen pathway or network if the group comprises a cDNA ID that also appears in Knock-in or Knock-out tables that causes one or more of the phenotypes described in section above. 
     Nitrogen Genes Identified by Amino Acid Sequence Similarity 
     Nitrogen genes from other plant species typically encode polypeptides that share amino acid similarity to the sequences encoded by corn and  Arabidopsis  Nitrogen genes. Groups of Nitrogen genes are identified in the Protein Group table. In this table, any protein group that comprises a peptide ID that corresponds to a cDNA ID member of a Nitrogen pathway or network is a group of proteins that also exhibits Nitrogen functions/utilities. 
     Such “nitrogen responsive” genes and gene products can function either to either increase or dampen the phenotypes and activities below, either in response to changes in nitrogen concentration or in the absence of nitrogen fluctuations. 
     Further, promoters of nitrogen responsive genes, as described in the Reference tables, for example, are useful to modulate transcription that is induced by nitrogen or any of the following phenotypes or biological activities below. 
     III.D.5.a. Use of Nitrogen-Responsive Genes to Modulate Phenotypes 
     “Nitrogen responsive” genes and gene products can be used to alter or modulate one or more phenotypes including plant development, initiation of the reproduction cycle from a vegetative state (such as flower development time and time to fruit maturity); root development and initiation (such as root branching, lateral root, initiation and/or development, nodule formation and nitrogen assimilation from any nitrogen-fixing symbions), growth rate, whole plant (including height, flowering time, etc.), organs (such as flowers, fruits, stems, leaves, roots, and lateral roots), biomass (such as fresh and dry weight during any time in plant life, such as maturation); number, size, and weight of flowers; seeds; branches, and leaves); total plant nitrogen content, amino acid/protein content of whole plant or parts, seed yield (such as number, size, weight, harvest index and content and composition, e.g., amino acid, nitrogen, oil, protein, and carbohydrate) and fruit yield (such as number, size, weight, harvest index, content and composition, e.g., amino acid, nitrogen, oil, protein, carbohydrate, and water. 
     To regulate any of the phenotype(s) above, activities of one or more of the nitrogen responsive genes or gene products can be modulated and the plants can be tested by screening for the desired trait. Specifically, the gene, mRNA levels, or protein levels can be altered in a plant utilizing the procedures described herein and the phenotypes can be screened for variants as in Winkler et al. (1998) Plant Physiol 118: 743-50 and assayed, for example, in accordance to Zhang (1999) Proc. Natl. Acad. Sci. 96(11): 6529-34; or Zhang and Forde (1998) Science 279(5349):407-9; Scheible, W., Lauerer, M., Schultze, E.-D., Caboche, M., and Sitt, M. (1997). Plant J. 11, 671-691; Chevalier C, Bourgeois E, Just D, Raymond P. Plant J. 1996 January; 9(1):1-11. 
     III.D.5.b. Use of Nitrogen-Responsive Genes to Modulate Biochemical Activities 
     The activities of one or more of the nitrogen responsive genes can be modulated to change biochemical or metabolic activities and/or pathways such as those noted below. Such biological activities are documented and can be measured according to the citations included in the Table below: 
     
       
         
           
               
               
               
             
               
                   
               
               
                   
                 Biochemical Or Metabolic 
                   
               
               
                   
                 Activities And/Or 
               
               
                 Process 
                 Pathways 
                 Citations including assays 
               
               
                   
               
             
            
               
                 Nitrate And Ammonium 
                 NO 3   −  Influx And Efflux 
                 Lejay et al. (1999) Plant J. 18(5): 
               
               
                 Uptake and Assimilation 
                   
                 509-519 
               
               
                   
                 Nitrate Channels 
                 Liu et al. (1999) Plant Cell 11: 865-874; 
               
               
                   
                   
                 and 
               
               
                   
                   
                 Wang et al.(1998) Proc. Natl. Acad. 
               
               
                   
                   
                 Sci. USA 95: 15134-15139 
               
               
                   
                 Changes In Membrane- 
                 Meharg et al. (1995) J. Membr. 
               
               
                   
                 Potential 
                 Biol. 145: 49-66; and 
               
               
                   
                   
                 Wang et al. (1998), supra 
               
               
                 Amino Acid Synthesis 
                 Glutamine Synthesis And 
                 Coruzzi et al. U.S. Pat. No. 
               
               
                   
                 Then Biosynthesis Of Other 
                 5,955,651; and 
               
               
                   
                 Amino Acids 
                 Oliveira et al. (1999) Plant. Phys. 
               
               
                   
                   
                 121: 301-309 
               
               
                   
                 Asparagine Synthesis And 
                 LAM ET AL. (1998) PLANT J. 
               
               
                   
                 Then Biosynthesis Of Other 
                 16(3): 345-353 
               
               
                   
                 Amino Acids 
               
               
                 Coordination Of Carbon 
                 Light-Regulation Of Major 
                 Lam et al. (1998), supra; 
               
               
                 And Nitrogen Metabolism 
                 Central Carbon And 
                 Lejay et al. (1999), supra; and 
               
               
                   
                 Nitrogen Metabolic 
                 Oliveira et al. (1999), supra 
               
               
                   
                 Pathways To Coordinate 
               
               
                   
                 Growth 
               
               
                   
                 Carbohydrate And Nitrogen 
                 Lam et al. (1998) supra; 
               
               
                   
                 Control Of Carbohydrate 
                 Lejay et al. (1999) supra; and 
               
               
                   
                 And Organic Nitrogen 
                 Oliveira et al. (1999) supra 
               
               
                   
                 Accumulation Pathways 
               
               
                 Nitrogen Loading And 
                 Nitrogen Transport From 
                 Walker et al. (1999) 210(1): 9-18 
               
               
                 Unloading 
                 Source To Sinks 
                 Elsheikh et al. (1997) 
               
               
                   
                   
                 51(2): 137-44. 
               
               
                 Nitrogen Storage 
                 Accumulation Of Amino 
                 Johnson et al. (1990) Plant Cell 
               
               
                   
                 Acids And/Or Storage 
                 2(6): 525-32. 
               
               
                   
                 Proteins In Vacuoles 
                 Herman and Larkins (1999) Plant 
               
               
                   
                   
                 Cell. 11(4): 601-14. 
               
               
                 Ammonium 
                 Plastid Ammonium 
                 Crawford (1995) Plant Cell 
               
               
                 Detoxification 
                 Storage/Glutamine 
                 7(7): 859-68. 
               
               
                   
                 Synthesis 
                 Zhang and Forde (1998) Science 
               
               
                   
                   
                 279: 407-409. 
               
               
                 Cell Growth 
                 DIVISION AND/OR 
                 Zhang and Forde (1998) Science 
               
               
                   
                 ELONGATION 
                 279: 407-409. 
               
               
                   
                   
                 Coruzzi et al. U.S. Pat. No. 
               
               
                   
                   
                 5,955,651 
               
               
                   
               
            
           
         
       
     
     Other biological activities that can be modulated by the nitrogen responsive genes and their products are listed in the Reference tables. Assays for detecting such biological activities are described in the Domain section above. 
     Nitrogen responsive genes are characteristically differentially transcribed in response to fluctuating nitrogen levels or concentrations, whether internal or external to an organism or cell. The MA_diff table reports the changes in transcript levels of various nitrogen responsive genes in the aerial parts of a seedling at 2, 6, 9 and 12 hours after a plant was sprayed with a solution enriched with ammonium nitrate as compared to seedlings sprayed with water. The MA_diff reports the changes in transcript levels of various nitrogen responsive genes in roots at 12 and 24 hours that were cut from seedlings transferred from a high to low potassium nitrate environment compared to control seedlings transferred to a high potassium nitrate environment. 
     The data from this time course reveal a number of types of nitrogen responsive genes and gene products, including “early responders,” and “delayed nitrogen responders”. Profiles of the individual categories of nitrogen responsive genes are shown in the Tables below together with examples of the kinds of associated biological activities that are modulated when the activities of one or more such genes vary in plants. 
     
       
         
           
               
            
               
                   
               
               
                 Low to High Ammonium Nitrate Experiment 
               
            
           
           
               
               
               
               
            
               
                   
                 Functional 
                   
                   
               
               
                 Gene Expression 
                 Category Of 
                 Physiological 
                 Examples Of Gene 
               
               
                 Levels 
                 Gene 
                 Consequences 
                 Products 
               
               
                   
               
               
                 Upregulated 
                 Early 
                 Perception Of 
                 Transcription Factors 
               
               
                 Transcripts 
                 Responders To 
                 Nitrogen 
                 Transporters 
               
               
                 (Level At 2 h ≅ 6, 
                 Nitrogen 
                 Induced Nitrogen 
                 Inhibitors Of Nitrogen 
               
               
                 9 Or 12 h) Or 
                   
                 Uptake Into Cells 
                 Fixation 
               
               
                 (Level At 2 h &gt; 6, 
                   
                 Induction Of Nitrogen 
                 Components Of Pathways 
               
               
                 9 Or 12 h) 
                   
                 Response Transduction 
                 Released From Repression 
               
               
                   
                   
                 Pathways 
                 Transaminases 
               
               
                   
                   
                 Initiation Of Specific 
                 Amino Acid Biosynthetic 
               
               
                   
                   
                 Gene Transcription 
                 Enzymes 
               
               
                 Upregulated 
                 Delayed 
                 Maintenance Of High 
                 Nitrogen Metabolic 
               
               
                 Transcripts 
                 Nitrogen 
                 Nitrogen Metabolism 
                 Pathway Enzymes 
               
               
                 (Level At 2 h &lt; 6, 
                 Responders 
                 And Growth 
                 Transaminases 
               
               
                 9, Or 12 h 
                   
                   
                 Amino Acid Biosynthetic 
               
               
                   
                   
                   
                 Enzymes 
               
               
                   
                   
                   
                 Factors Induced In 
               
               
                   
                   
                   
                 Coordination And Control 
               
               
                   
                   
                   
                 Of Central Carbon And 
               
               
                   
                   
                   
                 Nitrogen Metabolism 
               
               
                   
                   
                   
                 Cell Wall And Cell 
               
               
                   
                   
                   
                 Growth-Promoting 
               
               
                   
                   
                   
                 Pathway Enzymes 
               
               
                   
                   
                   
                 Storage Proteins 
               
               
                 Down Regulated 
                 Early 
                 Negative Regulation 
                 Transcription Factors 
               
               
                 Transcripts 
                 Responder 
                 Of Nitrogen Utilization 
                 Kinases And Phosphatases 
               
               
                 (Level At 2 h ≅ 6, 
                 Repressors Of 
                 Pathways Released 
                 Cytoskeletal Proteins 
               
               
                 9 Or 12 h) Or 
                 Nitrogen 
                 Pathways Of C And N 
                 Modulating Cell Structure 
               
               
                 (Level At 6, 9 Or 
                 Utilization 
                 Metabolism Required 
                 Chromatin Structure 
               
               
                 12 h &gt; 2 h) 
                 Pathways 
                 At Lower Levels 
                 Regulatory Proteins 
               
               
                   
                 Genes With 
                 Decline In Presence Of 
                 Metabolic Enzymes 
               
               
                   
                 Discontinued 
                 High Nitrogen 
                 Transporters 
               
               
                   
                 Expression Or 
                   
                 Proteins And Rna 
               
               
                   
                 UnsTable Mrna 
                   
                 Turnover Systems 
               
               
                   
                 Following 
               
               
                   
                 Nitrogen 
               
               
                   
                 Uptake 
               
               
                 Level At 2 Hours &gt; 
                 Delayed 
                 Negative Regulation 
                 Transcription Factors 
               
               
                 6, 9 Or 12 Hours 
                 Response 
                 Of Nitrogen Utilization 
                 Kinases And Phosphatases 
               
               
                   
                 Repressors Of 
                 Pathways Released 
                 Cytoskeletal Proteins 
               
               
                   
                 Nitrogen 
                 Pathways Of C And N 
                 Modulating Cell Structure 
               
               
                   
                 Utilization 
                 Metabolism Required 
                 Chromatin Structure 
               
               
                   
                 Pathways 
                 At Lower Levels 
                 Regulatory Proteins 
               
               
                   
                 Genes With 
                 Decline In Presence Of 
                 Metabolic Enzymes 
               
               
                   
                 Discontinued 
                 High Nitrogen 
                 Transporters 
               
               
                   
                 Expression Or 
                   
                 Protein And Rna Turnover 
               
               
                   
                 UnsTable Mrna 
                   
                 Systems 
               
               
                   
                 Following 
               
               
                   
                 Nitrogen 
               
               
                   
                 Uptake 
               
               
                   
               
            
           
         
       
     
     
       
         
           
               
            
               
                   
               
               
                 High to Low Potassium Nitrate Experiments 
               
            
           
           
               
               
               
               
            
               
                   
                 Functional 
                   
                 Examples Of Biochemical 
               
               
                 Gene Expression 
                 Category Of 
                 Type Of Biological 
                 Activities Of Gene 
               
               
                 Levels 
                 Gene 
                 Activity 
                 Products 
               
               
                   
               
               
                 Upregulated 
                 Early Responders 
                 Perception Of Low 
                 Transcription Factors - 
               
               
                 Transcripts (Level 
                 To Low Nitrate 
                 Nitrate 
                 Controlling Transcription 
               
               
                 At 12 h~24 h) 
                   
                 Nitrogen Uptake Into 
                 Transporters - Facilitating 
               
               
                 (Level At 
                   
                 Cells 
                 Transport 
               
               
                 12 h &gt; 24 h) 
                   
                 Low Nitrogen Signal 
                 Cell Wall/Membrane 
               
               
                   
                   
                 Transduction Response 
                 Structure Determining 
               
               
                   
                   
                 Pathways 
                 Proteins 
               
               
                   
                   
                 Initiation Of Specific 
                 Kinases And 
               
               
                   
                   
                 Gene Transcription 
                 Phosphatases- 
               
               
                   
                   
                 Initiation Of Nitrogen 
                 Regulating Signal 
               
               
                   
                   
                 Fixation 
                 Transduction Pathways 
               
               
                   
                   
                   
                 Cytoskeletal Proteins- 
               
               
                   
                   
                   
                 Modulating Cell Structure 
               
               
                   
                   
                   
                 Chromatin Structure 
               
               
                   
                   
                   
                 And/Or Dna Topology 
               
               
                   
                   
                   
                 Proteins 
               
               
                   
                   
                   
                 Protein-Protein Interaction 
               
               
                   
                   
                   
                 Participants 
               
               
                   
                   
                   
                 Metabolic Enzymes- 
               
               
                   
                   
                   
                 Nitrogen Turnover Enzymes 
               
               
                   
                   
                   
                 And Pathway Components 
               
               
                 Upregulated 
                 Delayed Low 
                 Maintenance Of Low 
                 Transcription Factors - 
               
               
                 Transcripts 
                 Nitrate 
                 Nitrogen Response 
                 Controlling Transcription 
               
               
                 (Level 12 h &lt; 24 h) 
                 Responders 
                 Pathways (See the Table 
                 Transporters - Facilitating 
               
               
                   
                   
                 Above) 
                 Transport 
               
               
                   
                   
                   
                 Cell Wall/Membrane 
               
               
                   
                   
                   
                 Structure Determining 
               
               
                   
                   
                   
                 Proteins 
               
               
                   
                   
                   
                 Kinases And 
               
               
                   
                   
                   
                 Phosphatases- 
               
               
                   
                   
                   
                 Regulating Signal 
               
               
                   
                   
                   
                 Transduction Pathways 
               
               
                   
                   
                   
                 Cytoskeletal Proteins- 
               
               
                   
                   
                   
                 Modulating Cell Structure 
               
               
                   
                   
                   
                 Chromatin Structure 
               
               
                   
                   
                   
                 And/Or Dna Topology 
               
               
                   
                   
                   
                 Proteins 
               
               
                   
                   
                   
                 Protein-Protein Interaction 
               
               
                   
                   
                   
                 Participants 
               
               
                   
                   
                   
                 Metabolic Enzymes- 
               
               
                   
                   
                   
                 Nitrogen Turnover Enzymes 
               
               
                   
                   
                   
                 And Pathway Components 
               
               
                 Down-Regulated 
                 Early Repressor 
                 Negative Regulation Of 
                 Transcription Factors 
               
               
                 Transcripts (Level 
                 Responders To 
                 Low Nitrogen-Mediated 
                 Cell Wall/Membrane 
               
               
                 At 12 h~24 h) 
                 Low Nitrate 
                 Pathways And/Or 
                 Structure Determining 
               
               
                 (Level At 
                 Genes Whose 
                 Responses Released 
                 Proteins 
               
               
                 12 h &gt; 24 h) 
                 Expression Is 
                 Pathways In C And N 
                 Factors For Promoting 
               
               
                   
                 Discontinued Or 
                 Metabolism Required At 
                 Protein Translation 
               
               
                   
                 Mrna Is UnsTable 
                 Lower Levels Decline In 
                 Kinases And 
               
               
                   
                 In Presence Of 
                 The Presence Of Low 
                 Phosphatases 
               
               
                   
                 Low Nitrate 
                 Nitrate 
                 Cytoskeletal Proteins- 
               
               
                   
                   
                   
                 Modulating Cell Structure 
               
               
                   
                   
                   
                 Protein And Rna Turnover 
               
               
                   
                   
                   
                 Systems 
               
               
                 Down-Regulated 
                 Delayed 
                 Negative Regulation Of 
                 Transcription Factors 
               
               
                 Transcripts 
                 Repressor 
                 Low Nitrogen-Mediated 
                 Cell Wall/Membrane 
               
               
                 (Level At 
                 Responders To 
                 Pathways And/Or 
                 Structure Determining 
               
               
                 12 h &lt; 24 h) 
                 Low Nitrate 
                 Responses Released 
                 Proteins 
               
               
                   
                 Genes Whose 
                 Pathways In C And N 
                 Factors For Promoting 
               
               
                   
                 Expression Is 
                 Metabolism Required At 
                 Protein Translation 
               
               
                   
                 Discontinued Or 
                 Lower Levels Decline In 
                 Kinases And 
               
               
                   
                 mRNA Is 
                 The Presence Of Low 
                 Phosphatases 
               
               
                   
                 UnsTable In 
                 Nitrate 
                 Cytoskeletal Proteins- 
               
               
                   
                 Presence Of Low 
                   
                 Modulating Cell Structure 
               
               
                   
                 Nitrate 
                   
                 Protein And Rna Turnover 
               
               
                   
                   
                   
                 Systems 
               
               
                   
                   
                   
                 Chromatin Structure 
               
               
                   
                   
                   
                 And/Or Dna Topology 
               
               
                   
                   
                   
                 Proteins 
               
               
                   
               
            
           
         
       
     
     Further, any desired sequence can be transcribed in similar temporal, tissue, or environmentally specific patterns as the nitrogen responsive genes when the desired sequence is operably linked to a promoter of a nitrogen responsive gene. 
     III.D.2. Circadian Rhythm (Clock) Responsive Genes, Gene Components and Products 
     Often growth and yield are limited by the ability of a plant to tolerate stress conditions, including water loss. To combat such conditions, plant cells deploy a battery of responses that are controlled by an internal circadian clock, including the timed movement of cotyledons and leaves, timed movements in guard cells in stomata, and timed biochemical activities involved with sugar and nitrogen metabolism. These responses depend on the functioning of an internal circadian clock, that becomes entrained to the ambient light/dark cycle, and a series of downstream signaling events leading to transcription independent and transcription dependent stress responses. 
     A functioning circadian clock can anticipate dark/light transitions and prepare the physiology and biochemistry of a plant accordingly. For example, expression of a chlorophyll a/b binding protein (CAB) is elevated before daybreak, so that photosynthesis can operate maximally as soon as there is light to drive it. Similar considerations apply to light/dark transitions and to many areas of plant physiology such as sugar metabolism, nitrogen metabolism, water uptake and water loss, flowering and flower opening, epinasty, germination, perception of season, and senescence. 
     Manipulation of one or more clock gene activities is useful to modulate the biological processes and/or phenotypes listed below. Clock responsive genes and gene products can act alone or in combination. Useful combinations include clock responsive genes and/or gene products with similar transcription profiles, similar biological activities, or members of the same or functionally related biochemical pathways. Whole pathways or segments of pathways are controlled by transcription factor proteins and proteins controlling the activity of signal transduction pathways. Therefore, manipulation of such protein levels is especially useful for altering phenotypes and biochemical activities of plants. The MA_diff Table(s) reports the transcript levels of the experiment (see EXPT ID: Circadian (relating to SMD 2344, SMD 2359, SMD 2361, SMD 2362, SMD 2363, SMD 2364, SMD 2365, SMD 2366, SMD 2367, SMD 2368, SMD 3242)). For transcripts that had higher levels in the samples than the control, a “+” is shown. A “−” is shown for when transcript levels were reduced in root tips as compared to the control. For more experimental detail see the Example section below. 
     Circadian genes are those sequences that showed differential expression as compared to controls, namely those sequences identified in the MA_diff tables with a “+” or “−” indication. 
     Circadian Genes Identified by Cluster Analyses of Differential Expression 
     Circadian Genes Identified by Correlation to Genes that are Differentially Expressed 
     As described above, the transcription profiles of genes that act together are well correlated. Applicants not only have identified the genes that are differentially expressed in the microarray experiments, but also have identified the genes that act in concert with them. The MA_clust table indicates groups of genes that have well correlated transcription profiles and therefore participate in the same pathway or network. 
     A pathway or network of Circadian genes is any group in the MA_clust that comprises a cDNA ID that also appears in Expt ID Circadian (relating to SMD 2344, SMD 2359, SMD 2361, SMD 2362, SMD 2363, SMD 2364, SMD 2365, SMD 2366, SMD 2367, SMD 2368, SMD 3242) of the MA_diff table(s). 
     Circadian Genes Identified by Correlation to Genes that Cause Physiological Consequences 
     Additionally, the differential expression data and the phenotypic observations can be merged to identify pathways or networks of Circadian genes. A group in the MA_clust is considered a Circadian pathway or network if the group comprises a cDNA ID that also appears in Knock-in or Knock-out tables that causes one or more of the phenotypes described in section above. 
     Circadian Genes Identified by Amino Acid Sequence Similarity 
     Circadian genes from other plant species typically encode polypeptides that share amino acid similarity to the sequences encoded by corn and  Arabidopsis  Circadian genes. Groups of Circadian genes are identified in the Protein Group table. In this table, any protein group that comprises a peptide ID that corresponds to a cDNA ID member of a Circadian pathway or network is a group of proteins that also exhibits Circadian functions/utilities. 
     Such clock responsive genes and gene products can function to either increase or dampen the above phenotypes or activities either in response to changes in daylength or in response to changes in light quality. Further, promoters of cirdadian (clock) responsive genes, as described in the Reference tables, for example, are useful to modulate transcription that is induced by circadian or any of the following phenotypes or biological activities below. Further, any desired sequence can be transcribed in similar temporal, tissue, or environmentally specific patterns as the circadian (clock) responsive genes when the desired sequence is operably linked to a promoter of a circadian (clock) responsive gene. 
     The expression of many genes is modulated by the clock. Microarray technology allows monitoring of gene expression levels for thousands of genes in a single experiment. This is achieved by hybridizing labeled fluorescent cDNA pools to glass slides that contain spots of DNA (Schena et al. (1995) Science 270: 467-70). The US  Arabidopsis  Functional Genomics Consortium (AFGC) has recently made public the results from such microarray experiments conducted with AFGC chips containing some 10,000 non-redundant ESTs, selected from about 37,000 randomly sequenced ESTs generated from mRNA of different tissues and developmental stages. 
     The sequences of the ESTs showing at least two-fold increases or decreases in response to the circadian rhythm clock at various times through the 24 hour cycle relative to the controls were identified, compared to the Ceres full length cDNA and genomic sequence databanks, and equivalent Ceres clones identified. The MA_diff table reports the results of this analysis, indicating those Ceres clones which are up or down regulated over controls, thereby indicating the Ceres clones which represent clock responsive genes. 
     III.D.2.a. Use of Circadian Rhythm (Clock) Responsive Genes to Modulate Phenotypes 
     Clock responsive genes and gene products are useful to or modulate one or more phenotypes including timing phenotypes, dormancy, germination, cotyledon opening, first leaves, juvenile to adult transition, bolting, flowering, pollination, fertilization, seed development, seed set, fruit drop, senescence, epinasty, biomass, fresh and dry weight during any time in plant life, such as maturation, number of flowers, seeds, branches, and/or leaves, seed yield, including number, size, weight, and/or harvest index, fruit yield, including number, size, weight, and/or harvest index, plant development, time to fruit maturity, cell wall strengthening and reinforcement, stress tolerance, drought tolerance, flooding tolerance, and uv tolerance 
     To regulate any of the phenotype(s) above, activities of one or more of the clock responsive genes or gene products can be modulated and the plants can be tested by screening for the desired trait. Specifically, the gene, mRNA levels, or protein levels can be altered in a plant utilizing the procedures described herein and the phenotypes can be screened for variants as in Anderson et al. (1997) Plant Cell 9: 1727-1743; Heintzen et al. (1997) Proc. Natl. Acad. Sci. USA 94: 8515-20; Schaffer et al. (1998) Cell 93:1219-1229; Somers et al. (1998) Development 125: 485-494; Somers et al. (1998) Science 282: 1488-1490; Wang and Tobin (1998) Cell 93: 1207-1217; Zhong et al. (1998) Plant Cell 10: 2005-2017; Sugano et al. (1998) Proc. Natl. Acad. Sci. USA 95: 11020-11025; Dowson-Day and Millar (1999) Plant J 17: 63-71; Green and Tobin (1999) Proc. Natl. Acad. Sci. USA 96: 4176-419; Staiger and Apel (1999) Mol. Gen. Genet. 261: 811-819; Strayer and Kay (1999) Curr. Opin. Plant Biol. 2:114-120; Strayer et. al. (2000) Science 289:768-771; Kreps et al. (2000) J Biol Rhythms (2000) 15:208-217; Nelson et al. (2000) Cell 101:331-340; Somers et al. (2000) Cell 101:319-329. 
     III.D.2.b. Use of Active Clock Responsive Genes to Modulate Biochemical Activities 
     The activities of one or more of the clock responsive genes can be modulated to change biochemical or metabolic activities and/or pathways such as those noted below. Such biological activities are documented and can be measured according to the citations above and included in the Table below: 
     
       
         
           
               
               
               
             
               
                   
               
               
                   
                 BIOCHEMICAL OR 
                   
               
               
                   
                 METABOLIC 
               
               
                   
                 ACTIVITIES 
                 CITATIONS INCLUDING 
               
               
                 PROCESS 
                 AND/OR PATHWAYS 
                 ASSAYS 
               
               
                   
               
             
            
               
                 Germination and seedling 
                 Cold, light and water modulated 
                 Bognar et al. (1999) Proc. 
               
               
                 development 
                 signal transduction pathways, 
                 Natl. Acad. Sci. USA 
               
               
                   
                 receptors, kinases, PAS domain 
                 96: 14652-14657; Sugano et al 
               
               
                   
                   
                 (1999) Proc. Natl. Acad. Sci. 
               
               
                   
                   
                 USA 96: 12362-12366; 
               
               
                   
                   
                 Dowson-Day and Millar 
               
               
                   
                   
                 (1999) Plant J 17: 63-71; 
               
               
                   
                   
                 Somers et al. (2000) Cell 
               
               
                   
                   
                 101: 319-329; Zhong et al. 
               
               
                   
                   
                 (1998) Plant Cell 10: 2005-2017 
               
               
                 Growth transitions and 
                 Cold and light modulated signal 
                 Nelson et al. (2000) Cell 
               
               
                 flowering 
                 transduction pathways, 
                 101: 331-340; Fowler et al. 
               
               
                   
                 receptors, kinases, PAS domain 
                 (1999) EMBO J. 18: 4679-4688 
               
               
                 Tuber formation 
                 Cold and light modulated signal 
                 Yanovsky et al. (2000) Plant 
               
               
                   
                 transduction pathways 
                 J. 23: 223-232 
               
               
                 METABOLISM 
               
               
                 Lipid metabolism 
                 Membrane lipid synthesis 
                 Bradley and Reddy (1997) J. 
               
               
                   
                 including omega-3 fatty acid 
                 Bacteriol. 179: 4407-4410; 
               
               
                   
                 desaturase, lipases, lipid 
                 Martin, M et al. 1999 Europe 
               
               
                   
                 transfer proteins 
                 J. Biochem 262: 283-290 
               
               
                 Sugar metabolism 
                 Glycosylhydrolases, 
                 Liu et al. (1996) Plant 
               
               
                   
                 glycosyltransferases, amylases, 
                 Physiol. 112: 43-51; Millar 
               
               
                   
                 sucrose synthase, CAB, 
                 and Kay (1996) Proc Natl 
               
               
                   
                 Rubisco, light signal 
                 Acad Sci USA 93: 15491-15496; 
               
               
                   
                 transduction 
                 Wang et al. (1997) 
               
               
                   
                   
                 Plant Cell 9: 491-507; 
               
               
                   
                   
                 Shinohara et al (1999) J. Biol. 
               
               
                   
                   
                 Chem. 273: 446-452 
               
               
                 Nitrogen metabolism 
                 Aminotransferases, arginase, 
                 Bradley and Reddy (1997) J. 
               
               
                   
                 proteases and vegetative storage 
                 Bacteriol. 179: 4407-4410 
               
               
                   
                 proteins, aromatic amino acid 
               
               
                   
                 synthesis 
               
               
                 Photorespiration 
                 Mitochondrial, chloroplast and 
                 Zhong and McClung (1996) 
               
               
                   
                 peroxisomal photorespiratory 
                 Mol. Gen. Genet. 251: 196-203; 
               
               
                   
                 enzymes, serine hydroxymethyl 
                 McClung (1997) Free. 
               
               
                   
                 transferases, catalase 
                 Radic. Biol. Med. 23: 489-496; 
               
               
                   
                   
                 McClung et al. (2000) 
               
               
                   
                   
                 Plant Physiol. 123: 381-392 
               
               
                 Responses to Environmental 
                 Expression of genes involved in 
                 McClung (1997) Free Radic 
               
               
                 Stress 
                 responses to drought, salt, UV 
                 Biol Med 23: 489-496; Shi et 
               
               
                   
                   
                 al. (2000) Proc. Natl. Acad. 
               
               
                   
                   
                 Sci. USA 97: 6896-6901 
               
               
                   
               
            
           
         
       
     
     Other biological activities that can be modulated by the clock responsive genes and their products are listed in the Reference tables. Assays for detecting such biological activities are described in the Protein Domain table. 
     Clock responsive genes are characteristically differentially transcribed in response to fluctuations in an entrained oscillator, which is internal to an organism and cell. The MA_diff table(s) report(s) the changes in transcript levels of various clock responsive genes in a plant. 
     Profiles of clock responsive genes are shown in the table below with examples of which associated biological activities are modulated when the activities of one or more such genes vary in plants. 
                                                     EXAMPLES OF       TRANSCRIPT       PHYSIOLOGICAL   BIOCHEMICAL       LEVELS   TYPE OF GENES   CONSEQUENCES   ACTIVITY                  Up regulated   Responders to   Circadian rhythm   Metabolic enzymes       transcripts   circadian rhythm   perception   Change in cell           Genes induced by rythm   Metabolisms   membrane structure               affected by   and potential               Circadian rhythm   Kinases and               Synthesis of   phosphatases               secondary   Transcription               metabolites   activators               and/or proteins   Change in               Modulation of   chromatin structure               clock response   and/or localized               transduction   DNA topology               pathways   Enzymes in lipid,               Specific gene   sugar and nitrogen               transcription   metabolism               initiation   Enzymes in                   photorespiration                   and photosynthesis       Down-regulated   Responders to   Negative   Transcription       transcripts   circadian rhythm.   regulation of   factors           Repressors of   circadian   Change in protein           circadian “state” of   pathways released   structure by           metabolism   Changes in   phosphorylation           Genes repressed by   pathways and   (kinases) or           rhythm   processes   dephosphoryaltion           Genes with   operating in cells   (phosphatases)           discontinued   Changes in   Change in           expression or   metabolism other   chromatin structure           unsTable mRNA in   than circadian   and/or DNA           presence of zinc   pathways   topology                   Stability of factors                   for protein                   synthesis and                   degradation                   Metabolic enzymes                   in light, sugar, lipid                   and nitrogen                   metabolism                    
Use of Promoters of Clock Responsive Genes
 
     Promoters of Clock responsive genes are useful for transcription of any desired polynucleotide or plant or non-plant origin. Further, any desired sequence can be transcribed in a similar temporal, tissue, or environmentally specific patterns as the Clock responsive genes where the desired sequence is operably linked to a promoter of a Clock responsive gene. The protein product of such a polynucleotide is usually synthesized in the same cells, in response to the same stimuli as the protein product of the gene from which the promoter was derived. Such promoter are also useful to produce antisense mRNAs to down-regulate the product of proteins, or to produce sense mRNAs to down-regulate mRNAs via sense suppression. 
     III.D.3. Blue Light (Phototropism) Responsive Genes, Gene Components and Products 
     Phototropism is the orientation or growth of a cell, an organism or part of an organism in relation to a source of light. Plants can sense red (R), far-red (FR) and blue light in their environment and respond differently to particular ratios of these. For example, a low R:FR ratio enhances cell elongation and favors flowering over leaf production, but blue light regulated cryptochromes also appear to be involved in determining hypocotyl growth and flowering time. 
     Phototropism of  Arabidopsis thaliana  seedlings in response to a blue light source is initiated by nonphototropic hypocotyl 1 (NPH1), a blue light-activated serine-threonine protein kinase, but the downstream signaling events are not entirely known. Blue light treatment leads to changes in gene expression. These genes have been identified by comparing the levels of mRNAs of individual genes in dark-grown seedlings, compared with in dark grown seedlings treated with 1 hour of blue light. Auxin also affects blue light phototropism. The effect of Auxin on gene expression stimulated by blue light has been explored by studying mRNA levels in a mutant of  Arabidopsis thaliana  nph4-2, grown in the dark and, treated with blue light for 1 hour compared with wild type seedlings treated similarly. This mutant is disrupted for Auxin-related growth and Auxin-induced gene transcription. Gene expression was studied using microarray technology. 
     Microarray technology allows monitoring of gene expression levels for thousands of genes in a single experiment. This is achieved by hybridizing labeled fluorescent cDNA pools to glass slides that contain spots of DNA (Schena et al. (1995) Science 270: 467-70). The US  Arabidopsis  Functional Genomics Consortium (AFGC) has recently made public the results from such microarray experiments conducted with AFGC chips containing some 10,000 non-redundant ESTs, selected from about 37,000 randomly sequenced ESTs generated from mRNA of different tissues and developmental stages. 
     The sequences of the ESTs showing at least two-fold increases or decreases over the controls were identified, compared to the Ceres full-length cDNA and genomic sequence databanks, and the equivalent Ceres clones identified. The MA_diff table(s)report(s) the results of this analysis, indicating those Ceres clones which are up or down regulated over controls, thereby indicating the Ceres clones which represent blue light responsive genes and of those which are blue light responsive in the absence of nph4 gene activity. The MA_diff Table(s) reports the transcript levels of the experiment (see EXPT ID: Phototropism (relating to SMD 4188, SMD 6617, SMD 6619)). For transcripts that had higher levels in the samples than the control, a “+” is shown. A “−” is shown for when transcript levels were reduced in root tips as compared to the control. For more experimental detail see the Example section below. 
     Blue Light genes are those sequences that showed differential expression as compared to controls, namely those sequences identified in the MA_diff tables with a “+” or “−” indication. 
     Blue Light Genes Identified by Cluster Analyses of Differential Expression 
     Blue Light Genes Identified by Correlation to Genes that are Differentially Expressed 
     As described above, the transcription profiles of genes that act together are well correlated. Applicants not only have identified the genes that are differentially expressed in the microarray experiments, but also have identified the genes that act in concert with them. The MA_clust table indicates groups of genes that have well correlated transcription profiles and therefore participate in the same pathway or network. 
     A pathway or network of Blue Light genes is any group in the MA_clust that comprises a cDNA ID that also appears in Expt ID Phototropism (relating to SMD 4188, SMD 6617, SMD 6619) of the MA_diff table(s). 
     Blue Light Genes Identified by Correlation to Genes that Cause Physiological Consequences 
     Additionally, the differential expression data and the phenotypic observations can be merged to identify pathways or networks of Blue Light genes. A group in the MA_clust is considered a Blue Light pathway or network if the group comprises a cDNA ID that also appears in Knock-in or Knock-out tables that causes one or more of the phenotypes described in section above. 
     Blue Light Genes Identified by Amino Acid Sequence Similarity 
     Blue Light genes from other plant species typically encode polypeptides that share amino acid similarity to the sequences encoded by corn and  Arabidopsis  Blue Light genes. Groups of Blue Light genes are identified in the Protein Group table. In this table, any protein group that comprises a peptide ID that corresponds to a cDNA ID member of a Blue Light pathway or network is a group of proteins that also exhibits Blue Light functions/utilities. 
     III.D.3.a. Use of Blue Light Responsive Genes, Gene Components and Products to Modulate Phenotypes 
     Changes in blue light in a plant&#39;s surrounding environment result in modulation of many genes and gene products. Examples of such blue light response genes and gene products are shown in the REFERENCE and SEQUENCE Tables. These genes and/or products are responsible for effects on traits such as plant vigor and seed yield. 
     While blue light responsive polynucleotides and gene products can act alone, combinations of these polynucleotides also affect growth and development. Useful combinations include different blue light responsive polynucleotides and/or gene products that have similar transcription profiles or similar biological activities, and members of the same or similar biochemical pathways. Whole pathways or segments of pathways are controlled by transcription factor proteins and proteins controlling the activity of signal transduction pathways. Therefore, manipulation of such protein levels is especially useful for altering phenotypes and biochemical activities of plants. In addition, the combination of a blue light responsive polynucleotides and/or gene product with other environmentally responsive polynucleotide is also useful because of the interactions that exist between hormone-regulated pathways, stress and pathogen induced pathways, nutritional pathways and development. Here, in addition to polynucleotides having similar transcription profiles and/or biological activities, useful combinations include polynucleotides that may have different transcription profiles but which participate in common or overlapping pathways. 
     III.D.3.b. Use of Blue Light Responsive Genes, Gene Components and Products to Modulate Phenotypes 
     Blue light responsive genes and gene products can function to either increase or dampen the above phenotypes or activities either in response to changes in blue light response concentration or in the absence of blue light responsive fluctuations. Further, promoters of blue light responsive genes, as described in the Reference tables, for example, are useful to modulate transcription that is induced by blue light or any of the following phenotypes or biological activities below. Further, any desired sequence can be transcribed in similar temporal, tissue, or environmentally specific patterns as the blue light responsive genes when the desired sequence is operably linked to a promoter of a blue light responsive gene. 
     Blue light responsive genes and gene products can be used to alter or modulate one or more phenotypes including growth, roots (elongation or gravitropism) and stems (such as elongation), development of cell (such as growth or elongation), flower (including flowering time), seedling (including elongation), plant yield, and seed and fruit yield. 
     To regulate any of the phenotype(s) above, activities of one or more of the blue light responsive genes or gene products can be modulated and the plants tested by screening for the desired trait. Specifically, the gene, mRNA levels, or protein levels can be altered in a plant utilizing the procedures described herein and the phenotypes can be assayed. As an example, a plant can be transformed according to Bechtold and Pelletier (1998, Methods. Mol. Biol. 82:259-266) and/or screened for variants as in Winkler et al. (1998) Plant Physiol 118: 743-50 and visually inspected for the desired phenotype or metabolically and/or functionally assayed according to Liscum and Briggs (1995, Plant Cell 7: 473-85), Vitha et al. (2000, Plant Physiol 122: 453-61), Stowe-Evance et al. (1998, Plant Physiol 118: 1265-75), Baum et al. (1999, PNAS USA 96: 13554-9), Huala et al. (1997) Science 278: 2120-2123), Kanegae et al. (2000, Plant Cell Physiol 41: 415-23), Khanna et al. (1999, Plant Mol Biol 39: 231-42), Sakai et al. (2000, Plant Cell 12: 225-36), Parks et al (1996, Plant Physiol 110: 155-62) and Janoudi et al. (1997, Plant Physiol 113: 975-79). 
     III.D.3.c. Use of Blue Light Responsive Genes, Gene Components and Products to Modulate Biochemical Activities 
     The activities of one or more of the blue light responsive genes can be modulated to change biochemical or metabolic activities and/or pathways such as those noted below. Such biological activities can be measured according to the citations included in the Table below: 
     
       
         
           
               
               
               
             
               
                   
               
               
                   
                 BIOCHEMICAL OR 
                   
               
               
                   
                 METABOLIC 
               
               
                   
                 ACTIVITIES 
                 CITATIONS INCLUDING 
               
               
                 PROCESS 
                 AND/OR PATHWAYS 
                 ASSAYS 
               
               
                   
               
             
            
               
                 Cell Growth 
                 Cell Elongation 
                 Liscum and Briggs (1995) Plant 
               
               
                 and 
                 Seedling 
                 Cell 7: 473-85 
               
               
                 Development 
                 Stem 
               
               
                   
                 Root 
                 Vitha et al. (2000) Plant Physiol 
               
               
                   
                   
                 122: 453-61 
               
               
                 Signalling 
                 UV light Perception 
                 Liscum and Briggs (1996) Plant 
               
               
                   
                   
                 Physiol 112: 291-96 
               
               
                   
                 Far-red/Red light 
                 Parks et al. (1996) Plant Physiol 
               
               
                   
                 Perception 
                 110: 155-62 
               
               
                   
                 Phosphorylation of 
                 Liscum and Briggs (1996) Plant 
               
               
                   
                 cellular and 
                 Physiol 112: 291-96 
               
               
                   
                 nuclear-localized proteins 
               
               
                   
                 Activation and Synthesis 
                 Sakae et al. (2000) Plant Cell 
               
               
                   
                 of Transcription Factors 
                 12: 225-36 
               
               
                   
                 Ca + 2 levels 
                 Baum et al. (1999) PNAS USA 
               
               
                   
                   
                 96: 13554-9 
               
               
                   
                   
                 Pu and Robinson (1998) J Cell 
               
               
                   
                   
                 Sci 111: 3197-3207 
               
               
                   
                 Auxin Concentration 
                 Estelle (1998) Plant Cell 10: 
               
               
                   
                   
                 1775-8 
               
               
                   
                   
                 Reed et al. (1998) Plant Physiol 
               
               
                   
                   
                 118: 1369-78 
               
               
                   
                 Inter-photoreceptors 
                 Janoudi et al. (1997) Plant 
               
               
                   
                   
                 Physiol 113: 975-79 
               
               
                   
               
            
           
         
       
     
     Other biological activities that can be modulated by blue light response genes and their products are listed in the REF Tables. Assays for detecting such biological activities are described in the Domain section of the REF Table. 
     The specific genes modulated by blue light, in wild type seedlings and in the mutant deficient in transmitting Auxin effects are given in the Reference and Sequence Tables. The kinds of genes discovered and some of their associated effects are given in the Table below. 
                                                     EXAMPLES OF       TRANSCRIPT       PHYSIOLOGICAL   BIOCHEMICAL       LEVELS   TYPE OF GENES   CONSEQUENCES   ACTIVITY                  Up regulated   Responders to no   Blue light   Transporters       transcripts   blue light in wild type   perception   Metabolic enzymes           or to blue light in   Metabolism   Change in cell           mutant lacking Auxin   affected by blue   membrane structure           effects   light   and potential               Synthesis of   Kinases and               secondary   phosphatases               metabolites and/or   Transcription               proteins   activators               Modulation of blue   Change in chromatin               light transduction   structure and/or               pathways   localized DNA               Specific gene   topology               transcription               initiation       Down-regulated   Responders to no   Blue light   Transcription factors       transcripts   blue light in wild type   perception   Change in protein           or to blue light in   Metabolism   structure by           mutants lacking   affected by blue   phosphorylation           Auxin effects   light   (kinases) or           Genes with   Synthesis of   dephosphorylation           discontinued   secondary   (phosphatases)           expression or   metabolites and/or   Change in chromatin           unsTable mRNA   proteins   structure and/or           during response   Modulation of blue   DNA topology               light transduction   Stability factors for               pathways   protein synthesis and               Specific gene   degradation               transcription   Metabolic enzymes               initiation               Changes in               pathways and               processes               operating in cells               Changes in               metabolic               pathways other               than phototropic               blue light               responsive               pathways                    
Use of Promoters of Blue Light Responsive Genes
 
     Promoters of Blue Light responsive genes are useful for transcription of any desired polynucleotide or plant or non-plant origin. Further, any desired sequence can be transcribed in a similar temporal, tissue, or environmentally specific patterns as the Blue Light responsive genes where the desired sequence is operably linked to a promoter of a Blue Light responsive gene. The protein product of such a polynucleotide is usually synthesized in the same cells, in response to the same stimuli as the protein product of the gene from which the promoter was derived. Such promoter are also useful to produce antisense mRNAs to down-regulate the product of proteins, or to produce sense mRNAs to down-regulate mRNAs via sense suppression. 
     III.D.4 Responsive Genes, Gene Components and Products 
     There has been a recent and significant increase in the level of atmospheric carbon dioxide. This rise in level is projected to continue over the next 50 years. The effects of the increased level of carbon dioxide on vegetation are just now being examined, generally in large scale, whole plant (often trees) experiments. Some researchers have initiated physiological experiments in attempts to define the biochemical pathways that are either affected by and/or are activated to allow the plant to avert damage from the elevated carbon dioxide levels. A genomics approach to this issue, using a model plant system, allows identification of those pathways affected by and/or as having a role in averting damage due to the elevated carbon dioxide levels and affecting growth. Higher agronomic yields can be obtained for some crops grown in elevated CO 2 . 
     Microarray technology allows monitoring of gene expression levels for thousands of genes in a single experiment. This is achieved by hybridizing labeled fluorescent cDNA pools to glass slides that contain spots of DNA (Schena et al. (1995) Science 270: 467-70). The U.S.  Arabidopsis  Functional Genomics Consortium (AFGC) has recently made public the results from such microarray experiments conducted with AFGC chips containing about 10,000 non-redundant ESTs, selected from about 37,000 randomly sequenced ESTs generated from mRNA of different tissues and developmental stages. 
     The sequences of the ESTs showing at least two-fold increases or decreases in plants grown in higher CO 2  levels compared with plants grown at more normal CO 2  levels, were compared to the Ceres full length cDNA and genomic sequence databanks, and equivalent Ceres clones were identified. The MA_diff table reports the results of this analysis, indicating those Ceres clones which are up or down regulated over controls, thereby indicating the Ceres clones cDNA sequences that change in response to CO 2 . 
     Examples of CO 2  responsive genes and gene products are shown in the Reference, Sequence, Protein Group, Protein Group Matrix tables, MA_diff and MA_clust tables. While CO 2  responsive polynucleotides and gene products can act alone, combinations of these polynucleotides also affect growth and development. Useful combinations include different CO 2  responsive polynucleotides and/or gene products that have similar transcription profiles or similar biological activities, and members of the same or similar biochemical pathways. Whole pathways or segments of pathways are controlled by transcription factor proteins and proteins controlling the activity of signal transduction pathways. Therefore, manipulation of such protein levels is especially useful for altering phenotypes and biochemical activities of plants. 
     Manipulation of one or more CO 2  responsive gene activities is useful to modulate the biological processes and/or phenotypes listed below. CO 2  responsive genes and gene products can act alone or in combination. Useful combinations include genes and/or gene products with similar transcription profiles, similar biological activities, or members of the same or functionally related biochemical pathways. Here, in addition to polynucleotides having similar transcription profiles and/or biological activities, useful combinations include polynucleotides that may have different transcription profiles but which participate in common or overlapping pathways. 
     CO 2  responsive genes and gene products can function to either increase or dampen the above phenotypes or activities. Further, promoters of CO 2  responsive genes, as described in the Reference tables, for example, are useful to modulate transcription that is induced by CO 2  or any of the following phenotypes or biological activities below. Further, any desired sequence can be transcribed in similar temporal, tissue, or environmentally specific patterns as the CO 2  responsive genes when the desired sequence is operably linked to a promoter of a CO 2  responsive gene. The MA_diff Table(s) reports the transcript levels of the experiment (see EXPT ID: CO2 (relating to SMD7561, SMD 7562, SMD 7261, SMD 7263, SMD 3710, SMD 4649, SMD 4650)). For transcripts that had higher levels in the samples than the control, a “+” is shown. A “−” is shown for when transcript levels were reduced in root tips as compared to the control. For more experimental detail see the Example section below. 
     CO2 genes are those sequences that showed differential expression as compared to controls, namely those sequences identified in the MA_diff tables with a “+” or “−” indication. 
     CO2 Genes Identified by Cluster Analyses of Differential Expression 
     CO2 Genes Identified by Correlation to Genes that are Differentially Expressed 
     As described above, the transcription profiles of genes that act together are well correlated. Applicants not only have identified the genes that are differentially expressed in the microarray experiments, but also have identified the genes that act in concert with them. The MA_clust table indicates groups of genes that have well correlated transcription profiles and therefore participate in the same pathway or network. 
     A pathway or network of CO2 genes is any group in the MA_clust that comprises a cDNA ID that also appears in Expt ID CO2 (relating to SMD7561, SMD 7562, SMD 7261, SMD 7263, SMD 3710, SMD 4649, SMD 4650) of the MA_diff table(s). 
     CO2 Genes Identified by Correlation to Genes that Cause Physiological Consequences 
     Additionally, the differential expression data and the phenotypic observations can be merged to identify pathways or networks of CO2 genes. A group in the MA_clust is considered a CO2 pathway or network if the group comprises a cDNA ID that also appears in Knock-in or Knock-out tables that causes one or more of the phenotypes described in section above. 
     CO2 Genes Identified by Amino Acid Sequence Similarity 
     CO2 genes from other plant species typically encode polypeptides that share amino acid similarity to the sequences encoded by corn and  Arabidopsis  CO2 genes. Groups of CO2 genes are identified in the Protein Group table. In this table, any protein group that comprises a peptide ID that corresponds to a cDNA ID member of a CO2 pathway or network is a group of proteins that also exhibits CO2 functions/utilities. 
     III.D.4.a. Use of Co2 Responsive Genes to Modulate Phenotypes 
     CO 2  responsive genes and gene products are useful to or modulate one or more phenotypes including catabolism, energy generation, atp, etc., metabolism, carbohydrate synthesis, growth rate, whole plant, including height, flowering time, etc., organs, flowers, fruits, stems, leaves, roots, lateral roots, biomass, fresh and dry weight during any time in plant life, such as maturation; number, size, and weight of flowers; seeds; branches; leaves; total plant nitrogen content, amino acid/protein content of whole plant or parts, seed yield (such as number, size, weight, harvest index, and content and composition, e.g., amino acid, nitrogen, oil, protein, and carbohydrate); fruit yield; number, size, weight, harvest index; content and composition, e.g., amino acid, nitrogen, oil, protein, carbohydrate, water; and photosynthesis (such as carbon dioxide fixation). 
     To improve any of the phenotype(s) above, activities of one or more of the CO 2  responsive genes or gene products can be modulated and the plants tested by screening for the desired trait. Specifically, the gene, mRNA levels, or protein levels can be altered in a plant utilizing the procedures described herein and the phenotypes can be assayed. As an example, a plant can be transformed according to Bechtold and Pelletier (1998, Methods. Mol. Biol. 82:259-266) and/or screened for variants as in Winkler et al. (1998) Plant Physiol 118: 743-50 and visually inspected for the desired phenotype or metabolically and/or functionally assayed according to Saito et al. (1994, Plant Physiol. 106: 887-95), Takahashi et al (1997, Proc. Natl. Acad. Sci. USA 94: 11102-07) and Koprivova et al. (2000, Plant Physiol. 122: 737-46). 
     III.D.2. Use of Co 2  Responsive Genes to Modulate Biochemical Activities 
     The activities of one or more of the CO 2  responsive genes can be modulated to change biochemical or metabolic activities and/or pathways such as those noted below. Such biological activities can be measured according to the citations included in the Table below: 
     
       
         
           
               
               
               
             
               
                   
               
               
                   
                 BIOCHEMICAL OR 
                   
               
               
                   
                 METABOLIC 
               
               
                 GENERAL 
                 ACTIVITIES 
                 CITATIONS INCLUDING 
               
               
                 CATEGORY 
                 AND/OR PATHWAYS 
                 ASSAYS 
               
               
                   
               
             
            
               
                 Cell Division 
                 Cell Cycle Control Genes 
                 Masle (2000) Plant 
               
               
                   
                   
                 Physiol. 122: 1399-1415 
               
               
                 Starch 
                 Starch Biosynthesis 
                 Ludewig et al., (1998) 
               
               
                 Biosynthesis 
                 Enzymes And Pathways 
                 FEBS Lett. 429: 147-151 
               
               
                 Photosynthesis 
                 Photosynthetic Enzymes, 
                 Cheng et al., (1998) Plant 
               
               
                   
                 e.g., Rubisco 
                 Physiol 166: 715-723 
               
               
                 Respiration 
                 Energy Metabolism 
                 Musgrave et al., (1986) 
               
               
                   
                 Pathways 
                 Proc. Natl. Acad. Sci. USA 
               
               
                   
                   
                 83: 8157-8161 
               
               
                 CO 2 Uptake 
                 Guard Cell Stomata 
                 Allen et al., Plant Cell 
               
               
                   
                 Control Systems 
                 (1999) 11(9): 1785-1798 
               
               
                   
                   
                 Ichida et al., Plant Cell 
               
               
                   
                   
                 (1997) 9(10): 1843-1857 
               
               
                   
                   
                 Hedrich et al., EMBO J 
               
               
                   
                   
                 (1993) 12(3): 897-901 
               
               
                 Coordination 
                 Light-Regulation Of Major 
                 Lam et al. (1998) Plant J. 
               
               
                 Of Carbon And 
                 Central Carbon And 
                 16(3): 345-353 
               
               
                 Nitrogen 
                 Nitrogen Metabolic 
                 Lejay et al. (1999) Plant J. 
               
               
                 Metabolism 
                 Pathways To Coordinate 
                 18(5): 509-519; and 
               
               
                   
                 Growth 
                 Oliveira et al. (1999) Plant. 
               
               
                   
                   
                 Phys. 121: 301-309 
               
               
                   
                 Carbohydrate And 
                 Lam et al. (1998) supra; 
               
               
                   
                 Nitrogen Control Of 
                 Lejay et al. (1999) supra; 
               
               
                   
                 Carbohydrate And Organic 
                 and 
               
               
                   
                 Nitrogen Accumulation 
                 Oliveira et al. (1999) supra 
               
               
                   
                 Pathways 
               
               
                   
               
            
           
         
       
     
     Other biological activities that can be modulated by the CO 2  responsive genes and gene products are listed in the Reference tables. Assays for detecting such biological activities are described in the Protein Domain table. 
     CO 2  responsive genes are characteristically differentially transcribed in response to fluctuating CO 2  levels or concentrations, whether internal or external to an organism or cell. The MA_diff tables report the changes in transcript levels of various CO 2  responsive genes that are differentially expressed in response to high CO 2  levels. 
     Profiles of these different CO 2  responsive genes are shown in the Table below with examples of associated biological activities. 
                                                     EXAMPLES OF       TRANSCRIPT       PHYSIOLOGICAL   BIOCHEMICAL       LEVELS   TYPE OF GENES   CONSEQUENCES   ACTIVITY                  Up   Responders   Changes In   Transporters       Regulated   To Higher   Generation Of ATP   Catabolic And       Transcripts   Levels Of   Changes In Catabolism   Anabolic Enzymes           CO 2     And Anabolism   Change In Cell           Genes   Enzymes and   Membrane Structure           Induced By   Pathways   And Potential           CO 2     Activation Of Krebs   Kinases And               Cycle   Phosphatases               Specific Gene   Transcription               Transcription Initiation   Activators And               Changes In   Repressors               Carbohydrate   Change In               Synthesis   Chromatin Structure               Changes In   And/Or Localized               Chloroplast Structure   DNA Topology               Changes In   Redox Control               Photosynthesis               Changes In               Respiration       Down-   Responders   Changes In Pathways   Transcription       Regulated   To Higher   And Processes   Factors       Transcripts   Levels Of   Operating In Cells   Change In Protein           CO 2     Changes In Catabolism   Structure By           Genes   and Anabolism   Phosphorylation           Repressed   Changes in   (Kinases) Or           By CO 2     Chloroplast Structure   Dephosphorylation                   (Phosphatases)                   Change In                   Chromatin Structure                   And/Or DNA                   Topology                   Stability Of Factors                   For Protein                   Synthesis And                   Degradation                   Metabolic Enzymes                    
Use of Promoters of CO2 Responsive Genes
 
     Promoters of CO2 responsive genes are useful for transcription of any desired polynucleotide or plant or non-plant origin. Further, any desired sequence can be transcribed in a similar temporal, tissue, or environmentally specific patterns as the CO2 responsive genes where the desired sequence is operably linked to a promoter of a CO2 responsive gene. The protein product of such a polynucleotide is usually synthesized in the same cells, in response to the same stimuli as the protein product of the gene from which the promoter was derived. Such promoter are also useful to produce antisense mRNAs to down-regulate the product of proteins, or to produce sense mRNAs to down-regulate mRNAs via sense suppression. 
     III.D.5. Mitochondria Electron Transport (Respiration) Genes, Gene Components and Products 
     One means to alter flux through metabolic pathways is to alter the levels of proteins in the pathways. Plant mitochondria contain many proteins involved in various metabolic processes, including the TCA cycle, respiration, and photorespiration and particularly the electron transport chain (mtETC). Most mtETC complexes consist of nuclearly-encoded mitochondrial proteins (NEMPs) and mitochondrially-encoded mitochondrial proteins (MEMPs). NEMPs are produced in coordination with MEMPs of the same complex and pathway and with other proteins in multi-organelle pathways. Enzymes involved in photorespiration, for example, are located in chloroplasts, mitochondria, and peroxisomes and many of the proteins are nuclearly-encoded. Manipulation of the coordination of protein levels within and between organelles can have critical and global consequences to the growth and yield of a plant. Genes which are manipulated by interfering with the mtETC have been characterized using microarray technology. 
     Microarray technology allows monitoring of gene expression levels for thousands of genes in a single experiment. This is achieved by hybridizing labeled fluorescent cDNA pools to glass slides that contain spots of DNA (Schena et al. (1995) Science 270: 467-70). The US  Arabidopsis  Functional Genomics Consortium (AFGC) has recently made public the results from such microarray experiments conducted with AFGC chips containing about 10,000 non-redundant ESTs, selected from about 37,000 randomly sequenced ESTs generated from mRNA of different tissues and developmental stages. 
     The sequences of the ESTs showing at least two-fold increases or decreases in the presence of the ETC inhibitor, 10 mM antimycin A compared with the control lacking antimycin A. were identified, compared to the Ceres full length cDNA and genomic sequence databanks, and equivalent Ceres clones identified. The MA_diff table reports the results of this analysis, indicating those Ceres clones which are up or down regulated over controls, thereby indicating the Ceres clones that represent respiration responsive genes. 
     Examples of genes and gene products that are responsive to antimycin A block of respiration are shown in the Reference, Sequence, Protein Group, Protein Group Matrix, MA_diff and MA_clust tables. While respiration responsive polynucleotides and gene products can act alone, combinations of these polynucleotides also affect growth and development. Useful combinations include different respiration responsive polynucleotides and/or gene products that have similar transcription profiles or similar biological activities, and members of the same or similar biochemical pathways. Here, in addition to polynucleotides having similar transcription profiles and/or biological activities, useful combinations include polynucleotides that may have different transcription profiles but which participate in common or overlapping pathways. Whole pathways or segments of pathways are controlled by transcription factor proteins and proteins controlling the activity of signal transduction pathways. Therefore, manipulation of such protein levels is especially useful for altering phenotypes and biochemical activities of plants. Manipulation of one or more respiration responsive gene activities are useful to modulate the biological processes and/or phenotypes listed below. 
     Such respiration responsive genes and gene products can function to either increase or dampen the phenotypes or activities below. Further, promoters of respiration responsive genes, as described in the Reference tables, for example, are useful to modulate transcription that is induced by respiration or any of the following phenotypes or biological activities below. Further, any desired sequence can be transcribed in similar temporal, tissue, or environmentally specific patterns as the respiration responsive genes when the desired sequence is operably linked to a promoter of a respiration responsive gene. The MA_diff Table(s) reports the transcript levels of the experiment (see EXPT ID: Mitchondria-Electron Transport (relating to SMD 8061, SMD 8063)). For transcripts that had higher levels in the samples than the control, a “+” is shown. A “−” is shown for when transcript levels were reduced in root tips as compared to the control. For more experimental detail see the Example section below. 
     Mitchondria-Electron Transport genes are those sequences that showed differential expression as compared to controls, namely those sequences identified in the MA_diff tables with a “+” or “−” indication. 
     Mitchondria-Electron Transport Genes Identified by Cluster Analyses of Differential Expression 
     Mitchondria-Electron Transport Genes Identified by Correlation to Genes that are Differentially Expressed 
     As described above, the transcription profiles of genes that act together are well correlated. Applicants not only have identified the genes that are differentially expressed in the microarray experiments, but also have identified the genes that act in concert with them. The MA_clust table indicates groups of genes that have well correlated transcription profiles and therefore participate in the same pathway or network. 
     A pathway or network of Mitchondria-Electron Transport genes is any group in the MA_clust that comprises a cDNA ID that also appears in Expt ID Mitchondria-Electron Transport (relating to SMD 8061, SMD 8063) of the MA_diff table(s). 
     Mitchondria-Electron Transport Genes Identified by Correlation to Genes that Cause Physiological Consequences 
     Additionally, the differential expression data and the phenotypic observations can be merged to identify pathways or networks of Mitchondria-Electron Transport genes. A group in the MA_clust is considered a Mitchondria-Electron Transport pathway or network if the group comprises a cDNA ID that also appears in Knock-in or Knock-out tables that causes one or more of the phenotypes described in section above. 
     Mitchondria-Electron Transport Genes Identified by Amino Acid Sequence Similarity 
     Mitchondria-Electron Transport genes from other plant species typically encode polypeptides that share amino acid similarity to the sequences encoded by corn and  Arabidopsis  Mitchondria-Electron Transport genes. Groups of Mitchondria-Electron Transport genes are identified in the Protein Group table. In this table, any protein group that comprises a peptide ID that corresponds to a cDNA ID member of a Mitchondria-Electron Transport pathway or network is a group of proteins that also exhibits Mitchondria-Electron Transport functions/utilities. 
     III.D.5.a. Use of Respiration Responsive Genes to Modulate Phenotypes 
     Respiration responsive genes and gene products are useful to or modulate one or more phenotypes including catabolism; energy generation, ATP, etc.; growth rate; whole plant, including height, flowering time, etc.; organs; flowers; fruits; stems; leaves; roots, lateral roots; biomass; fresh and dry weight during any time in plant life, such as maturation; number, size, and weight of flowers; seeds; branches; leaves; total plant nitrogen content; amino acid/protein content of whole plant or parts; seed yield (such as number, size weight, harvest index, and content and composition, e.g., amino acid, nitrogen, oil, protein, and carbohydrate); fruit yield; number, size, weight, harvest index; content and composition, e.g., amino acid, nitrogen, oil, protein, carbohydrate, water; and photosynthesis (such as carbon dioxide fixation). 
     To improve any of the phenotype(s) above, activities of one or more of the respiration responsive genes or gene products can be modulated and the plants tested by screening for the desired trait. Specifically, the gene, mRNA levels, or protein levels can be altered in a plant utilizing the procedures described herein and the phenotypes can be assayed. As an example, a plant can be transformed according to Bechtold and Pelletier (1998, Methods. Mol. Biol. 82:259-266) and/or screened for variants as in Winkler et al. (1998) Plant Physiol 118: 743-50 and visually inspected for the desired phenotype or metabolically and/or functionally assayed according to Saito et al. (1994, Plant Physiol. 106: 887-95), Takahashi et al (1997, Proc. Natl. Acad. Sci. USA 94: 11102-07) and Koprivova et al. (2000, Plant Physiol. 122: 737-46). 
     III.D.5.b. Use of Respiration-Responsive Genes to Modulate Biochemical Activities 
     The activities of one or more of the respiration responsive genes can be modulated to change biochemical or metabolic activities and/or pathways such as those noted below. Such biological activities can be measured according to the citations included in the Table below: 
     
       
         
           
               
               
               
             
               
                   
               
               
                   
                 BIOCHEMICAL OR 
                   
               
               
                   
                 METABOLIC 
               
               
                   
                 ACTIVITIES 
                 CITATIONS INCLUDING 
               
               
                 PROCESS 
                 AND/OR PATHWAYS 
                 ASSAYS 
               
               
                   
               
             
            
               
                 Respiration and 
                 Mitochondrial Electron 
                 Passam et al. (1973) 
               
               
                 energy-related 
                 Transport Chain 
                 Biochem Biophys. Acta 
               
               
                 processes 
                   
                 325: 54-61 
               
               
                   
                 Alternative oxidase pathway 
                 Saisho et al. (1997) Plant 
               
               
                   
                   
                 Mol. Biol. 35: 585-600 
               
               
                   
                   
                 Vanlerberghe and 
               
               
                   
                   
                 McIntosh (1994) Plant 
               
               
                   
                   
                 Physiol. 105: 867-874 
               
               
                   
                 ATP generation pathways 
                 Mahler and Cordes (1966) 
               
               
                   
                 ATP utilization pathways 
                 In Biological Chemistry, 
               
               
                   
                   
                 Harper and Row 
               
               
                   
                 Chloroplast energy related 
                 Foyer et al. (1989) Arch. 
               
               
                   
                 pathways 
                 Biochem. Biophys. 268: 
               
               
                   
                   
                 687-697 
               
               
                   
                   
                 Mills et al. (1978) 
               
               
                   
                   
                 Biochem. Biophys. Acta 
               
               
                   
                   
                 504: 298-309 
               
               
                   
                 Peroxisome energy related 
                 Olsen (1998) Plant mol. 
               
               
                   
                 pathways 
                 Biol. 38: 163-89 
               
               
                   
                 Cytoplasmic energy related 
                 Roberts et al. (1995) Febs Letters 
               
               
                   
                 pathways 
                 373: 307-309 
               
               
                   
                 Catabolism and Anabolism 
                 Mahler and Cordes (1966) In 
               
               
                   
                   
                 Biological Chemistry, Harper and 
               
               
                   
                   
                 Row 
               
               
                   
                 Aerobic versus anaerobic 
                 Mahler and Cordes (1966) In 
               
               
                   
                 pathways 
                 Biological Chemistry, Harper and 
               
               
                   
                   
                 Row 
               
               
                 Coordination of 
                 Light-regulation of major 
                 Lam et al. (1998) Plant J. 16(3): 
               
               
                 Carbon and Nitrogen 
                 central carbon and nitrogen 
                 345-353 
               
               
                 Metabolism 
                 Metabolic pathways to 
                 Lejay et al. (1999) Plant J. 18(5): 
               
               
                   
                 coordinate growth 
                 509-519; and 
               
               
                   
                   
                 Oliveira et al. (1999) Plant. Phys. 
               
               
                   
                   
                 121: 301-309 
               
               
                   
                 Carbohydrate and nitrogen 
                 Lam et al. (1998) Plant J. 16(3): 
               
               
                   
                 control of carbohydrate and 
                 345-353 
               
               
                   
                 organic nitrogen accumulation 
                 Lejay et al. (1999) Plant J. 18(5): 
               
               
                   
                 pathways 
                 509-519; and 
               
               
                   
                   
                 Oliveira et al. (1999) Plant. Phys. 
               
               
                   
                   
                 121: 301-309 
               
               
                   
               
            
           
         
       
     
     Other biological activities that can be modulated by the respiration genes and gene products are listed in the REF Tables. Assays for detecting such biological activities are described in the Protein Domain table. 
     Respiration responsive genes are differentially expressed in response to inhibition of mitochondrial electron transport by antimycin A. The MA_diff table reports the changes in transcript levels of various respiration responsive genes that are differentially expressed in response to this treatment. 
     Profiles of these different respiration genes are shown in the Table below with examples of associated biological activities. 
                                                     EXAMPLES OF       TRANSCRIPT       PHYSIOLOGICAL   BIOCHEMICAL       LEVELS   TYPE OF GENES   CONSEQUENCES   ACTIVITY                  Up regulated   Responders to   Changes in   Transporters       transcripts   inhibition of   generation of ATP   Catabolic and           mitochondrial   Alternate oxidase   anabolic enzymes           electron transport   induction   Changes in cell           respiration   Changes in   and organelle           Genes induced by   catabolic and   membrane           inhibition of   anabolic enzymes   structures and           mitochondrial   and pathways   potentials           electron transport   Specific gene   Kinases and               transcription   phosphatases               initiation   Transcription               Changes in electron   activators               transport proteins   Change in                   chromatin                   structure and/or                   localized DNA                   topology                   Redox control       Down-regulated   Responders to   Changes in ATP   Transcription       transcripts   inhibition of   generating   factors           mitochondrial   pathways   Change in protein           electron transport   Changes in   structure by           Genes repressed by   pathways and   phosphorylation           inhibition of   processes operating   (kinases) or           mitochondrial   in cells   dephosphoryaltion           electron transport   Induction of   (phosphatases)               aerobic pathways   Transporters               Changes in   Catabolic and               catabolism and anabolism   anabolic enzymes                   Changes in cell                   and organelle                   membrane                   structures and                   potentials                   Change in                   chromatin                   structure and/or                   localized DNA                   topology                   changes                   Stability factors                   for protein                   synthesis and                   degradation                   Metabolic enzymes               Changes in redox   Changes in redox               activities   enzymes                    
Use of Promoters of Respiration Genes
 
     Promoters of Respiration genes are useful for transcription of any desired polynucleotide or plant or non-plant origin. Further, any desired sequence can be transcribed in a similar temporal, tissue, or environmentally specific patterns as the Respiration genes where the desired sequence is operably linked to a promoter of a Respiration gene. The protein product of such a polynucleotide is usually synthesized in the same cells, in response to the same stimuli as the protein product of the gene from which the promoter was derived. Such promoter are also useful to produce antisense mRNAs to down-regulate the product of proteins, or to produce sense mRNAs to down-regulate mRNAs via sense suppression. 
     III.D.6. Protein Degradation Genes, Gene Components and Products 
     One of the components of molecular mechanisms that operate to support plant development is the “removal” of a gene product from a particular developmental circuit once the substrate protein is not functionally relevant anymore in temporal and/or spatial contexts. The “removal” mechanisms can be accomplished either by protein inactivation (e.g., phosphorylation or protein-protein interaction) or protein degradation most notably via ubiquitination-proteasome pathway. The ubiquitination-proteasome pathway is responsible for the degradation of a plethora of proteins involved in cell cycle, cell division, transcription, and signal transduction, all of which are required for normal cellular functions. Ubiquitination occurs through the activity of ubiquitin-activating enzymes (E1), ubiquitin-conjugating enzymes (E2), and ubiquitin-protein ligases (E3), which act sequentially to catalyze the attachment of ubiquitin (or other modifying molecules that are related to ubiquitin) to substrate proteins (Hochstrasser 2000, Science 289: 563). Ubiquitinated proteins are then routed to proteasomes for degradation processing [2000, Biochemistry and Molecular Biology of Plants, Buchanan, Gruissem, and Russel (eds), Amer. Soc. of Plant Physiologists, Rockville, Md.]. The degradation mechanism can be selective and specific to the concerned target protein (Joazeiro and Hunter 2001, Science 289: 2061; Sakamoto et al., 2001, PNAS Online 141230798). This selectivity and specificity may be one of the ways that the activity of gene products is modulated. 
     III.D.6.a. Identification of Protein Degradation Genes, Gene Components and Products 
     “Protein degradation” genes identified herein are defined as genes, gene components and products associated with or dependant on the ubiquitination—proteasome protein degradation process. Examples of such “protein degradation” genes and gene products are shown in the Reference and Sequence Tables. The biochemical functions of the protein products of many of these genes are also given in the Reference, Sequence, Protein Group, Protein Group Matrix tables, MA_diff and MA_clust tables. Selected genes, gene components and gene products of the invention can be used to modulate many plant traits from architecture to yield to stress tolerance. 
     “Protein Degradation” Genes, Gene Components and Products Identified by Phenotypic Observations 
     “Protein degradation” genes herein were discovered and characterized from a much larger set of genes in experiments designed to find the genes associated with the increased number of lateral branches (and secondary inflorescences) that are formed per cauline node. In these experiments, “protein degradation” genes were identified using a mutant with these characteristics. The gene causing the changes was identified from the mutant gene carrying an inserted tag. The mutant plant was named 13B12-1 and the mutant was in the E2 conjugating enzyme gene of the ubiquitination process. Compared to “wild-type” parental plants, the mutant plants exhibited multiple lateral stems per node and multi-pistillated flowers. For more experimental detail, see Example section below. 
     Protein Degradation Genes, Gene Components and Products Identified by Differential Expression 
     “Protein degradation” genes were also identified by measuring the relative levels of mRNA products in the mutant plant 13B12-1 lacking the E2 conjugating enzyme versus a “wild-type” parental plant. Specifically, mRNAs were isolated from 13B12-1 and compared with mRNAs isolated from wild-type plants utilizing microarray procedures. The MA_diff Table(s) reports the transcript levels of the experiment (see EXPT ID: 108451). For transcripts that had higher levels in the samples than the control, a “+” is shown. A “−” is shown for when transcript levels were reduced in root tips as compared to the control. For more experimental detail see the Example section below. 
     Protein Degradation genes are those sequences that showed differential expression as compared to controls, namely those sequences identified in the MA_diff tables with a “+” or “−” indication. 
     Protein Degradation Genes Identified by Cluster Analyses of Differential Expression 
     Protein Degradation Genes Identified By Correlation To Genes That Are Differentially Expressed 
     As described above, the transcription profiles of genes that act together are well correlated. Applicants not only have identified the genes that are differentially expressed in the microarray experiments, but also have identified the genes that act in concert with them. The MA_clust table indicates groups of genes that have well correlated transcription profiles and therefore participate in the same pathway or network. 
     A pathway or network of Protein Degradation genes is any group in the MA_clust that comprises a cDNA ID that also appears in Expt ID 108451 of the MA_diff table(s). 
     Protein Degradation Genes Identified by Correlation to Genes that Cause Physiological Consequences 
     Additionally, the differential expression data and the phenotypic observations can be merged to identify pathways or networks of Protein Degradation genes. A group in the MA_clust is considered a Protein Degradation pathway or network if the group comprises a cDNA ID that also appears in Knock-in or Knock-out tables that causes one or more of the phenotypes described in section above. 
     Protein Degradation Genes Identified by Amino Acid Sequence Similarity 
     Protein Degradation genes from other plant species typically encode polypeptides that share amino acid similarity to the sequences encoded by corn and  Arabidopsis  Protein Degradation genes. Groups of Protein Degradation genes are identified in the Protein Group table. In this table, any protein group that comprises a peptide ID that corresponds to a cDNA ID member of a Protein Degradation pathway or network is a group of proteins that also exhibits Protein Degradation functions/utilities. 
     These differentially expressed genes include genes associated with the degradation process and the genes whose expression is disturbed by the aberrant ubiquitination. 
     Examples of phenotypes, biochemical activities, and transcription profiles that can be modulated using these genes, gene components and gene products are described above and below. 
     III.D.6.b. Use of “Protein Degradation” Genes, Gene Components and Products to Modulate Phenotypes 
     The “protein degradation” genes, their components and products of the instant invention are useful for modulating one or more processes required for post-translational modification (e.g., ubiquitination) and degradation or inactivation of substrate proteins and also the pathways and processes that are associated with protein inactivation that are important for either or all of the following: (i) cell proliferation; (ii) cell differentiation; and (iii) cell death. The “protein degradation” genes, gene components and gene products are useful to alter or modulate one or more phenotypes including cell proliferation and cell size. 
     The intracellular levels of many proteins are regulated by ubiquitin-proteasome proteolysis. Without proper regulation of protein levels, normal cell differentiation can be altered. Examples of cell differentiation and development can be modulated by the genes and gene products of this invention include root size (such as length of primary roots or length of lateral roots) and function; branching and stem formation (such as multiple pistils, multiple lateral stems or secondary inflorescence per cauline node, and internode length) and cell differentiation and/or development in response to hormones (such as Auxin). 
     Programmed cell death can result from specific and targeted degradation of critical substrate proteins (e.g., transcription factors, enzymes, and proteins involved in signal transduction). Thus, alteration of “protein degradation” genes, their gene products, and the corresponding substrate proteins that they are acting upon are useful to modulate the vigor and yield of the plant overall as well as distinct cells, organs, or tissues. Traits that can be modulated by these genes and gene products include sterility or reproduction and seedling lethality. 
     Uses of Plants that are Modified as Described Above 
     Genes that control fundamental steps in regulatory pathways, such as protein inactivation, that in turn influence cascades and networks of other genes and processes are extremely useful. They and their component parts can be used selectively to manipulate development in specific cells, tissues and organs, including meristems when genes are designed to inactivate the normal genes only in specific cells, tissues and organs or to promote protein production where it is not normally produced. They can also be used to promote/control cell death. 
     Other “protein degradation” genes described here are components of the pathways determining organ identity and phenotypes. These and their component parts are also useful for modifying the characteristics of specific cells, tissues and organs when regulated appropriately. Thus “protein degradation” genes have wide utility for achieving the following: better plant survival by decreased lodging; better responses to high plant density; better stress tolerance; better animal (including human) nutrition values; improved dietary mineral nutrition; more vigor, growth rate and yield in terms of biomass; root/tuber yield (in terms of number, size, weight, or harvest index); content and composition, e.g. amino acid, jasmonate, oil, protein and starch; number of flowers; seed yield (e.g. number, size, weight, harvest index, content and composition, e.g. amino acid, jasmonate, oil, protein and starch); and fruit yield (e.g. number, size, weight, harvest index, post harvest quality, content and composition, e.g. amino acid, jasmonate, oil, protein and starch). 
     To regulate any of the phenotype(s) above, activities of one or more of the “protein degradation” genes or gene products can be modulated and tested by screening for the desired trait. Specifically, the gene, mRNA levels, or protein levels can be altered in a plant utilizing the procedures described herein and the phenotypes can be assayed. In addition, a synthetic molecule containing specific domains from “protein degradation” genes or gene product and/or in combination with other domains from gene products that are not necessarily related to protein degradation pathway can be constructed to target the degradation or inactivation of specific substrate proteins. As an example, a plant can be transformed according to Bechtold and Pelletier (1998, Methods. Mol. Biol. 82:259-266) and/or screened for variants as in Winkler et al. (1998) Plant Physiol 118: 743-50 and visually inspected for the desired phenotype or metabolically and/or functionally assayed according to Dolan et al. (1993, Development 119: 71-84), Dolan et al. (1997, Development 124: 1789-98), Crawford and Glass (1998, Trends Plant Science 3: 389-95), Wang et al. (1998, PNAS USA 95: 15134-39), Gaxiola et al. (1998, PNAS USA 95: 4046-50), Apse et al. (1999, Science 285: 1256-58), Fisher and Long (1992, Nature 357: 655-60), Schneider et al. (1998, Genes Devel 12: 2013-21) and Hirsch (1999, Curr Opin Plant Biol. 2: 320-326). 
     Use of Protein Degradation Genes, Gene Components and Products to Modulate Biochemical Activities 
     One or more of the “protein degradation” genes and their components can be used to modulate biochemical or metabolic activities, processes and/or pathways such as those noted below. Such biological activities can be measured according to the citations included in the Table below: 
     
       
         
           
               
               
               
             
               
                   
               
               
                   
                 BIOCHEMICAL OR 
                   
               
               
                   
                 METABOLIC 
               
               
                   
                 ACTIVITIES 
                 CITATIONS INCLUDING 
               
               
                 PROCESS 
                 AND/OR PATHWAYS 
                 ASSAYS 
               
               
                   
               
             
            
               
                 Growth, 
                 Auxin response 
                 Schwechheimer et al, Science 292: 
               
               
                 Differenti- 
                   
                 1379 (2001); 
               
               
                 ation and 
                   
                 Leyser et al, Nature 8: 161 (1993); 
               
               
                 Development 
                   
                 Lasswell et al, Plant Cell 12: 2395 
               
               
                   
                   
                 (2000) 
               
               
                   
                 Photomorphogenesis via leaf 
                 Schwechheimer et al, Science 292: 
               
               
                   
                 cells and meristems 
                 1379 (2001) 
               
               
                   
                 Apical dominance via shoot 
                 Schwechheimer et al, Science 292: 
               
               
                   
                 meristems 
                 1379 (2001) 
               
               
                   
                 Lateral root development via root 
                 Xie et al, Genes Dev 14: 3024 
               
               
                   
                 meristem 
                 (2000) 
               
               
                   
                 Hypocotyl, shoot elongation by 
                 Nagpal et al, Plant Physiol 123: 563 
               
               
                   
                 hormone controlled process 
                 (2000) 
               
               
                 Gene Expression 
                 mRNA stability 
                 Johnson et al, PNAS 97: 13991 
               
               
                 and related 
                   
                 (2000); 
               
               
                 cellular 
                 Gene activation 
                 Pham and Sauer, 289: 2357 (2000) 
               
               
                 processes 
                 Cell division and cell cycle 
                 King et al, Cell 81: 279 (1995); 
               
               
                   
                 control in meristems 
                 Ciechanover et al, Cell 37: 57 
               
               
                   
                   
                 (1984); 
               
               
                   
                   
                 Finley et al, Cell 37: 43 (1984); 
               
               
                   
                   
                 Robzyk et al, Science 287: 501 
               
               
                   
                   
                 (2000) 
               
               
                   
                 Chromatin remodeling 
                 Roest et al, Cell 86: 799 (1996) 
               
               
                   
                 Post-translational modification 
                 Biederer et al, Science 278: 1806 
               
               
                   
                 and organelle targeting of 
                 (1997) 
               
               
                   
                 proteins 
               
               
                   
               
            
           
         
       
     
     Other biological activities that can be modulated by the “protein degradation” gene, gene components and products are listed in the Reference tables. Assays for detecting such biological activities are described in the Protein Domain table. 
     III.D.6.d. Use of Protein Degradation Genes, Gene Components and Products to Modulate Transcription Levels of Other Genes 
     The expression of many genes is “up regulated” or “down regulated” in the 13B12-1 mutant because some protein degradation genes and their products are integrated into complex networks that regulate transcription of many other genes. Some protein degradation genes are therefore useful for modifying the transcription of other genes and hence complex phenotypes, as described above. Profiles of “protein degradation” genes are described in the Table below with associated biological activities. “Up-regulated” profiles are those where the gene produces mRNA levels that are higher in the 13B12-1 as compared to wild-type plant; and vice-versa for “down-regulated” profiles. 
     
       
         
           
               
               
               
               
             
               
                   
               
               
                   
                   
                   
                 EXAMPLES OF 
               
               
                   
                 TYPE OF GENES 
                 PHYSIOLOGICAL 
                 BIOCHEMICAL 
               
               
                   
                 WHOSE 
                 CONSEQUENCES OF 
                 ACTIVITIES WHOSE 
               
               
                 TRANSCRIPT 
                 TRANSCRIPTS 
                 MODIFYING GENE 
                 TRANSCRIPTS ARE 
               
               
                 LEVELS 
                 ARE CHANGED 
                 PRODUCT LEVELS 
                 CHANGED 
               
               
                   
               
             
            
               
                 Up Regulated 
                 Genes induced as 
                 Shoot formation 
                 Transcription 
               
               
                 Transcripts 
                 a consequence of 
                 Lateral stem, lateral 
                 Activators and 
               
               
                   
                 mutant 
                 and main 
                 Repressors 
               
               
                   
                 ubiquitination 
                 inflorescence 
                 Chromatin Structure 
               
               
                   
                 degradation 
                 development 
                 and/or Localized 
               
               
                   
                 system 
                 Internode 
                 DNA Topology 
               
               
                   
                 Genes repressed 
                 elongation 
                 determining proteins 
               
               
                   
                 by “protein 
                 Node determination 
                 Methylated DNA 
               
               
                   
                 degradation” 
                 and development 
                 binding proteins 
               
               
                   
                 system directly or 
                 Root formation 
                 Kinases, 
               
               
                   
                 indirectly 
                 Lateral root 
                 Phosphatases 
               
               
                   
                 Genes repressed 
                 development 
                 Signal transduction 
               
               
                   
                 or mRNAs 
                 Proper response to 
                 pathway proteins 
               
               
                   
                 degraded as a 
                 Auxin and other 
                 Transporters 
               
               
                   
                 consequence of 
                 growth regulators 
                 Metabolic Enzymes 
               
               
                   
                 mutant 
                 Seed dormancy and 
                 Cell cycle 
               
               
                   
                 ubiquitination 
                 seed development 
                 checkpoint proteins 
               
               
                   
                 degradation 
                 Resistance to 
                 Cell Membrane 
               
               
                   
                 process 
                 drought and other 
                 Structure And 
               
               
                   
                   
                 forms of stress 
                 Proteins 
               
               
                   
                   
                 Secondary 
                 Cell Wall Proteins 
               
               
                   
                   
                 metabolite 
                 Proteins involved in 
               
               
                   
                   
                 biosynthesis 
                 secondary 
               
               
                   
                   
                   
                 metabolism 
               
               
                   
                   
                   
                 Seed storage 
               
               
                   
                   
                   
                 metabolism 
               
               
                 Down 
                 Genes activated 
               
               
                 Regulated 
                 by “protein 
               
               
                 Transcripts 
                 degradation” 
               
               
                   
                 systems directly 
               
               
                   
                 or indirectly 
               
               
                   
               
            
           
         
       
     
     “Protein degradation” genes and gene products can be modulated alone or in combination as described in the introduction. Of particular interest are combination of these genes and gene products with those that modulate hormone responses and/or metabolism. Hormone responsive and metabolism genes and gene products are described in more detail in the sections above. Such modification can lead to major changes in plant architecture and yield. 
     Use of Promoters and “Protein Degradation Genes, Gene Components and Products” 
     Promoters of “protein degradation” genes, as described in the Reference tables, for example, can be used to modulate transcription of any polynucleotide, plant or non plant to achieve synthesis of a protein in association with production of the ubiquitination—proteasome pathway or the various cellular systems associated with it. Additionally such promoters can be used to synthesize antisense RNA copies of any gene to reduce the amount of protein product produced, or to synthesize RNA copies that reduce protein formation by RNA interference. Such modifications can make phenotypic changes and produce altered plants as described above. 
     III.D.7. Carotenogenesis Responsive Genes, Gene Components and Products 
     Carotenoids serve important biochemical functions in both plants and animals. In plants, carotenoids function as accessory light harvesting pigments for photosynthesis and to protect chloroplasts and photosystem II from heat and oxidative damage by dissipating energy and scavenging oxygen radicals produced by high light intensities and other oxidative stresses. Decreases in yield frequently occur as a result of light stress and oxidative stress in the normal growth ranges of crop species. In addition light stress limits the geographic range of many crop species. Modest increases in oxidative stress tolerance would greatly improve the performance and growth range of many crop species. The development of genotypes with increased tolerance to light and oxidative stress would provide a more reliable means to minimize crop losses and diminish the use of energy-costly practices to modify the soil environment. 
     In animals carotenoids such as beta-carotene are essential provitamins required for proper visual development and function. In addition, their antioxidative properties are also thought to provide valuable protection from diseases such as cancer. Modest increases in carotenoid levels in crop species could produce a dramatic effect on plant nutritional quality. The development of genotypes with increased carotenoid content would provide a more reliable and effective nutritional source of Vitamin A and other carotenoid derived antioxidants than through the use of costly nutritional supplements. 
     Genetic changes produced through DNA mutation in a plant can result in the modulation of many genes and gene products. Examples of such mutation altered genes and gene products are shown in the Reference and Sequence Tables. These genes and/or products are responsible for effects on traits such as plant vigor, nutritional content and seed yield. 
     While carotenoid synthesis and/or oxidative stress responsive polynucleotides and gene products can act alone, combinations of these polynucleotides also affect growth and development. Useful combinations include different carotenoid biosynthetic polynucleotides and/or gene products that have similar transcription profiles or similar biological activities, and members of the same or similar biochemical pathways. In addition, the combination of an carotenoid synthesis or oxidative stress protective polynucleotide and/or gene product with another environmentally responsive polynucleotide is also useful because of the interactions that exist between hormone-regulated pathways, stress pathways, nutritional pathways and development. Here, in addition to polynucleotides having similar transcription profiles and/or biological activities, useful combinations include polynucleotides that may have different transcription profiles but which participate in a common pathway. 
     Such carotenoid synthesis/oxidative stress tolerance genes and gene products can function to either increase or dampen the above phenotypes or activities either in response to changes in light intensity or in the absence of osmotic fluctuations. They were discovered and characterized from a much larger set of genes by experiments designed to find genes whose mRNA products participate in carotenogenesis. These experiments made use of an  Arabidopsis  mutant (Or) having an accumulation of up to 500 times more beta-carotene than wild-type in non-photosynthetic tissues. 
     Microarray technology allows monitoring of gene expression levels for thousands of genes in a single experiment. This is achieved by hybridizing labeled fluorescent cDNA pools to glass slides that contain spots of DNA (Schena et al. (1995) Science 270: 467-70). The USArabidopsis Functional Genomics Consortium (AFGC) has recently made public the results from such microarray experiments conducted with AFGC chips containing some 10,000 non-redundant ESTs, selected from about 37,000 randomly sequenced ESTs generated from mRNA of different tissues and developmental stages. 
     The sequences of the ESTs showing at least two-fold increases or decreases in the mutant plant compared with wild type seedlings were identified, compared to the Ceres full length cDNA and genomic sequence databanks, and equivalent Ceres clones identified. MA_diff Table reports the results of this analysis, indicating those Ceres clones which are up or down regulated over controls, thereby indicating the Ceres clones which represent Carotenoid synthesis/oxidative stress tolerance responsive genes. The MA_diff Table(s) reports the transcript levels of the experiment (see EXPT ID: Cauliflower (relating to SMD 5329, SMD 5330)). For transcripts that had higher levels in the samples than the control, a “+” is shown. A “−” is shown for when transcript levels were reduced in root tips as compared to the control. For more experimental detail see the Example section below. 
     Carotenogenesis genes are those sequences that showed differential expression as compared to controls, namely those sequences identified in the MA_diff tables with a “+” or “−” indication. 
     Carotenogenesis Genes Identified by Cluster Analyses of Differential Expression 
     Carotenogenesis Genes Identified by Correlation to Genes that are Differentially Expressed 
     As described above, the transcription profiles of genes that act together are well correlated. Applicants not only have identified the genes that are differentially expressed in the microarray experiments, but also have identified the genes that act in concert with them. The MA_clust table indicates groups of genes that have well correlated transcription profiles and therefore participate in the same pathway or network. 
     A pathway or network of Carotenogenesis genes is any group in the MA_clust that comprises a cDNA ID that also appears in Expt ID Cauliflower (relating to SMD 5329, SMD 5330) of the MA_diff table(s). 
     Carotenogenesis Genes Identified by Correlation to Genes that Cause Physiological Consequences 
     Additionally, the differential expression data and the phenotypic observations can be merged to identify pathways or networks of Carotenogenesis genes. A group in the MA_clust is considered a Carotenogenesis pathway or network if the group comprises a cDNA ID that also appears in Knock-in or Knock-out tables that causes one or more of the phenotypes described in section above. 
     Carotenogenesis Genes Identified by Amino Acid Sequence Similarity 
     Carotenogenesis genes from other plant species typically encode polypeptides that share amino acid similarity to the sequences encoded by corn and  Arabidopsis  Carotenogenesis genes. Groups of Carotenogenesis genes are identified in the Protein Group table. In this table, any protein group that comprises a peptide ID that corresponds to a cDNA ID member of a Carotenogenesis pathway or network is a group of proteins that also exhibits Carotenogenesis functions/utilities. 
     III.D.7.a. Use of Carotenoid Synthesis/Oxidative Stress Tolerance Responsive Genes, Gene Components and Products to Modulate Phenotypes 
     Carotenoid synthesis/oxidative stress tolerance genes and gene products are useful to or modulate one or more phenotypes including growth rate; whole plant, including height, flowering time, etc.); seedling; organ (such as stem, leaves, roots, flowers, fruits, or seed yield, size, or weight); seed development; embryo; germination; cell differentiation; chloroplasts; plant nutrition; uptake and assimilation of organic compounds; uptake and assimilation of inorganic compounds; animal (including human) nutrition; improved dietary mineral nutrition; stress responses; drought; cold; and osmotic. 
     To improve any of the phenotype(s) above, activities of one or more of the Carotenoid synthesis/oxidative stress tolerance genes or gene products can be modulated and tested by screening for the desired trait. Specifically, the gene, mRNA levels, or protein levels can be altered in a plant utilizing the procedures described herein and the phenotypes can be assayed. As an example, a plant can be transformed according to Bechtold and Pelletier (1998, Methods. Mol. Biol. 82:259-266) and/or screened for variants as in Winkler et al. (1998) Plant Physiol 118: 743-50 and visually inspected for the desired phenotype or metabolically and/or functionally assayed according to Friedrich, (1999, JAMA 282: 1508), Kumar et al. (1999, Phytochemistry 51: 847-51), La Rocca et al. (2000, Physiologia Plantarum 109: 51-7) and Bartley (1994, In: Ann Rev Plant Physiol Plant Molec Biol, Jones and Somerville, eds, Annual Reviews Inc, Palo Alto, Calif.). 
     III.D.7.b. Use of Carotenoid Synthesis/Oxidative Stress Tolerance Responsive Genes, Gene Components and Products to Modulate Biochemical Activities 
     The activities of one or more of the carotenoid synthesis/oxidative stress tolerance genes can be modulated to change biochemical or metabolic activities and/or pathways such as those noted below. Such biological activities can be measured according to the citations included in the Table below: 
     
       
         
           
               
               
               
             
               
                   
               
               
                   
                 BIOCHEMICAL OR 
                   
               
               
                   
                 METABOLIC 
               
               
                   
                 ACTIVITIES 
                 CITATIONS INCLUDING 
               
               
                 PROCESS 
                 AND/OR PATHWAYS 
                 ASSAYS 
               
               
                   
               
             
            
               
                 Growth, 
                 Chloroplast 
                 Kumar et al. (1999) 
               
               
                 Differenti- 
                 biosynthesis 
                 Phytochemistry 51: 847-51 
               
               
                 ation and 
                   
                 Fraser et al. (1994) Plant 
               
               
                 Development 
                   
                 Physiol 105: 405-13 
               
               
                 Metabolism 
                 Carotenoid 
                 Kumar et al. (1999) 
               
               
                   
                 biosynthesis 
                 Phytochemistry 51: 847-51 
               
               
                   
                 Herbicide resistance 
                 La Rocca et al. (2000) 
               
               
                   
                   
                 Physiolgia 
               
               
                   
                   
                 Plantarum 109: 51-57 
               
               
                   
                 Regulate abscisic 
                 Tan et al. (1997) PNAS USA 
               
               
                   
                 acid levels 
                 94: 12235-40 
               
               
                   
                 Drought, cold and 
                 Tan et al. (1997) PNAS USA 
               
               
                   
                 osmotic tolerance 
                 94: 12235-40 
               
               
                   
               
            
           
         
       
     
     Other biological activities that can be modulated by the Carotenoid synthesis, oxidative stress tolerance genes and gene products are listed in the Reference Tables. Assays for detecting such biological activities are described in the Protein Domain table. 
     Profiles of these different carotenoid synthesis/oxidative stress tolerance responsive genes are shown in the Table below together with examples of the kinds of associated biological activities. 
                                                     EXAMPLES OF       TRANSCRIPT       PHYSIOLOGICAL   BIOCHEMICAL       LEVELS   TYPE OF GENES   CONSEQUENCES   ACTIVITY                  Up regulated   Genes induced during   Gene   Transporters       transcripts   carotenoid synthesis/   Repression/Induction   Metabolic           oxidative stress   activity   enzymes           tolerance activity   Cell cycle progression   Kinases and               Chromatin   phosphatases               condensation   Transcription               Synthesis of   activators               metabolites and/or   Change in               proteins   chromatin               Modulation of   structure and/or               transduction pathways   localized DNA               Specific gene   topology               transcription initiation       Down-regulated   Genes repressed   Gene   Transcription       transcripts   during carotenoid   repression/induction   factors           synthesis/oxidative   activity   Change in           stress tolerance   Changes in pathways   protein structure           activity   and processes   by           Genes with   operating in cells   phosphorylation           discontinued   Changes in   (kinases) or           expression or   metabolism other than   dephosphorylation           unsTable mRNA in   carotenoid   (phosphatases)           conditions of reduced   synthesis/oxidative   Change in           carotenoid   stress tolerance   chromatin           synthesis/oxidative       structure and/or           stress tolerance       DNA topology                   Stability of                   factors for                   protein synthesis                   and degradation                   Metabolic                   enzymes                    
Use of Promoters of Carotenogenesis Responsive Genes
 
     Promoters of Carotenogenesis responsive genes are useful for transcription of any desired polynucleotide or plant or non-plant origin. Further, any desired sequence can be transcribed in a similar temporal, tissue, or environmentally specific patterns as the Carotenogenesis responsive genes where the desired sequence is operably linked to a promoter of a Carotenogenesis responsive gene. The protein product of such a polynucleotide is usually synthesized in the same cells, in response to the same stimuli as the protein product of the gene from which the promoter was derived. Such promoter are also useful to produce antisense mRNAs to down-regulate the product of proteins, or to produce sense mRNAs to down-regulate mRNAs via sense suppression. 
     III.D.8. Viability Genes, Gene Components and Products 
     Plants contain many proteins and pathways that when blocked or induced lead to cell, organ or whole plant death. Gene variants that influence these pathways can have profound effects on plant survival, vigor and performance. The critical pathways include those concerned with metabolism and development or protection against stresses, diseases and pests. They also include those involved in apoptosis and necrosis. The applicants have elucidated many such genes and pathways by discovering genes that when inactivated lead to cell or plant death. 
     Herbicides are, by definition, chemicals that cause death of tissues, organs and whole plants. The genes and pathways that are activated or inactivated by herbicides include those that cause cell death as well as those that function to provide protection. The applicants have elucidated these genes. 
     The genes defined in this section have many uses including manipulating which cells, tissues and organs are selectively killed, which are protected, making plants resistant to herbicides, discovering new herbicides and making plants resistant to various stresses. 
     III.D.8.a. Identification of Viability Genes, Gene Components and Products 
     Viability genes identified here are defined as genes, gene components and products capable of inhibiting cell, tissue, organ or whole plant death or protecting cells, organs and plants against death and toxic chemicals or stresses. Examples of such viability genes and gene products are shown in the Reference, Sequence, Protein Group, Protein Group Matrix tables, MA_diff, MA_clust, Knock-in and Knock-out tables. The biochemical functions of the protein products of many of these genes determined from comparisons with known proteins are also given in the Reference tables. 
     Viability Genes, Gene Components and Products Identified by Phenotypic Observations 
     These genes were discovered and characterized from a much larger set of genes by experiments designed to find genes that cause serious disturbances in progeny survival, seed germination, development, embryo and/or seedling growth. In these experiments, viability genes were identified by either (1) ectopic expression of a cDNA in a plant or (2) mutagenesis of a plant genome. The plants were then cultivated and one or more of the following phenotypes, which varied from the parental wild-type was observed:
         A. Gametophytic loss of progeny seedlings (detected from a parent on the basis of a linked herbicide resistance gene showing abnormal segregation ratios, as revealed by treating with herbicide)   B. Embryo death, resulting in some cases to loss of seed   C. Pigment variation in cotyledons and leaves, including absence of chlorophyll, which leads to seedling death.
           1. Abinos   2. Yellow/greens   
           D. Cotyledons produced but no or few leaves and followed by seedling death.   E. Very small plantlets       

     The genes identified in these experiments are shown in Tables X. 
     Viability Genes, Gene Components and Products Identified by Differential Expression 
     Viability genes were also identified from a much larger set of genes by experiments designed to find genes whose mRNA products changed in concentration in response to applications of different herbicides to plants. Viability genes are characteristically differentially transcribed in response to fluctuating herbicide levels or concentrations, whether internal or external to an organism or cell. The MA_diff Table reports the changes in transcript levels of various viability genes in entire seedlings at 0, 4, 8, 12, 24, and 48 hours after a plant was sprayed with a Hoagland&#39;s nutrient solution enriched with either 2,4 D (Trimec), GLEAN®, Grassgetter, ROUNDUP®, or Finale herbicides as compared to seedlings sprayed with Hoagland&#39;s solution only. 
     The MA_diff Table(s) reports the transcript levels of the experiment (see EXPT ID: 108467, 107871, 107876, 108468, 107881, 108465, 107896, 108466, 107886, 107891, 108501). For transcripts that had higher levels in the samples than the control, a “+” is shown. A “−” is shown for when transcript levels were reduced in root tips as compared to the control. For more experimental detail see the Example section below. 
     Viability genes are those sequences that showed differential expression as compared to controls, namely those sequences identified in the MA_diff tables with a “+” or “−” indication. 
     Viability Genes Identified by Cluster Analyses of Differential Expression 
     Viability Genes Identified by Correlation to Genes that are Differentially Expressed 
     As described above, the transcription profiles of genes that act together are well correlated. Applicants not only have identified the genes that are differentially expressed in the microarray experiments, but also have identified the genes that act in concert with them. The MA_clust table indicates groups of genes that have well correlated transcription profiles and therefore participate in the same pathway or network. 
     A pathway or network of Viability genes is any group in the MA_clust that comprises a cDNA ID that also appears in Expt ID 108467, 107871, 107876, 108468, 107881, 108465, 107896, 108466, 107886, 107891, 108501 of the MA_diff table(s). 
     Viability Genes Identified by Correlation to Genes that Cause Physiological Consequences 
     Additionally, the differential expression data and the phenotypic observations can be merged to identify pathways or networks of Viability genes. A group in the MA_clust is considered a Viability pathway or network if the group comprises a cDNA ID that also appears in Knock-in or Knock-out tables that causes one or more of the phenotypes described in section above. 
     Viability Genes Identified by Amino Acid Sequence Similarity 
     Viability genes from other plant species typically encode polypeptides that share amino acid similarity to the sequences encoded by corn and  Arabidopsis  Viability genes. Groups of Viability genes are identified in the Protein Group table. In this table, any protein group that comprises a peptide ID that corresponds to a cDNA ID member of a Viability pathway or network is a group of proteins that also exhibits Viability functions/utilities. 
     It is assumed that those gene activity changes in response to the toxic herbicides are either responsible, directly or indirectly, for cell death or reflect activation of defense pathways. These genes are therefore useful for controlling plant viability. 
     Examples of phenotypes, biochemical activities, or transcript profiles that can be modulated using selected viability gene components are described above and below. 
     III.D.8.b. Use of Viability Genes, Gene Components and Products to Modulate Phenotypes 
     Deficiencies in viability genes can cause cell death at various rates and under various conditions. Viability genes can be divided into two classes; (1) those that lead to cell death under permissive growth conditions and (2) those that cause cell demise under restrictive conditions. Examples of the first class are viability genes which encode toxins or which participate in the programmed cell death pathway(s). Disruption of metabolic pathways, such as amino acid synthesis, may not cause death when the cell is supplemented with appropriate amino acids, but can cause death under more restrictive conditions. 
     Some deficiencies in viability genes identified cause the organism as a whole to die, while other genes cause death only of a specific subset of cells or organs. For example, genes identified from embryo viability phenotypes can cause an entire organism to die. In contrast, genes characterized from gametophytic lethals may inhibit cell growth only in a select set of cells. In addition, some viability genes may not cause an immediate demise. A seedling lethal phenotype is one such example, where a seed germinates and produces cotyledons but the plant dies before producing any true leaves. Yellow-green pigment mutants provide yet another set of examples. In some cases, the plant produces a number of yellow-green leaves but dies before producing any seed, due in part, to the necessity to produce chlorophyll in functioning chloroplasts to fix CO 2 . 
     Viability genes, in which mutational deficiencies lead to death, carry no duplicates in the haploid plant genome. They thus may be especially likely to promote viability and vigor when expressed more optimally in a plant, in specific tissues or throughout the plant. 
     Proteins which lead to death when inactivated, and other proteins in the pathways in which they act, are potential targets for herbicides. In this kind of application, chemicals specifically capable of interacting with such proteins are discovered. Typically, this could be done by designing a gene involving the relevant viability gene, that also facilitates a rapid easily measured assay for the functioning of the protein product, and treating plants containing the new genes with the potential herbicides. Those chemicals specifically interfering with the protein activity can then easily be selected for further development. 
     Genes whose products interact directly with a herbicide can also be modified such that the herbicide no longer inactivates the protein. Such genes are useful for making herbicide resistant plants, valuable in agriculture. 
     Many of the genes activated or inactivated by the herbicides define genes involved in the pathways that protect the plant against damage and stresses. These genes and gene components, especially those regulating such pathways, are especially useful for enhancing the ability of plants to withstand specific stresses, including herbicides. [See the sections on Stress responsive genes, gene components and products.] 
     Genes that cause cellular death can be used to design new genes that cause death of specific cells and tissues and hence new valuable products. For example, activation of genes causing death in cells specifying seeds can be used to produce fruits lacking seeds. They can also be used to prevent cell death by pathogens and pests. 
     The genes and gene components of the instant invention are useful to modulate one or more processes that affect viability and vigor at the (1) cellular level; (2) organelle level; (3) organ level; or (4) overall organism level. 
     Phenotypes that are modulated by these genese and gene components include (1) at the cellular level: cell size, cell differentiation, cell division, cell longevity, cell position, and cytotoxins; (2) at the organelle level: chloroplasts and/or mitochondria; (3) at the organ level: flower number or size; seed size, number or composition (amino Acid, carbohydrates, lipid, and secondary metabolites); fruit size, number, or composition (amino Acid, carbohydrates, lipid, and secondary metabolites); fruit drop, fruit ripening; leaf (size, composition, amino acid, carbohydrates, lipid, and secondary metabolites, photoefficiency, abscission, or senescence); stem; or root; and (4) at the overall organism level: vigor (e.g. increased biomass), stress tolerance (e.g. cold, drought, heat, herbicide, oxidative, and salt); and pathogen resistance 
     To regulate any of the phenotype(s) above, activities of one or more of the viability genes or gene products can be modulated in an organism and tested by screening for the desired trait. Specifically, the gene, mRNA levels, or protein levels can be altered in a plant utilizing the procedures described herein and the phenotypes can be assayed. As an example, a plant can be transformed according to Bechtold and Pelletier (Methods. Mol. Biol. 82:259-266 (1998)) and/or screened for variants as in Winkler et al., Plant Physiol. 118: 743-50 and visually inspected for the desired phenotype or metabolically and/or functionally assayed. 
     III.D.8.c. Use of Viability Genes, Gene Components and Products to Modulate Biochemical Activities 
     The viability genes, their components and/or products can be used to modulate processes, biochemical or metabolic activities and/or pathways such as those noted below. Such biological activities can be measured according to the citations included in the table below: 
     
       
         
           
               
               
               
             
               
                   
               
               
                   
                 BIOCHEMICAL OR 
                   
               
               
                   
                 METABOLIC 
               
               
                   
                 ACTIVITIES 
                 CITATIONS INCLUDING 
               
               
                 PROCESS 
                 AND/OR PATHWAYS 
                 ASSAYS 
               
               
                   
               
             
            
               
                 Amino Acid Synthesis 
                 Aceto -lactate synthase 
                 Hershey et al. (1999) Plant 
               
               
                   
                   
                 Mol. Biol. 40, 795-806 
               
               
                 Cell Wall Synthesis 
                 Cellulose synthase 
                 Peng et al. (2001) Plant 
               
               
                   
                   
                 Physiol. 126, 981-982 
               
               
                   
                   
                 Kawagoe and Delmer 
               
               
                   
                   
                 (1997) Genet Eng. 19, 63-87 
               
               
                 Nucleotide Synthesis 
                 Coenzyme A biosynthesis 
                 Kupke et al. (2001) J. Biol. 
               
               
                   
                   
                 Chem. 276, 19190-19196 
               
               
                 Lipid Synthesis 
                 Oleosin biosynthesis 
                 Singh et al. (2000) 
               
               
                   
                   
                 Biochem. Soc. Trans. 28, 
               
               
                   
                   
                 925-927 
               
               
                   
                   
                 Zou et al. (1996). Plant Mol. 
               
               
                   
                   
                 Biol. 31, 429-433 
               
               
                 Hormone Signaling 
                 Brassinolide and light signal 
                 Kang et al. (2001) Cell 105, 
               
               
                 Pathways 
                 transduction 
                 625-636 
               
               
                 Hormone Biosynthesis 
                 Cytokinin biosynthesis 
                 Takei et al, (2001) J. Biol. 
               
               
                   
                   
                 Chem. 276, 26405-26410 
               
               
                 Secondary Metabolites 
                 Carotenoid biosynthesis 
                 Estevez et al. (2001) J. Biol. 
               
               
                   
                   
                 Chem. 276, 22901-22909 
               
               
                   
                   
                 Carol and Kuntz (2001) 
               
               
                   
                   
                 Trendy Plant Sci. 6, 31-36 
               
               
                   
                   
                 Pogson and Rissler (2001) 
               
               
                   
                   
                 Phil. Trans. Roy. Soc. Lord. 
               
               
                   
                   
                 B 355, 1395-1400 
               
               
                 Clearing of Toxic 
                 Ubiquitination 
               
               
                 Substances 
               
               
                 Growth, Differenti- 
                 Farnesylation 
                 Pei et al (1998) Science 282: 
               
               
                 ation And 
                 Nitrogen Metabolism 
                 287-290; Cutler et al. (1996) 
               
               
                 Development 
                   
                 Science 273: 1239 
               
               
                   
                   
                 Goupil et al (1998) J Exptl 
               
               
                   
                   
                 Botany 49: 1855-62 
               
               
                 Water Conservation And 
                 Stomatal Development And 
                 Allen et al. (1999) Plant 
               
               
                 Resistance To Drought 
                 Physiology 
                 Cell 11: 1785-1798 
               
               
                 And Other Related 
                 Stress Response Pathways 
                 Li et al. 2000 Science 287: 
               
               
                 Stresses 
                 Inhibition Of Ethylene 
                 300-303 
               
               
                   
                 Production Under Low Water 
                 Burnett Et Al 2000. J. Exptl 
               
               
                   
                 Potential 
                 Botany 51: 197-205 
               
               
                   
                 Proline And Other Osmolite 
                 Raschke (1987) In: Stomatal 
               
               
                   
                 Synthesis And Degradation 
                 Function Zeiger et al. Eds., 
               
               
                   
                   
                 253-279 
               
               
                   
                   
                 Bush And Pages (1998) 
               
               
                   
                   
                 Plant Mol. Biol. 37: 425-35 
               
               
                   
                   
                 Spollen Et Al (2000) Plant 
               
               
                   
                   
                 Physiol. 122: 967-976 
               
               
                   
                   
                 Hare et al. (1998) Plant, Cell 
               
               
                   
                   
                 And Environment 21: 535-553; 
               
               
                   
                   
                 Hare et al. (1999) J. 
               
               
                   
                   
                 Exptl. Botany 50: 413-434 
               
               
                 Programmed cell death 
                 Proteases 
                 Kamens et al. (1995) J. Biol. 
               
               
                   
                 DNA endonucleases 
                 Chem. 270, 15250-15256 
               
               
                   
                 Mitochondriae uncoupling 
                 Wang et al. (2001) 
               
               
                   
                 proteins 
                 Anticancer Res. 21, 1789-1794 
               
               
                   
                   
                 Drake et al. (1996) Plant 
               
               
                   
                   
                 Mol. Biol 304, 755-767 
               
               
                   
                   
                 Mittler and Lam (1995) 
               
               
                   
                   
                 Plant Cell 7, 1951-1962 
               
               
                   
                   
                 Mittler and Lam (1995) 
               
               
                   
                   
                 Plant Physiol. 108, 489-493 
               
               
                   
                   
                 Thelen and Northcote 
               
               
                   
                   
                 (1989) Planta 179, 181-195 
               
               
                   
                   
                 Hanak and Jezek (2001) 
               
               
                   
                   
                 FEBS Lett. 495, 137-141 
               
               
                   
                 Plasmalemma and Tonoplast 
                 Macrobbie (1998) Philos 
               
               
                   
                 Ion Channel Changes 
                 Trans R Soc Lond B Biol 
               
               
                   
                 Ca2+ Accumulation 
                 Sci 353: 1475-88; Li et al 
               
               
                   
                 K+ Efflux 
                 (2000) Science 287: 300-303; 
               
               
                   
                 Activation Of Kinases And 
                 Barkla et al. (1999) 
               
               
                   
                 Phosphatases 
                 Plant Physiol. 120: 811-819 
               
               
                   
                   
                 Lacombe et al. (2000) Plant 
               
               
                   
                   
                 Cell 12: 837-51; Wang et 
               
               
                   
                   
                 al. (1998) Plant Physiol 
               
               
                   
                   
                 118: 1421-1429; Shi et al. 
               
               
                   
                   
                 (1999) Plant Cell 11: 2393-2406 
               
               
                   
                   
                 Gaymard et al. (1998) Cell 
               
               
                   
                   
                 94: 647-655 
               
               
                   
                   
                 Jonak et al. (1996) Proc. 
               
               
                   
                   
                 Natl. Acad. Sci 93: 11274-79; 
               
               
                   
                   
                 Sheen (1998) Proc. Natl. 
               
               
                   
                   
                 Acad. Sci. 95: 975-80; Allen 
               
               
                   
                   
                 et al. (1999) Plant Cell 11: 
               
               
                   
                   
                 1785-98 
               
               
                   
               
            
           
         
       
     
     Other biological activities that can be modulated by the viability genes, their components and products are listed in the Reference tables. Assays for detecting such biological activities are described in the Protein Domain table. 
     III.D.8.d. Use of Viability Genes, Gene Components and Products to Modulate Transcript Levels of Other Genes 
     The expression of many genes is “up regulated” or “down regulated” following herbicide treatment and also in the leaf mutants, because some “viability” genes and their products are integrated into complex networks that regulate transcription of many other genes. Some “viability genes” are therefore useful for modifying the transcription of other genes and hence complex phenotypes, as described above. The data from differential expression experiments can be used to identify a number of types of transcript profiles of “viability genes”, including “early responders,” and “delayed responders”, “early responder repressors” and “delayed repressors”. Profiles of these different types responsive genes are shown in the Table below together with examples of the kinds of associated biological activities. “Up-regulated” profiles are those where the mRNA transcript levels are higher in the herbicide treated plants as compared to the untreated plants. “Down-regulated” profiles represent higher transcript levels in the untreated plant as compared to the herbicide treated plants. 
     
       
         
           
               
               
               
               
             
               
                   
               
               
                   
                   
                   
                 EXAMPLES OF 
               
               
                   
                   
                 PHYSIOLOGICAL 
                 BIOCHEMICAL 
               
               
                   
                 TYPE OF GENES 
                 CONSEQUENCES 
                 ACTIVITIES 
               
               
                   
                 WHOSE 
                 OF MODIFYING 
                 WHOSE 
               
               
                 TRANSCRIPT 
                 TRANSCRIPTS ARE 
                 GENE PRODUCT 
                 TRANSCRIPTS ARE 
               
               
                 LEVELS 
                 CHANGED 
                 LEVELS 
                 CHANGED 
               
               
                   
               
             
            
               
                 Up Regulated 
                 Early Responders 
                 Suppression of 
                 Transcription 
               
               
                 Transcripts 
                 To: 
                 cell, tissue, organ 
                 Factors 
               
               
                 (Level At 4 Hr ≅ 0 Hr) 
                  Gluphosinate 
                 or plant death 
                 Transporters 
               
               
                 or 
                  Chlorsulfuron 
                 following: 
                 Change In Cell 
               
               
                 (Level At 4 Hr &gt; 0 Hr) 
                  Glyphosate 
                  Herbicide 
                 Membrane Structure 
               
               
                   
                  and/or 2,4-D 
                  treatment or 
                 Kinases And 
               
               
                   
                   
                  under stress 
                 Phosphatases 
               
               
                   
                   
                 Activation of cell, 
                 Germins, Germin- 
               
               
                   
                   
                 tissue, organ or 
                 like proteins, 
               
               
                   
                   
                 plant death 
                 Calcium-binding 
               
               
                   
                   
                 following: 
                 proteins and H 2 O 2   
               
               
                   
                   
                  Herbicide 
                 generating and 
               
               
                   
                   
                  treatment or 
                 H 2 O 2  neutralizing 
               
               
                   
                   
                  under stress 
                 proteins. 
               
               
                   
                   
                   
                 Transcription 
               
               
                   
                   
                   
                 Activators 
               
               
                   
                   
                   
                 Change In 
               
               
                   
                   
                   
                 Chromatin Structure 
               
               
                   
                   
                   
                 And/Or Localized 
               
               
                   
                   
                   
                 DNA Topology 
               
               
                   
                   
                   
                 Annexins, cell wall 
               
               
                   
                   
                   
                 structural proteins 
               
               
                 Up Regulated 
                 Delayed Responders to 
                 Suppression of 
                 Transcription 
               
               
                 Transcripts 
                 Gluphosinate, 
                 cell, tissue, organ 
                 Factors 
               
               
                 (Level At 4 Hr &lt; 12 Hr) 
                 Chlorsulfuron, 
                 or plant death 
                 Specific Factors 
               
               
                   
                 Glyphosate and/or 2,4-D 
                 following: 
                 (Initiation And 
               
               
                   
                   
                  Herbicide 
                 Elongation) For 
               
               
                   
                   
                  treatment or 
                 Protein Synthesis 
               
               
                   
                   
                  under stress 
                 Lipid transfer 
               
               
                   
                   
                 Activation of cell, 
                 proteins 
               
               
                   
                   
                 tissue, organ or 
                 Myrosinase-binding 
               
               
                   
                   
                 plant death 
                 proteins 
               
               
                   
                   
                 following: 
                 Sugar 
               
               
                   
                   
                 Herbicide 
                 interconverting 
               
               
                   
                   
                 treatment or 
                 enzymes 
               
               
                   
                   
                 under stress 
                 Maintenance Of 
               
               
                   
                   
                   
                 mRNA Stability 
               
               
                   
                   
                   
                 Maintenance Of 
               
               
                   
                   
                   
                 Protein Stability 
               
               
                   
                   
                   
                 Maintenance Of 
               
               
                   
                   
                   
                 Protein-Protein 
               
               
                   
                   
                   
                 Interaction 
               
               
                   
                   
                   
                 Protein 
               
               
                   
                   
                   
                 translocation factors 
               
               
                   
                   
                   
                 RNA-binding 
               
               
                   
                   
                   
                 proteins 
               
               
                   
                   
                   
                 Centromere and 
               
               
                   
                   
                   
                 cytoskeleton 
               
               
                   
                   
                   
                 proteins 
               
               
                   
                   
                   
                 Lipases 
               
               
                   
                   
                   
                 Zn/Cu transporters 
               
               
                   
                   
                   
                 Cell wall structural 
               
               
                   
                   
                   
                 proteins 
               
               
                 Down-Regulated 
                 Early Responder 
                 Suppression of 
                 Transcription 
               
               
                 Transcripts 
                 Repressors Of Stress 
                 cell, tissue, organ 
                 Factors 
               
               
                 (Level At 0 Hr ≅ 4 Hr) 
                 Response State Of 
                 or plant death 
                 Change In Protein 
               
               
                 or 
                 Metabolism 
                 following: 
                 Structure By 
               
               
                 (Level At 0 Hr &gt; 4 Hr) 
                 Genes With 
                  Herbicide 
                 Phosphorylation 
               
               
                   
                 Discontinued 
                  treatment or 
                 (Kinases) Or 
               
               
                   
                 Expression Or UnsTable 
                  under stress 
                 Dephosphoryaltion 
               
               
                   
                 mRNA In Presence Of 
                 Activation of cell, 
                 (Phosphatases) 
               
               
                   
                 Herbicide or Abiotic 
                 tissue, organ or 
                 Change In 
               
               
                   
                 Stress 
                 plant death 
                 Chromatin Structure 
               
               
                   
                   
                 following: 
                 And/Or DNA 
               
               
                   
                   
                  Herbicide 
                 Topology 
               
               
                   
                   
                  treatment or 
                 H 2 O 2  neutralizing 
               
               
                   
                   
                  under stress 
                 proteins 
               
               
                   
                   
                 Zn/Cu transporters 
                 Neutralizing 
               
               
                   
                   
                 Cell wall 
                 proteins including 
               
               
                   
                   
                 structural proteins 
                 SOD and GST 
               
               
                 Down-Regulated 
                 Delayed Responder 
                 Suppression of 
                 Transcription 
               
               
                 Transcripts 
                 Repressors Of ABA 
                 cell, tissue, organ 
                 Factors 
               
               
                 (Level At 4 Hr &gt; 12 Hr) 
                 Function State Of 
                 or plant death 
                 Kinases And 
               
               
                   
                 Metabolism 
                 following: 
                 Phosphatases 
               
               
                   
                 Genes With 
                  Herbicide 
                 Stability Of Factors 
               
               
                   
                 Discontinued 
                  treatment or 
                 For Protein 
               
               
                   
                 Expression Or Unstable 
                  under stress 
                 Synthesis And 
               
               
                   
                 mRNA In Presence Of 
                 Activation of cell, 
                 Degradation 
               
               
                   
                 herbicide or Abiotic 
                 tissue, organ or 
                 Amino Acid 
               
               
                   
                 Stress 
                 plant death 
                 biosynthesis 
               
               
                   
                   
                 following: 
                 proteins including 
               
               
                   
                   
                  Herbicide 
                 aspargive synthase 
               
               
                   
                   
                  treatment or 
                 Ca-binding proteins 
               
               
                   
                   
                  under stress 
                 Lipid biosynthesis 
               
               
                   
                   
                   
                 proteins 
               
               
                   
                   
                   
                 Lipases 
               
               
                   
                   
                   
                 Zn/Cu transporters 
               
               
                   
                   
                   
                 Cell wall structural 
               
               
                   
                   
                   
                 proteins 
               
               
                   
               
            
           
         
       
     
     While viability modulating polynucleotides and gene products can act alone, combinations of these polynucleotides also affect growth and development. 
     Use of Promoters of Viability Genes, Gene Components and Products 
     Promoters of viability genes can include those that are induced by (1) destructive chemicals, e.g. herbicides, (2) stress, or (3) death. These promoters can be linked operably to achieve expression of any polynucleotide from any organism. Specific promoters from viability genes can be selected to ensure transcription in the desired tissue or organ. Proteins expressed under the control of such promoters can include those that can induce or accelerate death or those that can protect plant cells organ death. For example, stress tolerance can be increased by using promoters of viability genes to drive transcription of cold tolerance proteins, for example. Alternatively, promoters induced by apoptosis can be utilized to drive transcription of antisense constructs that inhibit cell death. 
     III.D.9. Histone Deacetylase (Axel) Responsive Genes, Gene Components and Products 
     The deacetylation of histones is known to play an important role in regulating gene expression at the chromatin level in eukaryotic cells. Histone deacetylation is catalyzed by proteins known as histone deacetylases (HDAcs). HDAcs are found in multisubunit complexes that are recruited to specific sites on nuclear DNA thereby affecting chromatin architecture and target gene transcription. Mutations in plant HDAc genes cause alterations in vegetative and reproductive growth that result from changes in the expression and activities of HDAc target genes or genes whose expression is governed by HDAc target genes. For example, transcription factor proteins control whole pathways or segments of pathways and proteins also control the activity of signal transduction pathways. Therefore, manipulation of these types of protein levels is especially useful for altering phenotypes and biochemical activities. 
     Manipulation of one or more HDAc gene activities is useful to modulate the biological activities and/or phenotypes listed below. HDAc genes and gene products can act alone or in combination. Useful combinations include HDAc genes and/or gene products with similar biological activities, or members of the same, co-regulated or functionally related biochemical pathways. Such HDAc genes and gene products can function to either increase or dampen these phenotypes or activities. 
     Examples of genes whose expression is affected by alterations in HDAc activity are shown in the Reference and Sequence Tables. These genes and/or gene products are responsible for effects on traits such as inflorescence branching and seed production. They were discovered and characterized from a much larger set of genes by experiments designed to find genes whose mRNA products are affected by a decrease in HDAc gene activity. These experiments made use of an  Arabidopsis  mutant having severely reduced mRNA levels for the histone deactylase gene AtHDAC1. 
     Microarray technology allows monitoring of gene expression levels for thousands of genes in a single experiment. This is achieved by simultaneously hybridizing two differentially labeled fluorescent cDNA pools to glass slides that contain spots of DNA (Schena et al. (1995) Science 270: 467-70). The  Arabidopsis  Functional Genomics Consortium (AFGC) has recently made public the results from such microarray experiments conducted with AFGC chips containing 10,000 non-redundant ESTs, selected from 37,000 randomly sequenced ESTs generated from mRNA of different tissues and developmental stages. 
     The sequences of the ESTs showing at least two-fold increases or decreases over the controls were identified, compared to the Ceres full-length cDNA and genomic sequence databanks, and identical Ceres clones identified. MA_diff table reports the results of this analysis, indicating those Ceres clones which are up or down regulated over controls, thereby indicating the Ceres clones which are HDAc genes. The MA_diff Table(s) reports the transcript levels of the experiment (see EXPT ID: Axel (relating to SMD 6654, SMD 6655)). For transcripts that had higher levels in the samples than the control, a “+” is shown. A “−” is shown for when transcript levels were reduced in root tips as compared to the control. For more experimental detail see the Example section below. 
     Histone Deacetylase genes are those sequences that showed differential expression as compared to controls, namely those sequences identified in the MA_diff tables with a “+” or “−” indication. 
     Histone Deacetylase Genes Identified by Cluster Analyses of Differential Expression 
     Histone Deacetylase Genes Identified by Correlation to Genes that are Differentially Expressed 
     As described above, the transcription profiles of genes that act together are well correlated. Applicants not only have identified the genes that are differentially expressed in the microarray experiments, but also have identified the genes that act in concert with them. The MA_clust table indicates groups of genes that have well correlated transcription profiles and therefore participate in the same pathway or network. 
     A pathway or network of Histone Deacetylase genes is any group in the MA_clust that comprises a cDNA ID that also appears in Expt ID Axel (relating to SMD 6654, SMD 6655) of the MA_diff table(s). 
     Histone Deacetylase Genes Identified by Correlation to Genes that Cause Physiological Consequences 
     Additionally, the differential expression data and the phenotypic observations can be merged to identify pathways or networks of Histone Deacetylase genes. A group in the MA_clust is considered a Histone Deacetylase pathway or network if the group comprises a cDNA ID that also appears in Knock-in or Knock-out tables that causes one or more of the phenotypes described in section above. 
     Histone Deacetylase Genes Identified by Amino Acid Sequence Similarity 
     Histone Deacetylase genes from other plant species typically encode polypeptides that share amino acid similarity to the sequences encoded by corn and  Arabidopsis  Histone Deacetylase genes. Groups of Histone Deacetylase genes are identified in the Protein Group table. In this table, any protein group that comprises a peptide ID that corresponds to a cDNA ID member of a Histone Deacetylase pathway or network is a group of proteins that also exhibits Histone Deacetylase functions/utilities. 
     III.D.9.a. Use of Hdac Genes, Gene Components and Products to Modulate Phenotypes 
     HDAc Genes and Gene Products are Useful to or Modulate One or More Phenotypes including growth rate; whole plant, including height, flowering time, etc.; seedling; organ; seed development; embryo; germination, and cell differentiation. 
     To improve any of the phenotype(s) above, activities of one or more of the HDAc genes or gene products can be modulated and tested by screening for the desired trait. Specifically, the gene, mRNA levels, or protein levels can be altered in a plant utilizing the procedures described herein and the phenotypes can be assayed. As an example, a plant can be transformed according to Bechtold and Pelletier (1998, Methods. Mol. Biol. 82:259-266) and visually inspected for the desired phenotype or metabolically and/or functionally assayed according to Wu et al. (2000, Plant J 22: 19-27), Hu et al. (2000, J Biol Chem 275: 15254-64), Johnson and Turner (1999, Semin Cell Dev Biol 10: 179-88), Koyama et al. (2000, Blood 96: 1490-5), Wu et al. (2000, Plant J 22: 19-27), Li (1999, Nature Genetics 23: 5-6), Adams et al. (2000, Development 127: 2493-2502) and Lechner et al. (2000, Biochemistry 39: 1683-92). 
     III.D.9.b. Use of Hdac Development Genes, Gene Components and Products to Modulate Biochemical Activities 
     The activities of one or more of the HDAc genes can be modulated to change biochemical or metabolic activities and/or pathways such as those noted below. Such biological activities can be measured according to the citations included in the Table below: 
     
       
         
           
               
               
               
             
               
                   
               
               
                   
                 BIOCHEMICAL OR 
                   
               
               
                   
                 METABOLIC ACTIVITIES 
                 CITATIONS INCLUDING 
               
               
                 PROCESS 
                 AND/OR PATHWAYS 
                 ASSAYS 
               
               
                   
               
             
            
               
                 Growth, Differentiation 
                 Cell Differentiation 
                 Koyama et al. (2000) Blood 
               
               
                 And Development 
                   
                 96: 1490-5 
               
               
                   
                 Cell Cycle Progression 
                 Hu et al. (2000) J Biol Chem 
               
               
                   
                   
                 275: 15254-64 
               
               
                 Metabolism 
                 Chromatin Structure 
                 Hu et al. (2000) J Biol Chem 
               
               
                   
                   
                 275: 15254-64 
               
               
                   
                 Gene Transcription And 
                 Johnson and Turner (1999) 
               
               
                   
                 Chromatin Assembly 
                 Semin Cell Dev Biol 10: 179-88 
               
               
                 Reproduction And Seed 
                 Seed Development 
                 Wu et al. (2000) Plant J 22: 19-27 
               
               
                 Development 
                 Seed Germination 
                 Lechner et al. (2000) 
               
               
                   
                   
                 Biochemistry 39: 1683-92 
               
               
                   
                 Independent Embryo 
                 Ohad et al. (1996) PNAS USA 
               
               
                   
                 Fertilization 
                 93: 5319-24 
               
               
                   
                 Fertilization Independent 
                 Chaudhury et al. (1997) PNAS 
               
               
                   
                 Seed Development 
                 USA 94: 4222-28 
               
               
                   
                 Megagametogenesis 
                 Christensen et al. (1997) Sex 
               
               
                   
                   
                 Plant Reproduc 10: 49-64 
               
               
                   
               
            
           
         
       
     
     Other biological activities that can be modulated by the HDAc genes and gene products are listed in the REFERENCE Table. Assays for detecting such biological activities are described in the Protein Domain table. 
     Profiles of these different HDAc genes are shown in the Table below with examples of associated biological activities. 
                                         TRAN-           EXAMPLES OF       SCRIPT   TYPE OF   PHYSIOLOGICAL   BIOCHEMICAL       LEVELS   GENES   CONSEQUENCES   ACTIVITY                  Up   Responders To   Gene Repression   Transporters       Regulated   HDAc Activity   Activity   Metabolic enzymes       Transcripts       Cell Cycle   Kinases and               Progression   phosphatases               Chromatin   Transcription               Condensation   activators               Synthesis Of   Change in               Metabolites   chromatin structure               And/Or Proteins   and/or localized               Modulation Of   DNA topology               Transduction               Pathways               Specific Gene               Transcription               Initiation       Down-   Responder To   Negative   Transcription       Regulated   Hdac Inhibitors   Regulation Of   factors       Transcripts   Genes With   Acetylation   Change in protein           Discontinued   Pathways   structure by           Expression Or   Changes In   phosphorylation           UnsTable   Pathways And   (kinases) or           Mrna In   Processes   dephosphorylation           Presence   Operating In Cells   (phosphatases)           Of Hdac   Changes In   Change in               Metabolism   chromatin structure                   and/or DNA                   topology                   Stability of factors                   for protein synthesis                   and degradation                   Metabolic enzymes                    
Use of Promoters of Histone Deacetylase Responsive Genes
 
     Promoters of Histone Deacetylase responsive genes are useful for transcription of any desired polynucleotide or plant or non-plant origin. Further, any desired sequence can be transcribed in a similar temporal, tissue, or environmentally specific patterns as the Histone Deacetylase responsive genes where the desired sequence is operably linked to a promoter of a Histone Deacetylase responsive gene. The protein product of such a polynucleotide is usually synthesized in the same cells, in response to the same stimuli as the protein product of the gene from which the promoter was derived. Such promoter are also useful to produce antisense mRNAs to down-regulate the product of proteins, or to produce sense mRNAs to down-regulate mRNAs via sense suppression. 
     III.E. Stress Responsive Genes, Gene Components and Products 
     III.E.1. Cold Responsive Genes, Gene Components and Products 
     The ability to endure low temperatures and freezing is a major determinant of the geographical distribution and productivity of agricultural crops. Even in areas considered suiTable for the cultivation of a given species or cultivar, can give rise to yield decreases and crop failures as a result of aberrant, freezing temperatures. Even modest increases (1-2° C.) in the freezing tolerance of certain crop species would have a dramatic impact on agricultural productivity in some areas. The development of genotypes with increased freezing tolerance would provide a more reliable means to minimize crop losses and diminish the use of energy-costly practices to modify the microclimate. 
     Sudden cold temperatures result in modulation of many genes and gene products, including promoters. Examples of such cold responsive genes and gene products are shown in the Reference, Sequence, Protein Group, Protein Group Matrix tables, MA_diff and MA_clust tables. These genes and/or products are responsible for effects on traits such as plant vigor and seed yield. They were discovered and characterized from a much larger set by experiments designed to find genes whose mRNA products changed in response to cold treatment. 
     Manipulation of one or more cold responsive gene activities is useful to modulate the biological activities and/or phenotypes listed below. Cold responsive genes and gene products can act alone or in combination. Useful combinations include cold responsive genes and/or gene products with similar transcription profiles, similar biological activities, or members of the same or functionally related biochemical pathways. Whole pathways or segments of pathways are controlled by transcription factor proteins and proteins controlling the activity of signal transduction pathways. Therefore, manipulation of the levels of such proteins is especially useful for altering phenotypes and biochemical activities of plants. The MA_diff Table(s) reports the transcript levels of the experiment (see EXPT ID: 108578, 108579, 108533, 108534). For transcripts that had higher levels in the samples than the control, a “+” is shown. A “−” is shown for when transcript levels were reduced in root tips as compared to the control. For more experimental detail see the Example section below. 
     Cold genes are those sequences that showed differential expression as compared to controls, namely those sequences identified in the MA_diff tables with a “+” or “−” indication. 
     Cold Genes Identified by Cluster Analyses of Differential Expression 
     Cold Genes Identified By Correlation To Genes That Are Differentially Expressed 
     As described above, the transcription profiles of genes that act together are well correlated. Applicants not only have identified the genes that are differentially expressed in the microarray experiments, but also have identified the genes that act in concert with them. The MA_clust table indicates groups of genes that have well correlated transcription profiles and therefore participate in the same pathway or network. 
     A pathway or network of Cold genes is any group in the MA_clust that comprises a cDNA ID that also appears in Expt ID 108578, 108579, 108533, 108534 of the MA_diff table(s). 
     Cold Genes Identified by Correlation to Genes that Cause Physiological Consequences 
     Additionally, the differential expression data and the phenotypic observations can be merged to identify pathways or networks of Cold genes. A group in the MA_clust is considered a Cold pathway or network if the group comprises a cDNA ID that also appears in Knock-in or Knock-out tables that causes one or more of the phenotypes described in section above. 
     Cold Genes Identified by Amino Acid Sequence Similarity 
     Cold genes from other plant species typically encode polypeptides that share amino acid similarity to the sequences encoded by corn and  Arabidopsis  Cold genes. Groups of Cold genes are identified in the Protein Group table. In this table, any protein group that comprises a peptide ID that corresponds to a cDNA ID member of a Cold pathway or network is a group of proteins that also exhibits Cold functions/utilities. 
     Such cold responsive genes and their products can function to either increase or dampen the phenotypes and activities below either in response to cold treatment or in the absence of cold temperature fluctuations. 
     Further, promoters of cold responsive genes, as described in the Reference tables, for example, are useful to modulate transcription that is induced by ABA or any of the following phenotypes or biological activities below. 
     III.E.1.a. Use of Cold-Responsive Genes to Modulate Phenotypes 
     Cold responsive genes and gene products are useful to or modulate one or more phenotypes including cold tolerance, below 7° C., for example, cells, organelles, proteins, dehydration resistance, growth rate, whole plant, including height, bolting time, etc., organs, biomass, fresh and dry weight during any time in plant life, such as maturation, number, size, and/or weight of flowers, seeds, branches, or leaves; seed yield in terms of number, size, weight, harvest index, or water content, fruit yield in terms of number, size, weight, harvest index, water content. 
     To regulate any of the phenotype(s) above, activities of one or more of the cold responsive genes or gene products can be modulated and the plants can be tested by screening for the desired trait. Specifically, the gene, mRNA levels, or protein levels can be altered in a plant utilizing the procedures described herein and the phenotypes can be screened for variants as in Winkler et al. (1998) Plant Physiol 118: 743-50 and assayed, for example, in accordance to Steponokus et al. (1993) Biochimica et Biophysica Acta 1145: 93-104; Quinn (1988) Symp Soc. Exp. Biol. 42: 237-258; Bectold and Pelletier (1998) Methods Mol. Biol. 82: 259-266; Kasuga et al. (1999) Nature Biotechnology 17: 287-291; Guy et al. (1998) Cryobiology 36: 301-314; or Liu et al. (1998) Plant Cell 10: 1391-1406. 
     III.E.1.b. Use of Cold-Responsive Genes to Modulate Biochemical Activities 
     The activities of one or more of the cold responsive genes can be modulated to change biochemical or metabolic activities and/or pathways such as those noted below. Such biological activities are documented and can be measured according to the citations above and those included in the Table below: 
     
       
         
           
               
               
               
             
               
                   
               
               
                   
                 BIOCHEMICAL OR 
                   
               
               
                   
                 METABOLIC ACTIVITIES 
                 CITATIONS INCLUDING 
               
               
                 PROCESS 
                 AND/OR PATHWAYS 
                 ASSAYS 
               
               
                   
               
             
            
               
                 Cold Tolerance 
                 Viability Of Plant Protoplasts At 
                 Steponkus (1998) PNAS USA 
               
               
                   
                 Low Temperatures. 
                 95: 14570-14575 
               
               
                   
                 Viability Of Yeast At Low 
                 Schirmer et al. (1994) Plant Cell 
               
               
                   
                 Temperatures. 
                 6: 1899-1909 
               
               
                   
                 Complementation Of Yeast Tsp 
                 Zentella et al. (1999) Plant 
               
               
                   
                 Mutant 
                 Physiology, 119: 1473-1482 
               
               
                   
                 Viability Of  E. Coli  At Low 
                 Yeh et. al. (1997) PNAS 94: 
               
               
                   
                 Temperatures. 
                 10967-10972 
               
               
                   
                 Induction Of Cold Shock 
                 Pearce (1999) Plant Growth 
               
               
                   
                 Response Genes 
                 Regulation 29: 47-76. 
               
               
                 Lipid Composition 
                 Altered Composition Of 
                 Sayanova et al. (1999) Journal of 
               
               
                   
                 Membrane Fatty Acids 
                 Experimental Botany 50: 1647-1652 
               
               
                   
                   
                 Sayanova (1997) PNAS 
               
               
                   
                   
                 USA 94: 4211-4216 
               
               
                   
                 ALTERATION OF 
                 Porta et al. (1999) Plant and Cell 
               
               
                   
                 LIPOXYGENASE ENZYME 
                 Physiology 40: 850-858. 
               
               
                   
                 ACCUMULATION AND 
               
               
                   
                 ACTIVITY 
               
               
                 Protein 
                 PROTEIN 
                 Wisniewski et al.(1999) 
               
               
                 Composition 
                 DENATURATION 
                 Physiologia Plantarum 105: 600-608 
               
               
                   
                 Protein Hydrophilicity 
                 Steponkus (1998) PNAS USA 95: 
               
               
                   
                   
                 14570-14575 
               
               
                 Modulation of 
                 Induced Transcription 
                 Current Protocols in Molecular 
               
               
                 Transcription 
                 Factors And Other Dna 
                 Biology/edited by Frederick M. 
               
               
                 Induced by Low 
                 Binding Proteins 
                 Ausubel . . . [et al.]. New York: 
               
               
                 Temperatures 
                 Transcription Of Specific 
                 Published by Greene Pub. 
               
               
                   
                 Genes 
                 Associates and Wiley- 
               
               
                   
                   
                 Interscience: J. Wiley, c1987. 
               
               
                   
                   
                 Steponkus (1998) PNAS USA 95: 
               
               
                   
                   
                 14570-14575 
               
               
                   
                   
                 Kadyrzhanova et al., Plant Mol 
               
               
                   
                   
                 Biol (1998) 36(6): 885-895; and 
               
               
                   
                   
                 Pearce et al., Plant Physiol (1998) 
               
               
                   
                   
                 117(3): 787-795 
               
               
                 Signal 
                 Plasma Membrane Proteins 
                 Goodwin et al., Plant Mol Biol 
               
               
                 Transduction 
                   
                 (1996) 31(4) 777-781; and 
               
               
                   
                   
                 Koike et al., Plant Cell Physiol 
               
               
                   
                   
                 (1997) 38(6): 707-716 
               
               
                 Oxygen 
                 Glutathione 
                 Kocsy et al., Planta (2000) 
               
               
                 Scavengers 
                   
                 210(2): 295-301 
               
               
                   
                 Accumulation Active O 2  and 
                 Tao et al., Cryobiology (1998) 
               
               
                   
                 H 2 O 2  Scavengers 
                 37(1): 38-45 
               
               
                 Dehydration 
                 Dehydrin 
                 Ismail et al., Plant Physiol (1999) 
               
               
                   
                   
                 120(1): 237-244 
               
               
                   
                 Transcription of mRNA 
                 Kaye et al., Plant Physiol (1998) 
               
               
                   
                   
                 116(4): 1367-1377 
               
               
                 Metabolism 
                 Soluble Sugars and/or 
                 Wanner et al., (1999) Plant 
               
               
                   
                 Proline 
                 Physiol 120(2): 391-400 
               
               
                 RNA/DNA 
                 Stabilization of RNA/DNA 
                 Jiang, Weining et al., (1997) 
               
               
                 Chaperone 
                 through RNA binding and 
                 Journal of Biological Chemistry, 
               
               
                   
                 modulation of RNA 
                 272: 196-202. 
               
               
                   
                 translation through RNA 
                 Fukunaga et al., (1999) Journal of 
               
               
                   
                 binding and or unwinding. 
                 Plant Research, 112: 263-272. 
               
               
                 Protein Chaperone 
                 Stabilize protein structure 
                 Forreiter and Nover (1998) Journal 
               
               
                   
                 and facilitate protein folding 
                 of Biosciences 23: 287-302 
               
               
                   
               
            
           
         
       
     
     Other biological activities that can be modulated by the cold responsive genes and their products are listed in the Reference tables. Assays for detecting such biological activities are described in the Protein Domain table. 
     Cold responsive genes are characteristically differentially expressed in response to fluctuating cold temperature levels, whether internal or external to an organism or cell. The MA_diff table reports the changes in transcript levels of various cold responsive genes in the aerial parts of seedlings at 1 and 6 hours at 4° C. in the dark as compared to aerial parts of seedlings covered with aluminium foil, and grown at 20° C. in the growth chamber. 
     The data from this time course can be used to identify a number of types of cold responsive genes and gene products, including “early responders” and “delayed responders”. Profiles of these different cold responsive genes are shown in the Table below together with examples of the kinds of associated biological activities. 
     
       
         
           
               
               
               
               
             
               
                   
               
               
                   
                   
                   
                 EXAMPLES OF 
               
               
                 GENE 
                 FUNCTIONAL 
                 TYPE OF 
                 BIOCHEMICAL 
               
               
                 EXPRESSION 
                 CATEGORY 
                 BIOLOGICAL 
                 ACTIVITIES OF GENE 
               
               
                 LEVELS 
                 OF GENE 
                 ACTIVITY 
                 PRODUCTS 
               
               
                   
               
             
            
               
                 Upregulated Genes 
                 Early 
                 Perception Of 
                 Transcription Factors 
               
               
                 (Level At 1 h ≅ 6 h) 
                 Responders To 
                 Cold 
                 Kinases And 
               
               
                 or 
                 Cold 
                 Induction Of 
                 Phosphatases 
               
               
                 (Level At 1 h &gt; 6 h) 
                   
                 Cold Response 
                 Amino Acid Sugar And 
               
               
                   
                   
                 Signal 
                 Metabolite Transporters 
               
               
                   
                   
                 Transduction 
                 Carbohydrate Catabolic 
               
               
                   
                   
                 Pathways 
                 And Anabolic Enzymes. 
               
               
                   
                   
                 Initiating 
                 Lipid Biosynthesis 
               
               
                   
                   
                 Specific Gene 
                 Enzymes 
               
               
                   
                   
                 Transcription 
                 Lipid Modification 
               
               
                   
                   
                 Osmotic 
                 Enzymes, Example 
               
               
                   
                   
                 Adjustment 
                 Desaturases 
               
               
                   
                   
                 Alteration Of 
                 Ice Crystal Binding 
               
               
                   
                   
                 Lipid 
                 Proteins 
               
               
                   
                   
                 Composition. 
                 Hydrophilic Proteins 
               
               
                   
                   
                 Ice Nucleation 
               
               
                   
                   
                 Inhibition 
               
               
                   
                   
                 Mitigation Of 
               
               
                   
                   
                 Dehydration By 
               
               
                   
                   
                 Sequestering 
               
               
                   
                   
                 Water 
               
               
                   
                 Stress Response 
                 Repression Of 
                 Transcription Factors 
               
               
                   
                   
                 General 
                 Kinases And 
               
               
                   
                   
                 Biochemical 
                 Phosphatases 
               
               
                   
                   
                 Pathways To 
                 Protein Stability Factors 
               
               
                   
                   
                 Optimize Cold 
                 mRNA Stability Factors 
               
               
                   
                   
                 Response 
                 mRNA Translation 
               
               
                   
                   
                 Pathways. 
                 Factors 
               
               
                   
                   
                 Stabilization Of 
                 Protein Turnover Factors 
               
               
                   
                   
                 Protein/Enzyme 
                 Oxygen Radical 
               
               
                   
                   
                 Activity At Low 
                 Scavengers, Example- 
               
               
                   
                   
                 Temperature 
                 Peroxidases 
               
               
                   
                   
                 Protection 
                 Energy Generation 
               
               
                   
                   
                 Against Oxidative 
                 Enzymes EtOH 
               
               
                   
                   
                 Stress 
                 Detoxification 
               
               
                   
                   
                 Anaerobic 
               
               
                   
                   
                 Metabolism 
               
               
                 Upregulated Genes 
                 Delayed 
                 Respiration, 
                 Transcription Factors 
               
               
                 (Level At 1 h &lt; 6 h) 
                 Responders To 
                 Photosynthesis 
                 Kinases And 
               
               
                   
                 Cold Stress 
                 And Protein 
                 Phosphatases 
               
               
                   
                 Cold 
                 Synthesis 
                 Protein Stability Factors 
               
               
                   
                 Acclimation 
                 Carbohydrate 
                 mRNA Stability Factors 
               
               
                   
                 Genes 
                 And Amino Acid 
                 mRNA Translation 
               
               
                   
                   
                 Solute 
                 Factors 
               
               
                   
                   
                 Accumulation 
                 Protein Turnover Factors 
               
               
                   
                   
                 Increased Fatty 
                 Oxygen Radical 
               
               
                   
                   
                 Acid Desaturation 
                 Scavengers, Peroxidase 
               
               
                   
                   
                 To Increase Lipid 
                 Metabolic Enzymes 
               
               
                   
                   
                 Membrane 
               
               
                   
                   
                 Stability 
               
               
                   
                   
                 Increased 
               
               
                   
                   
                 Accumulation Or 
               
               
                   
                   
                 Activity Of 
               
               
                   
                   
                 Oxidative Stress 
               
               
                   
                   
                 Protection Proteins 
               
               
                   
                   
                 Stabilization Of 
               
               
                   
                   
                 Protein/Enzyme 
               
               
                   
                   
                 Activity At Low 
               
               
                   
                   
                 Temperature 
               
               
                   
                   
                 Protection 
               
               
                   
                   
                 Against Oxidative 
               
               
                   
                   
                 Stress 
               
               
                   
                   
                 Extracellular 
               
               
                   
                   
                 Matrix 
               
               
                   
                   
                 Modification 
               
               
                   
                 Stress Response 
                 Stabilization Of 
                 Transcription Factors 
               
               
                   
                 Genes 
                 Protein/Enzyme 
                 Kinases And 
               
               
                   
                   
                 Activity At Low 
                 Phosphatases 
               
               
                   
                   
                 Temperature 
                 Protein Stability Factors 
               
               
                   
                   
                 Protection 
                 mRNA Stability Factors 
               
               
                   
                   
                 Against Oxidative 
                 mRNA Translation 
               
               
                   
                   
                 Stress 
                 Factors 
               
               
                   
                   
                 Anaerobic 
                 Protein Turnover Factors 
               
               
                   
                   
                 Metabolism 
                 Oxygen Radical 
               
               
                   
                   
                   
                 Scavengers, Example- 
               
               
                   
                   
                   
                 Peroxidase 
               
               
                   
                   
                   
                 Energy Generation 
               
               
                   
                   
                   
                 Enzymes, Etoh 
               
               
                   
                   
                   
                 Detoxification 
               
               
                 Downregulated 
                 Early 
                 Negative 
                 Transcription Factors 
               
               
                 (Level At 1 h ≅ 6 h) 
                 Responder 
                 Regulation Of 
                 Kinases And 
               
               
                 (Level At 6 h &gt; 1 h) 
                 Repressors Of 
                 Cold Signal 
                 Phosphatases 
               
               
                   
                 Cold Stress 
                 Transduction 
                 Protein Stability Factors 
               
               
                   
                 Metabolism 
                 Pathways Released 
                 mRNA Stability Factors 
               
               
                   
                   
                   
                 mRNA Translation 
               
               
                   
                   
                   
                 Factors 
               
               
                   
                   
                   
                 Protein Turnover Factors 
               
               
                   
                 Genes With 
                 Negative 
                 Cold Repressed 
               
               
                   
                 Discontinued 
                 Regulation Of 
                 Metabolic Pathway 
               
               
                   
                 Expression Or 
                 Cold Induced 
                 Proteins 
               
               
                   
                 UnsTable 
                 Transcription 
                 Factors Coordinating And 
               
               
                   
                 mRNA In Cold 
                 Reduced 
                 Controlling Central C and 
               
               
                   
                   
                 Reduction In 
                 N Metabolism 
               
               
                   
                   
                 Gene Expression 
                 Storage Proteins 
               
               
                   
                   
                 In Pathways Not 
               
               
                   
                   
                 Required Under 
               
               
                   
                   
                 Cold Conditions 
               
               
                   
                   
                 Induced mRNA 
               
               
                   
                   
                 Turnover 
               
               
                 Down-Regulated 
                 Delayed 
                 Maintenance Of 
                 Transcription Factors 
               
               
                 Transcripts 
                 Responder 
                 Cold Induced State 
                 Kinases And 
               
               
                 (Level At 1 h &gt; 6 h) 
                 Repressors Of 
                 Of Metabolism 
                 Phosphatases 
               
               
                   
                 Cold Stress 
                 Reduction In 
                 Protein Stability Factors 
               
               
                   
                 Metabolism 
                 Gene Expression 
                 mRNA Stability Factors 
               
               
                   
                 Genes With 
                 For Pathways Not 
                 mRNA Translation 
               
               
                   
                 Discontinued 
                 Required Under 
                 Factors 
               
               
                   
                 Expression Or 
                 Cold Conditions 
                 Protein Turnover Factors 
               
               
                   
                 UnsTable 
                 Induced mRNA 
                 Cold Repressed 
               
               
                   
                 mRNA In Cold 
                 Turnover 
                 Metabolic Pathway 
               
               
                   
                   
                   
                 Proteins 
               
               
                   
                   
                   
                 Factors Coordinating And 
               
               
                   
                   
                   
                 Controlling Central C and 
               
               
                   
                   
                   
                 N Metabolism 
               
               
                   
                   
                   
                 Storage Proteins 
               
               
                   
               
            
           
         
       
     
     Further, any desired sequence can be transcribed in similar temporal, tissue, or environmentally specific patterns as the cold responsive genes when the desired sequence is operably linked to a promoter of a cold responsive gene. 
     III.E.2. Heat Responsive Genes, Gene Components and Products 
     The ability to endure high temperatures is a major determinant of the geographical distribution and productivity of agricultural crops. Decreases in yield and crop failure frequently occur as a result of aberrant, hot conditions even in areas considered suiTable for the cultivation of a given species or cultivar. Only modest increases in the heat tolerance of crop species would have a dramatic impact on agricultural productivity. The development of genotypes with increased heat tolerance would provide a more reliable means to minimize crop losses and diminish the use of energy-costly practices to modify the microclimate. 
     Changes in temperature in the surrounding environment or in a plant microclimate results in modulation of many genes and gene products. Examples of such heat stress responsive genes and gene products are shown in the Reference, Sequence, Protein Group, Protein Group Matrix, MA_diff and MA_clust tables. These genes and/or products are responsible for effects on traits such as plant vigor and seed yield. They were discovered and characterized from a much larger set by experiments designed to find genes whose mRNA products changed in response to high temperatures. 
     While heat stress responsive polynucleotides and gene products can act alone, combinations of these polynucleotides also affect growth and development. Useful combinations include different heat stress responsive polynucleotides and/or gene products that have similar transcription profiles or similar biological activities, and members of the same or similar biochemical pathways. Whole pathways or segments of pathways are controlled by transcription factor proteins and proteins controlling the activity of signal transduction pathways. Therefore, manipulation of such protein levels is especially useful for altering phenotypes and biochemical activities of plants. In addition, the combination of a heat stress responsive polynucleotide and/or gene product with other environmentally responsive polynucleotide is also useful because of the interactions that exist between stress pathways, pathogen stimulated pathways, hormone-regulated pathways, nutritional pathways and development. Here, in addition to polynucleotides having similar transcription profiles and/or biological activities, useful combinations include polynucleotides that may have different transcription profiles, but which participate in common or overlapping pathways. The MA_diff Table(s) reports the transcript levels of the experiment (see EXPT ID: 108576, 108577, 108522, 108523). For transcripts that had higher levels in the samples than the control, a “+” is shown. A “−” is shown for when transcript levels were reduced in root tips as compared to the control. For more experimental detail see the Example section below. 
     Heat genes are those sequences that showed differential expression as compared to controls, namely those sequences identified in the MA_diff tables with a “+” or “−” indication. 
     Heat Genes Identified by Cluster Analyses of Differential Expression 
     Heat Genes Identified by Correlation to Genes that are Differentially Expressed 
     As described above, the transcription profiles of genes that act together are well correlated. Applicants not only have identified the genes that are differentially expressed in the microarray experiments, but also have identified the genes that act in concert with them. The MA_clust table indicates groups of genes that have well correlated transcription profiles and therefore participate in the same pathway or network. 
     A pathway or network of Heat genes is any group in the MA_clust that comprises a cDNA ID that also appears in Expt ID 108576, 108577, 108522, 108523 of the MA_diff table(s). 
     Heat Genes Identified by Correlation to Genes that Cause Physiological Consequences 
     Additionally, the differential expression data and the phenotypic observations can be merged to identify pathways or networks of Heat genes. A group in the MA_clust is considered a Heat pathway or network if the group comprises a cDNA ID that also appears in Knock-in or Knock-out tables that causes one or more of the phenotypes described in section above. 
     Heat Genes Identified by Amino Acid Sequence Similarity 
     Heat genes from other plant species typically encode polypeptides that share amino acid similarity to the sequences encoded by corn and  Arabidopsis  Heat genes. Groups of Heat genes are identified in the Protein Group table. In this table, any protein group that comprises a peptide ID that corresponds to a cDNA ID member of a Heat pathway or network is a group of proteins that also exhibits Heat functions/utilities. 
     Such heat stress responsive genes and gene products can function either to increase or dampen the above phenotypes or activities either in response to changes in temperature or in the absence of temperature fluctuations. 
     Further, promoters of heat responsive genes, as described in the Reference tables, for example, are useful to modulate transcription that is induced by heat or any of the following phenotypes or biological activities below. 
     III.E.2.a. Use of Heat Stress Responsive Genes to Modulate Phenotypes 
     Heat stress responsive genes and gene products can be used to alter or modulate one or more phenotypes including heat tolerance (above 20° C., 23° C., 27° C., 30° C., 33° C., 37° C., 40° C. or 42° C.), heat tolerance of of cells, of organelles, of proteins, of cells or organelles dehydration resistance, growth rate, whole plant, including height, bolting time, etc., organs, biomass, fresh and dry weight during any time in plant life, such as maturation, number, size, and weight of flowers, seeds, branches, or leaves; seed yield in number, size, weight, harvest index; fruit yield in terms of number, size, weight, or harvest index, stress responses such as mediation of response to desiccation, drought, salt, disease, wounding, cold and other stresses, and reproduction 
     To regulate any of the phenotype(s) above, activity of one or more of the heat stress responsive genes or gene products can be modulated and the plants tested by screening for the desired trait. Specifically, the gene, mRNA levels, or protein levels can be altered in a plant utilizing the procedures described herein and the phenotypes can be assayed. As an example, a plant can be transformed according to Bechtold and Pelletier (1998, Methods. Mol. Biol. 82:259-266) and/or screened for variants as in Winkler et al. (1998) Plant Physiol 118: 743-50 and visually inspected for the desired phenotype or metabolically and/or functionally assayed according to Queitsch et al. (2000, The Plant Cell 12: 479-92). 
     III.E.2.b. Use of Heat Stress Responsive Genes to Modulate Biochemical Activities 
     The activities of one or more of the heat stress responsive genes can be modulated to change biochemical or metabolic activities and/or pathways such as those noted below. Such biological activities can be measured according to the citations included in the Table below: 
     
       
         
           
               
               
               
             
               
                   
               
               
                   
                 BIOCHEMICAL OR 
                   
               
               
                   
                 METABOLIC ACTIVITIES 
                 CITATION INCLUDING 
               
               
                 PROCESS 
                 AND/OR PATHWAYS 
                 ASSAY 
               
               
                   
               
             
            
               
                 Cell Growth and 
                 Regulation And Molecular 
                 Wisniewski et al. 
               
               
                 Differentiation 
                 Chaperones 
                 (1999) Physiolgia 
               
               
                   
                 Maintenance Of Native 
                 Plantarum 105: 
               
               
                   
                 Conformation (Cytosolic 
                 600-608 
               
               
                   
                 Proteins) 
                 Queitsch et al. 
               
               
                   
                 Reactivation Of 
                 (2000) The Plant 
               
               
                   
                 Aggregation And Protein 
                 Cell 12: 479-92 
               
               
                   
                 Folding 
                 Lee and Vierling 
               
               
                   
                 Autoregulation Of Heat 
                 (2000) Plant 
               
               
                   
                 Shock Response 
                 Physiol. 122: 189-197 
               
               
                   
                 Regulation Of Translational 
                 Schwechheimer 
               
               
                   
                 Efficiency 
                 (1998) Plant Mol 
               
               
                   
                 Regulation Of Kinase 
                 Biol 36: 195-204 
               
               
                   
                 Activity 
                 Shi et al. (1998) 
               
               
                   
                 Regulation Of Calcium 
                 Genes and 
               
               
                   
                 Mediated Signal 
                 Development 12: 
               
               
                   
                 Transduction 
                 654-66 
               
               
                   
                   
                 Wells et al. (1998) 
               
               
                   
                   
                 Genes and 
               
               
                   
                   
                 Development 12: 
               
               
                   
                   
                 3236-51 
               
               
                   
                   
                 Lis et al. (2000) 
               
               
                   
                   
                 Genes and 
               
               
                   
                   
                 Development 14: 
               
               
                   
                   
                 792-803 
               
               
                   
                   
                 Malho, R.(1999) Plant 
               
               
                   
                   
                 Biology 1: 487-494. 
               
               
                   
                   
                 Sheen, Jen.(1996) 
               
               
                   
                   
                 Science 274: 1900-1902. 
               
               
                   
                   
                 Farmer, P. et al., (1999.) 
               
               
                   
                   
                 Biochimica et Biophysica 
               
               
                   
                   
                 Acta 1434: 6-17. 
               
               
                 Gene regulation 
                 Transcriptional Regulation Of 
                 Current Protocols in 
               
               
                   
                 Heat Induced Proteins 
                 Molecular Biology/edited 
               
               
                   
                 Through DNA Binding 
                 by Frederick M. Ausubel . . . 
               
               
                   
                 Proteins. 
                 [et al.]. New York: 
               
               
                   
                 Transcriptional Regulation Of 
                 Published by Greene Pub. 
               
               
                   
                 Heat Induced Proteins 
                 Associates and Wiley- 
               
               
                   
                 Through Protein-Protein 
                 Interscience: J. Wiley, 
               
               
                   
                 Interactions Between DNA 
                 c1987. 
               
               
                   
                 Binding Proteins And 
                 Steponkus (1998) PNAS 
               
               
                   
                 Coactivators. 
                 USA 95: 14570-14575 
               
               
                   
                 Transcriptional Regulation Of 
                 Gubler et al. (1999) Plant 
               
               
                   
                 Heat Induced Proteins 
                 Journal 17: 1-9 
               
               
                   
                 Through Protein 
                 Glenn et al. (1999) 
               
               
                   
                 Phosphorylation And 
                 Journal of Biological 
               
               
                   
                 Dephosphorylation 
                 Chemistry, 274: 36159-36167 
               
               
                   
                 Transcriptional Regulation Of 
                 Zhou et al., (1997) 
               
               
                   
                 Thermal Stress Induced 
                 EMBO Journal16: 3207-3218. 
               
               
                   
                 Genes By Protein-Protein 
                 Sessa et al., 
               
               
                   
                 Interactions. 
                 (2000) EMBO Journal 19: 
               
               
                   
                 Translational Regulation Of 
                 2257-2269. 
               
               
                   
                 Thermal Stress Induced 
                 Burnett et al., (2000) 
               
               
                   
                 Messenger Rnas. 
                 Journal of Experimental 
               
               
                   
                 Transcriptional Regulation Of 
                 Botany. 51: 197-205. 
               
               
                   
                 Heat Induced Genes Through 
                 Osterlund et al., (2000) 
               
               
                   
                 Chromatin Remodeling. 
                 Nature 405: 462-466. 
               
               
                   
                   
                 Gross and Watson (1998) 
               
               
                   
                   
                 Canadian Journal of 
               
               
                   
                   
                 Microbiology, 44: 341-350 
               
               
                   
                   
                 Luo, R. X., Dean, D. C. 
               
               
                   
                   
                 (1999) 
               
               
                   
                   
                 Journal of the National 
               
               
                   
                   
                 Cancer Institute 91: 1288-1294. 
               
               
                   
                   
                 Chromatin protocols 
               
               
                   
                   
                 (1999) edited by Peter B. 
               
               
                   
                   
                 Becker. Totowa, N. J.: 
               
               
                   
                   
                 Humana Press. 
               
               
                 Cell Structure 
                 Thermal Stress Protection By 
                 Goodwin et al. (1996) 
               
               
                   
                 Plasma Membrane Anchored 
                 Plant Mol Biol 31(4) 777-781; and 
               
               
                   
                 Or Secreted And/Or Cell 
                 Koike et al. (1997) Plant 
               
               
                   
                 Wall Associated Proteins. 
                 Cell Physiol 38(6): 707-716 
               
               
                 Signal Transduction 
                 Regulation Of Thermal Stress 
                 Jonak (1996) Proceedings 
               
               
                   
                 Pathways And Protein 
                 of the National Academy of 
               
               
                   
                 Activity By Protein Kinase 
                 Sciences of the United 
               
               
                   
                 And Protein Phosphatase 
                 States of America, 93: 
               
               
                   
                 Mediated Phosphorylation 
                 11274-11279. 
               
               
                   
                 And Dephosphorylation 
                 Monroy. et al., (1998) 
               
               
                   
                 Respectively. 
                 Analytical Biochemistry 
               
               
                   
                   
                 265: 183-185. 
               
               
                 Photosynthesis 
                 Regulation Of 
                 Schroda et al. (1999) The 
               
               
                   
                 Photoprotection And Repair 
                 Plant Cell 11: 1165-178 
               
               
                   
                 Of Photosystem II 
                 Oh and Lee (1996) J Plant 
               
               
                   
                   
                 Biol. 39: 301-07 
               
               
                 Stress Response 
                 Regulation Of Cytosol 
                 Dat et al. (1998) Plant 
               
               
                   
                 Peroxide Levels 
                 Physiol 116: 1351-1357 
               
               
                   
                 Regulation Of Heat Shock 
                 Kurek et al. (1999) Plant 
               
               
                   
                 Factor Binding 
                 Physiol 119: 693-703 
               
               
                   
                 Regulation Of Protein 
                 Storozhenko et al. (1998) 
               
               
                   
                 Stability During Thermal 
                 Plant Physiol 118: 1005-14 
               
               
                   
                 Stress 
                 Soto et al. (1999) Plant 
               
               
                   
                 Nucleocytoplasmic Export Of 
                 Physiol 120: 521-28 
               
               
                   
                 Heat Shock Protein Mrnas 
                 Yeh et al. (1997) PNAS 94: 
               
               
                   
                 Regulation/Reconfiguration 
                 10967-10972 
               
               
                   
                 Of Cell Architecture 
                 Winkler et al. (1998) Plant 
               
               
                   
                 Regulation Of Pathways For 
                 Physiol 118: 743-50 
               
               
                   
                 Reactivation Of “Damaged” 
                 Saavedra et al. (1997) 
               
               
                   
                 And/Or Denatured Proteins 
                 Genes and Development 
               
               
                   
                 Regulation Of Protein 
                 11: 2845-2856 
               
               
                   
                 Degradation During Thermal 
                 Parsell and Lindquist 
               
               
                   
                 Stress. 
                 (1993). Ann. Rev. Genet. 
               
               
                   
                 Regulation Of Osmotic 
                 27: 437-496. 
               
               
                   
                 Potential During Thermal 
                 Parsell and Lindquist 
               
               
                   
                 Stress. 
                 (1993). Ann. Rev. Genet. 
               
               
                   
                 Regulation Of Universal 
                 27: 437-496. 
               
               
                   
                 Stress Protein Homologue 
                 Georgopoulos and Welch 
               
               
                   
                 Activity By Phosphorylation 
                 (1993). Ann Rev. Cell Biol. 
               
               
                   
                 And Dephosphorylation. 
                 9: 601-634. 
               
               
                   
                 Regulation Of Dehydrin, 
                 Vierstra, Richard D. 
               
               
                   
                 LEA-Like And Other Heat 
                 (1996) Plant Molecular 
               
               
                   
                 STable Protein Accumulation 
                 Biology, 32: 275-302. 
               
               
                   
                   
                 Vierstra, Richard D.; 
               
               
                   
                   
                 Callis, Judy. (1999) Plant 
               
               
                   
                   
                 Molecular Biology, 
               
               
                   
                   
                 41: 435-442. 
               
               
                   
                   
                 Liu, J. et al., (1998)Plant 
               
               
                   
                   
                 Science 134: 11-20. 
               
               
                   
                   
                 Freestone, P. 1997et al., 
               
               
                   
                   
                 Journal of Molecular 
               
               
                   
                   
                 Biology, v. 274: 318-324. 
               
               
                   
                   
                 Robertson, A. J. (1994) 
               
               
                   
                   
                 Plant Physiology 105: 181-190. 
               
               
                   
               
            
           
         
       
     
     Other biological activities that can be modulated by the heat stress responsive genes and gene products are listed in the Reference tables. Assays for detecting such biological activities are described in the Protein Domain table. 
     Heat stress responsive genes are characteristically differentially transcribed in response to fluctuating temperatures, whether internal or external to an organism or cell. The MA_diff table reports the changes in transcript levels of various heat stress responsive genes in aerial tissues at 1 and 6 hours after plants were placed at 42° C. as compared to aerial tissues kept at 20° C. growth chamber temperature. 
     The data from this time course can be used to identify a number of types of heat stress responsive genes and gene products, including “early responders to heat stress,” “delayed responders to heat stress,” “early responder repressors,” and “delayed repressor responders.” Profiles of these different heat stress responsive genes are shown in the Table below together with examples of the kinds of associated biological activities. 
     
       
         
           
               
               
               
               
             
               
                   
               
               
                   
                   
                   
                 EXAMPLES OF 
               
               
                 GENE 
                 FUNCTIONAL 
                   
                 BIOCHEMICAL 
               
               
                 EXPRESSION 
                 CATEGORY OF 
                 PHYSIOLOGICAL 
                 ACTIVITIES/GENE 
               
               
                 LEVELS 
                 GENE 
                 CONSEQUENCES 
                 PRODUCTS 
               
               
                   
               
             
            
               
                 Up Regulated 
                 Early Responders 
                 Heat Stress Perception 
                 Transcription 
               
               
                 Transcripts 
                 To Heat Stress 
                 Modulation Of Heat 
                 Factors 
               
               
                 (Level At 1 h ≈ 6 h) 
                   
                 Stress Response 
                 Transporters 
               
               
                 Or 
                   
                 Transduction 
                 Changes In Cell 
               
               
                 (Level At 1 h &gt; 6 h) 
                   
                 Pathways 
                 Membrane Structure 
               
               
                   
                   
                 Specific Gene 
                 Kinases And 
               
               
                   
                   
                 Transcription 
                 Phosphatases 
               
               
                   
                   
                 Initiation 
                 Transcription 
               
               
                   
                   
                 Conditional Shift In 
                 Activators 
               
               
                   
                   
                 Preferential 
                 Changes In 
               
               
                   
                   
                 Translation Of 
                 Chromatin Structure 
               
               
                   
                   
                 Transcripts 
                 And/Or Localized 
               
               
                   
                   
                 Changes In Cell 
                 Dna Topology 
               
               
                   
                   
                 Architecture To 
                 Modification Of Pre- 
               
               
                   
                   
                 Optimize Cell 
                 Existing Translation 
               
               
                   
                   
                 Adaptation To Heat 
                 Factors By 
               
               
                   
                   
                 Stress 
                 Phosphorylation 
               
               
                   
                   
                   
                 (Kinases) Or 
               
               
                   
                   
                   
                 Dephosphorylation 
               
               
                   
                   
                   
                 (Phosphatases) 
               
               
                   
                   
                   
                 Synthesis Of New 
               
               
                   
                   
                   
                 Translation Factors 
               
               
                   
                   
                   
                 Stability Of 
               
               
                   
                   
                   
                 Mediators Of 
               
               
                   
                   
                   
                 Protein-Protein 
               
               
                   
                   
                   
                 Interaction 
               
               
                   
                   
                   
                 Heat Shock Proteins 
               
               
                   
                   
                   
                 Changes In 
               
               
                   
                   
                   
                 Organelle 
               
               
                   
                   
                   
                 Structures, 
               
               
                   
                   
                   
                 Membranes And 
               
               
                   
                   
                   
                 Energy-Related 
               
               
                   
                   
                   
                 Activities 
               
               
                   
                   
                   
                 Proteins To Catalyse 
               
               
                   
                   
                   
                 Metabolic Turnover 
               
               
                 Up Regulated 
                 “Delayed” 
                 Maintenance Of 
                 Transcription 
               
               
                 Transcripts 
                 Responders 
                 Response To Heat 
                 Factors 
               
               
                 (Level At 1 h &lt; 6 h) 
                 Maintenance Of 
                 Stress 
                 Specific Factors 
               
               
                   
                 Heat Stress 
                 Maintenance Of 
                 (Initiation And 
               
               
                   
                 Response 
                 Protein Stability And 
                 Elongation) For 
               
               
                   
                   
                 Conformation 
                 Protein Synthesis 
               
               
                   
                   
                   
                 Maintenance Of 
               
               
                   
                   
                   
                 Mrna Stability 
               
               
                   
                   
                   
                 Heat Shock Proteins 
               
               
                   
                   
                   
                 Changes In 
               
               
                   
                   
                   
                 Organelle 
               
               
                   
                   
                   
                 Structures, 
               
               
                   
                   
                   
                 Membranes And 
               
               
                   
                   
                   
                 Energy-Related 
               
               
                   
                   
                   
                 Activities 
               
               
                   
                   
                   
                 Proteins To Catalyse 
               
               
                   
                   
                   
                 Metabolic Turnover. 
               
               
                   
                   
                   
                 Stability Of 
               
               
                   
                   
                   
                 Mediators Of 
               
               
                   
                   
                   
                 Protein-Protein 
               
               
                   
                   
                   
                 Interaction 
               
               
                 Down-Regulated 
                 Early Responder 
                 Negative Regulation 
                 Transcription 
               
               
                 Transcripts 
                 Repressors Of 
                 Of Heat Stress 
                 Factors And 
               
               
                 (Level At 1 h ≈ 6 h) 
                 “Normal” State Of 
                 Response Released 
                 Activators 
               
               
                 Or 
                 Metabolism 
                 Changes In 
                 Change In Protein 
               
               
                 (Level At 6 h &gt; 1 h) 
                 Genes With 
                 Biochemical And 
                 Structure By 
               
               
                   
                 Discontinued 
                 Signal Transduction 
                 Phosphorylation 
               
               
                   
                 Expression Or 
                 Pathways And 
                 (Kinases) Or 
               
               
                   
                 UnsTable mRNA 
                 Processes Operating In 
                 Dephosphoryaltion 
               
               
                   
                 In Presence Of 
                 Cells 
                 (Phosphatases) 
               
               
                   
                 Heat Stress 
                 Reorientation Of 
                 Change In 
               
               
                   
                   
                 Metabolism 
                 Chromatin Structure 
               
               
                   
                   
                   
                 And/Or Dna 
               
               
                   
                   
                   
                 Topology 
               
               
                 Down-Regulated 
                 Delayed 
                 Maintenance Of Heat 
                 Transcription 
               
               
                 Transcripts 
                 Repressors Of 
                 Stress Response 
                 Factors And 
               
               
                 (Level At 1 hr &gt; 
                 “Normal” State Of 
                 Maintenance Of 
                 Activators 
               
               
                 6 hr) 
                 Metabolism 
                 Pathways Released 
                 Kinases And 
               
               
                   
                 Genes With 
                 From Repression 
                 Phosphatases 
               
               
                   
                 Discontinued 
                 Changes In Pathways 
                 Stability Of Factors 
               
               
                   
                 Expression Or 
                 And Processes 
                 For Protein 
               
               
                   
                 UnsTable mRNA 
                 Operating In Cells 
                 Translation 
               
               
                   
                 In Presence Of 
                 Reorientation Of 
               
               
                   
                 Heat Stress 
                 Metabolism 
               
               
                   
               
            
           
         
       
     
     Further, any desired sequence can be transcribed in similar temporal, tissue, or environmentally specific patterns as the heat responsive genes when the desired sequence is operably linked to a promoter of a heat responsive gene. 
     III.E.3. Drought Responsive Genes, Gene Components and Products 
     The ability to endure drought conditions is a major determinant of the geographical distribution and productivity of agricultural crops. Decreases in yield and crop failure frequently occur as a result of aberrant, drought conditions even in areas considered suiTable for the cultivation of a given species or cultivar. Only modest increases in the drought tolerance of crop species would have a dramatic impact on agricultural productivity. The development of genotypes with increased drought tolerance would provide a more reliable means to minimize crop losses and diminish the use of energy-costly practices to modify the microclimate. 
     Drought conditions in the surrounding environment or within a plant, results in modulation of many genes and gene products. Examples of such drought responsive genes and gene products are shown in the Reference and Sequence Tables. These genes and/or products are responsible for effects on traits such as plant vigor and seed yield. They were discovered and characterized from a much larger set by experiments designed to find genes whose mRNA products changed in response to availability of water. 
     While drought responsive polynucleotides and gene products can act alone, combinations of these polynucleotides also affect growth and development. Useful combinations include different drought responsive polynucleotides and/or gene products that have similar transcription profiles or similar biological activities, and members of the same or similar biochemical pathways. Whole pathways, or segments of pathways are controlled by transcription factor proteins and proteins controlling the activity of signal transduction pathways. Therefore, manipulation of the levels of such proteins is especially useful for altering phenotypes and biochemical activities of plants. In addition, the combination of a drought responsive polynucleotide and/or gene product with another environmentally responsive polynucleotide is also useful because of the interactions that exist between hormone-regulated pathways, stress pathways, nutritional pathways and development. Here, in addition to polynucleotides having similar transcription profiles and/or biological activities, useful combinations include polynucleotides that may have different transcription profiles but which participate in a common pathway. The MA_diff Table(s) reports the transcript levels of the experiment (see EXPT ID: 108572, 108573, 108502, 108503, 108504, 108556, 108482, 108483, 108473, 108474, 108477). For transcripts that had higher levels in the samples than the control, a “+” is shown. A “−” is shown for when transcript levels were reduced in root tips as compared to the control. For more experimental detail see the Example section below. 
     Drought genes are those sequences that showed differential expression as compared to controls, namely those sequences identified in the MA_diff tables with a “+” or “−” indication. 
     Drought Genes Identified by Cluster Analyses of Differential Expression 
     Drought Genes Identified by Correlation to Genes that are Differentially Expressed 
     As described above, the transcription profiles of genes that act together are well correlated. Applicants not only have identified the genes that are differentially expressed in the microarray experiments, but also have identified the genes that act in concert with them. The MA_clust table indicates groups of genes that have well correlated transcription profiles and therefore participate in the same pathway or network. 
     A pathway or network of Drought genes is any group in the MA_clust that comprises a cDNA ID that also appears in Expt ID 108572, 108573, 108502, 108503, 108504, 108556, 108482, 108483, 108473, 108474, 108477 of the MA_diff table(s). 
     Drought Genes Identified by Correlation to Genes that Cause Physiological Consequences 
     Additionally, the differential expression data and the phenotypic observations can be merged to identify pathways or networks of Drought genes. A group in the MA_clust is considered a Drought pathway or network if the group comprises a cDNA ID that also appears in Knock-in or Knock-out tables that causes one or more of the phenotypes described in section above. 
     Drought Genes Identified by Amino Acid Sequence Similarity 
     Drought genes from other plant species typically encode polypeptides that share amino acid similarity to the sequences encoded by corn and  Arabidopsis  Drought genes. Groups of Drought genes are identified in the Protein Group table. In this table, any protein group that comprises a peptide ID that corresponds to a cDNA ID member of a Drought pathway or network is a group of proteins that also exhibits Drought functions/utilities. 
     Such drought responsive genes and gene products can function to either increase or dampen the above phenotypes or activities either in response to drought conditions or in the absence of drought conditions. Further, promoters of drought responsive genes, as described in the Reference tables, for example, are useful to modulate transcription that is induced by drought or any of the following phenotypes or biological activities below. 
     More specifically, drought responsive genes and gene products are useful to or modulate one or more phenotypes including growth, roots, stems, buds, leaves, development, cell growth, leaves, fruit development, seed development, senescence, stress responses, and mediates response to desiccation, drought, salt and cold. 
     Further, any desired sequence can be transcribed in similar temporal, tissue, or environmentally specific patterns as the drought responsive genes when the desired sequence is operably linked to a promoter of a drought responsive gene. 
     To produce the desired phenotype(s) above, one or more of the drought response genes or gene products can be tested by screening for the desired trait. Specifically, the gene, mRNA levels, or protein levels can be altered in a plant utilizing the procedures described herein and the phenotypes can be assayed. As an example, a plant can be transformed according to Bechtold and Pelletier (1998, Methods. Mol. Biol. 82:259-266) and/or screened for variants as in Winkler et al. (1998) Plant Physiol 118: 743-50 and visually inspected for the desired phenotype or metabolically and/or functionally assayed according to Ruzin (1999, In: Plant Microtechnique and Microscopy, Oxford University Press, London) and Khanna-Chopra et al. (1999, BBRC 255:324-7). 
     Alternatively, the activities of one or more of the drought responsive genes can be modulated to change biochemical or metabolic activities and/or pathways such as those noted below. Such biological activities can be measured according to the citations included in the Table below: 
     
       
         
           
               
               
               
             
               
                   
               
               
                   
                 BIOCHEMICAL OR 
                   
               
               
                   
                 METABOLIC ACTIVITIES 
               
               
                 GENERAL CATEGORY 
                 AND/OR PATHWAYS 
                 ASSAY 
               
               
                   
               
             
            
               
                 Cell Growth and 
                 Preservation of Leaf Sub-Cellular 
                 Jagtap et al. (1998) J Exptl 
               
               
                 Differentiation 
                 Structures Including 
                 Botany 49: 1715-1721 
               
               
                   
                 Photosynthetic Apparatus 
               
               
                   
                 Preservation of Cell Membrane 
                 Munne-Bosch and Alegre 
               
               
                   
                 Structures 
                 (2000) Planta 210: 925-31 
               
               
                   
                 Regulation of Stomatal 
                 Menke et al. (2000) Plant 
               
               
                   
                 development and Physiology 
                 Physiol. 122: 677-686. 
               
               
                   
                 Regulation of Factors Involved in 
                 Harrak et al. (1999) Plant 
               
               
                   
                 the Drought-adapted change in 
                 Physiol. 121: 557-564. 
               
               
                   
                 cell ultrastructure 
               
               
                 Physiology 
                 Modulation of Transpiration 
                 Allen et al. (1999) Plant 
               
               
                   
                   
                 Cell 11: 1785-98 
               
               
                   
                   
                 Li et al. (2000) Science 
               
               
                   
                   
                 287: 300-303 
               
               
                   
                   
                 Burnett et al. (2000) J Exptl 
               
               
                   
                   
                 Bot 51: 197-205 
               
               
                   
                   
                 Raschke (1987) In: 
               
               
                   
                   
                 Stomatal function, Zeiger 
               
               
                   
                   
                 et al., Eds, 253-79 
               
               
                   
                 Modulation of Photosynthesis 
                 Sung and Krieg (1979) 
               
               
                   
                   
                 Plant Physiol 64: 852-56 
               
               
                   
                 Regulation of Epicuticular Wax 
                 Rhee et al. (1998) Plant 
               
               
                   
                 Biosynthesis 
                 Physiol 116: 901-11 
               
               
                   
                 Regulation of Carotenoid 
                 Alegre (2000) Planta 210: 
               
               
                   
                 Biosynthesis 
                 925-31 
               
               
                   
                   
                 Loggini et al (2000) Plant 
               
               
                   
                   
                 Physiol 119: 1091 
               
               
                 Stress Response 
                 Modulation of Leaf Rolling to 
                 Taiz and Zeiger (1991) In: 
               
               
                   
                 minimize water loss 
                 Plant Physiology, 
               
               
                   
                   
                 Benjamin/Cummings 
               
               
                   
                   
                 Publishing Co., Redwood 
               
               
                   
                   
                 City, pp 346-70 
               
               
                   
                 Modulation of Osmolite 
                 Hare et al. (1998) Plant, 
               
               
                   
                 Synthesis 
                 Cell and Environment 21: 
               
               
                   
                   
                 535-553 
               
               
                   
                   
                 Huan et al. (2000) Plant 
               
               
                   
                   
                 Physiol 122: 747-756 
               
               
                   
                 Regulation of gene 
                 Hare et al. (1999) J. Exptl. 
               
               
                   
                 transcriptional activity specific to 
                 Botany 333: 413-434. 
               
               
                   
                 the establishment of drought 
               
               
                   
                 tolerance 
               
               
                   
                 Regulation of protein degradation 
                 Lee and Vierling (2000) 
               
               
                   
                 and reactivation during drought 
                 Plant Physiol. 122: 189-197 
               
               
                   
                 stress condition 
               
               
                   
                 Modulation/reconfiguration of 
                 Lis et al. (2000) Genes and 
               
               
                   
                 translation machineries 
                 Development 14: 792-803 
               
               
                   
                 (“recycling” mechanisms) 
               
               
                   
                 adapTable to drought condition 
               
               
                 Signal Transduction 
                 Regulation of Ion Sequestration 
                 Bush and Jones (1987) Cell 
               
               
                   
                   
                 Calcium 8: 455-72 
               
               
                   
                 Regulation of Nuclear Targeted 
                 Ferringno and Silver 
               
               
                   
                 Protein Transport 
                 (1999) Methods in Cell 
               
               
                   
                   
                 Biology 58: 107-22 
               
               
                   
                 Regulation of Cytoplasmic Ca+2 
                 Shi et al. (1999) Plant Cell 
               
               
                   
                   
                 11: 2393-2406 
               
               
                   
                 Regulation of Kinase Synthesis 
                 Li et al. (2000) Science 
               
               
                   
                 and Activity 
                 287-300-03 
               
               
                   
                 Modulation of Molecular 
                 Mayhew et al (1996) 
               
               
                   
                 Chaperone Activity 
                 Nature 379: 420-26 
               
               
                   
                   
                 Kimura et al. (1995) 
               
               
                   
                   
                 Science 268: 1362-1365. 
               
               
                   
               
            
           
         
       
     
     Other biological activities that can be modulated by the drought responsive genes and gene products are listed in the Reference Tables. Assays for detecting such biological activities are described in the Protein Domain table. 
     Drought responsive genes are characteristically differentially transcribed in response to drought conditions, whether internal or external to an organism or cell. The MA_diff table(s) report(s) the changes in transcript levels of various drought responsive genes at 1 and 6 hours after aerial tissues were isolated and left uncovered at room temperature on 3 MM paper, as compared to isolated aerial tissues placed on 3 MM paper wetted with Hoagland&#39;s solution. The data from this time course can be used to identify a number of types of drought responsive genes and gene products, including “early responders,” and “delayed responders.” Profiles of these different drought responsive genes are shown in the Table below together with examples of the kinds of associated biological activities. 
                                                     EXAMPLES OF       GENE   FUNCTIONAL       BIOCHEMICAL       EXPRESSION   CATEGORY OF   PHYSIOLOGICAL   ACTIVITIES OF GENE       LEVELS   GENE   CONSEQUENCES   PRODUCTS                  Up regulated   Early responders to   Drought perception   Transcription factors       transcripts   drought   leading to the   Transporters       (level at 1 hr ≈ 6 hr)       establishment of       (level at 1 hr &gt; 6 hr)       tolerance to drought               Modulation of drought   Change in cell membrane               response transduction   structure               pathways   Kinases and phosphatases               Specific gene   Transcription activators               transcription initiation   Change in chromatin                   structure and/or localized                   DNA topology               Conditional shift in   Modification of pre-               preferential translation   existing translation factors               of transcripts   by phosphorylation                   (kinases) or                   dephosphorylation                   (phosphatases)                   Synthesis of new                   translation factors               Changes in cell   Stability of mediators of               architecture to optimize   protein-protein interaction               cell adaptation to heat               stress               Changes in cell   Synthesis and/or stability               division cycle   of factors regulating cell                   division       Up regulated   Maintenance of   Maintenance of   Transcription factors       transcripts   drought response   response to drought and   Specific factors (initiation       (level at 1 hr &lt; 6 hr)   “Delayed” responders   maintenance of   and elongation) for protein               drought-tolerance   synthesis               mechanisms   RNA-binding proteins                   effective for mRNA                   stability                   Change in chromatin                   structure and/or DNA                   topology               Maintenance of   Stability of mediators of               mechanisms effective   protein-protein interaction               for ions sequestration,   Stability of factors to               osmolite biosynthesis,   effectively utilize pre-               nuclear protein   existing translation               transport, regulation of   machinery (“recycling”               cytoplasmic Ca+2, and   mechanisms) under               regulation of proteins   drought condition               effective for               maintaining protein               stability and               conformation               Maintenance of cellular   Stability of mediators of               structures   protein-protein interaction       Down-regulated   Early responder   Negative regulation of   Transcription factors and       transcripts   repressors of “normal”   drought response   activators       (level at 1 hr ≈ 6 hr)   state of metabolism   inducible pathways   Change in protein structure       (level at 6 hr &gt; 1 hr)   Genes with   released   by phosphorylation           discontinued   Changes in   (kinases) or           expression or   biochemical and signal   dephosphoryaltion           unsTable mRNA in   transduction pathways   (phosphatases)           presence of water   and processes operating   Change in chromatin           stress   in cells   structure and/or DNA                   topology       Down-regulated   Delayed repressors of   Maintenance of   Transcription factors and       transcripts   “normal” state of   drought response   activators       (level at 1 hr &gt; 6 hr)   metabolism   Maintenance of   Kinases and phosphatases           Genes with   pathways released from   Stability of factors for           discontinued   repression   protein translation           expression or   Changes in pathways           unsTable mRNA in   and processes operating           presence of water   in cells           stress                    
Use of Promoters of Drought Responsive Genes
 
     Promoters of Drought responsive genes are useful for transcription of any desired polynucleotide or plant or non-plant origin. Further, any desired sequence can be transcribed in a similar temporal, tissue, or environmentally specific patterns as the Drought responsive genes where the desired sequence is operably linked to a promoter of a Drought responsive gene. The protein product of such a polynucleotide is usually synthesized in the same cells, in response to the same stimuli as the protein product of the gene from which the promoter was derived. Such promoter are also useful to produce antisense mRNAs to down-regulate the product of proteins, or to produce sense mRNAs to down-regulate mRNAs via sense suppression. 
     III.E.4. Wounding Responsive Genes, Gene Components and Products 
     Plants are continuously subjected to various forms of wounding from physical attacks including the damage created by pathogens and pests, wind, and contact with other objects. Therefore, survival and agricultural yields depend on constraining the damage created by the wounding process and inducing defense mechanisms against future damage. 
     Plants have evolved complex systems to minimize and/or repair local damage and to minimize subsequent attacks by pathogens or pests or their effects. These involve stimulation of cell division and cell elongation to repair tissues, induction of programmed cell death to isolate the damage caused mechanically and by invading pests and pathogens, and induction of long-range signaling systems to induce protecting molecules, in case of future attack. The genetic and biochemical systems associated with responses to wounding are connected with those associated with other stresses such as pathogen attack and drought. 
     Wounding results in the modulation of activities of specific genes and, in consequence, of the levels of key proteins and metabolites. These genes, called here wounding responsive genes, are important for minimizing the damage induced by wounding from pests, pathogens and other objects. Examples of such wounding responsive genes, gene components and products are shown in the Reference, Sequence, Protein Group, Protein Group Matrix, MA_diff, and MA_clust tables. They can be active in all parts of a plant and so where, when and to what extent they are active is crucial for agricultural performance and for the quality, visual and otherwise, of harvested products. They were discovered and characterized from a much larger set of genes by experiments designed to find genes whose products changed in response to wounding. 
     Manipulation of one or more wounding responsive gene activities is useful to modulate the biological activities and/or phenotypes listed below. Wounding responsive genes and gene products can act alone or in combination with genes induced in other ways. Useful combinations include wounding responsive genes and/or gene products with similar transcription profiles, similar biological activities, or members of functionally related biochemical pathways. Whole pathways or segments of pathways are controlled by transcription factor proteins and proteins controlling the activity of signal transduction pathways. Therefore, manipulation of the levels of such proteins is especially useful for altering phenotypes and biochemical activities of plants. The MA_diff Table(s) reports the transcript levels of the experiment (see EXPT ID: 108574, 108575, 108524, 108525, and Wounding (relating to SMD 3714, SMD 3715)). For transcripts that had higher levels in the samples than the control, a “+” is shown. A “−” is shown for when transcript levels were reduced in root tips as compared to the control. For more experimental detail see the Example section below. 
     Wounding genes are those sequences that showed differential expression as compared to controls, namely those sequences identified in the MA_diff tables with a “+” or “−” indication. 
     Wounding Genes Identified by Cluster Analyses of Differential Expression 
     Wounding Genes Identified by Correlation to Genes that are Differentially Expressed 
     As described above, the transcription profiles of genes that act together are well correlated. Applicants not only have identified the genes that are differentially expressed in the microarray experiments, but also have identified the genes that act in concert with them. The MA_clust table indicates groups of genes that have well correlated transcription profiles and therefore participate in the same pathway or network. 
     A pathway or network of Wounding genes is any group in the MA_clust that comprises a cDNA ID that also appears in Expt ID 108574, 108575, 108524, 108525, and Wounding (relating to SMD 3714, SMD 3715) of the MA_diff table(s). 
     Wounding Genes Identified by Correlation to Genes that Cause Physiological Consequences 
     Additionally, the differential expression data and the phenotypic observations can be merged to identify pathways or networks of Wounding genes. A group in the MA_clust is considered a Wounding pathway or network if the group comprises a cDNA ID that also appears in Knock-in or Knock-out tables that causes one or more of the phenotypes described in section above. 
     Wounding Genes Identified by Amino Acid Sequence Similarity 
     Wounding genes from other plant species typically encode polypeptides that share amino acid similarity to the sequences encoded by corn and  Arabidopsis  Wounding genes. Groups of Wounding genes are identified in the Protein Group table. In this table, any protein group that comprises a peptide ID that corresponds to a cDNA ID member of a Wounding pathway or network is a group of proteins that also exhibits Wounding functions/utilities. 
     Such wounding responsive genes and gene products can function either to increase or dampen the phenotypes and activities below, either in response to wounding or in the absence of wounding. 
     Further, promoters of wounding responsive genes, as described in the Reference tables, for example, are useful to modulate transcription that is induced by wounding or any of the following phenotypes or biological activities below. 
     III.E.4.a. Use of Wounding-Responsive Genes to Modulate Phenotypes 
     Wounding responsive genes and gene products can be used to alter or modulate one or more phenotypes including growth rate; whole plant height, width, or flowering time; organs (such as coleoptile elongation, young leaves, roots, lateral roots, tuber formation, flowers, fruit, and seeds); biomass; fresh and dry weight during any time in plant life, such as at maturation; number of flowers; number of seedsm seed yield, number, size, weight, harvest index (such as content and composition, e.g., amino acid, nitrogen, oil, protein, and carbohydrate); fruit yield, number, size, weight, harvest index, post harvest quality, content and composition (e.g., amino acid, carotenoid, jasmonate, protein, and starch); seed and fruit development; germination of dormant and non-dormant seeds; seed viability, seed reserve mobilization, fruit ripening, initiation of the reproductive cycle from a vegetative state, flower development time, insect attraction for fertilization, time to fruit maturity, senescence; fruits, fruit drop; leaves; stress and disease responses; drought; heat and cold; wounding by any source, including wind, objects, pests and pathogens; uv and high light damage (insect, fungus, virus, worm, nematode damage). 
     To regulate any of the phenotype(s) above, activities of one or more of the wounding responsive genes or gene products can be modulated and the plants can be tested by screening for the desired trait. Specifically, the gene, mRNA levels, or protein levels can be altered in a plant utilizing the procedures described herein and the phenotypes can be screened for variants as in Winkler et al. (1998) Plant Physiol 118: 743-50 and assayed, for example, in accordance with Johnson et. al. (1998) Plant Physiol 116:643-649, Reymond et. al. (2000) Plant Cell 12 707-720, or Keith et. al. (1991) Proc. Nat. Acad. Sci. USA 888821 8825. 
     III.E.4.b. Use of Wounding-Responsive Genes to Modulate Biochemical Activities 
     The activities of one or more of the wounding responsive genes can be modulated to change biochemical or metabolic activities and/or pathways such as those noted below. Such biological activities are documented and can be measured according to the citations included in the Table below: 
     
       
         
           
               
               
               
             
               
                   
               
               
                   
                 BIOLOGICAL OR 
                   
               
               
                   
                 METABOLIC 
               
               
                   
                 ACTIVITIES AND/OR 
                 CITATIONS INCLUDING 
               
               
                 PROCESS 
                 PATHWAYS 
                 ASSAYS 
               
               
                   
               
             
            
               
                 Plant Tissue 
                 Cell Damage Repair; Cell 
                 Flanders (1990) J. Cell Biol. 
               
               
                 Proliferation 
                 Division 
                 110: 1111-1122 
               
               
                 Wound Induced 
                 Synthesis Of Jasmonic And 
                 Reymond, P and Farmer E. E. 
               
               
                 Pathways Providing 
                 Salicylic Acids And The 
                 Current Opinion in Plant 
               
               
                 Defense Against 
                 Pathways Induced By These 
                 Biology 1998 1: 404-411 
               
               
                 Pests And Pathogens 
                 Signaling Molecules. 
                 Creelman, RA and Mullet, J. E. 
               
               
                   
                 Induction Of Jasmonic Acid 
                 (1997) Ann Rev. Plant 
               
               
                   
                 Independent Defense 
                 Physiol Mol Biol 48: 355-387 
               
               
                   
                 Pathways. 
                 Leon et al. 1998 Mol Gen 
               
               
                   
                 Induction Of Lipoxygenase, 
                 Genet 254: 412-419 
               
               
                   
                 Thionins And Nodulins 
                 Titarentko et al. 1997 Plant 
               
               
                   
                   
                 Physiol 115: 817-826 
               
               
                   
                 Cell Wall Degradation, 
                 Rojo, E. et al. 1998. Plant J 
               
               
                   
                 Ethylene Formation, Systemic 
                 13: 153-165 
               
               
                   
                 Signaling And Induction Of 
                 Ryan, CA and Pearce, G. 
               
               
                   
                 Defense Related Genes 
                 1998. Ann Rev. Cell Dev. 
               
               
                   
                   
                 Biol 14: 1-17 
               
               
                   
                 Specific Rnase Induction 
                 Reymond, P. et al. 2000. 
               
               
                   
                   
                 Plant Cell 12: 707-720 
               
               
                   
                   
                 Glazebrook, J. 1999. Current 
               
               
                   
                   
                 Opinion in Plant Biol. 2: 280-286 
               
               
                   
                   
                 O&#39;Donnel P. J., et al. 1996 
               
               
                   
                   
                 Science 274: 1914-1917 
               
               
                   
                   
                 Rojo et al. 1999. Plant J. 20: 
               
               
                   
                   
                 135-142 
               
               
                   
                   
                 Merkouropoulus G. et al. 
               
               
                   
                   
                 1999 Planta 208: 212-219 
               
               
                   
                   
                 Kariu et al. 1998. Bioscience 
               
               
                   
                   
                 Biotechnology and 
               
               
                   
                   
                 Biochemistry 62: 1144-1151 
               
               
                   
                   
                 Mcoann et al. 1997 PNAS 94: 
               
               
                   
                   
                 5473-5477 
               
               
                 Other Stress Induced 
                 Abscisic Acid Formation And 
                 Carrera, E and Prat, S. 1998. 
               
               
                 Pathways 
                 Its Signaling Pathway 
                 Plant J 15: 767-771 
               
               
                   
                 Cold Responsive Genes and 
                 Chao et. al. 1999. Plant 
               
               
                   
                 Pathways 
                 Physiol 120: 979-992 
               
               
                   
                 Drought Induced Dehydrins 
               
               
                   
                 And Pathways 
               
               
                 Modified Lipid 
                 Membrane Lipid Synthesis 
                 Martin, M et al. 1999 Europe 
               
               
                 Motabolism 
                 Including Omega-3 Fatty 
                 J. Biochem 262: 283-290 
               
               
                   
                 Acid Desaturase 
               
               
                   
                 Lipases 
               
               
                   
                 Lipid Transfer Proteins 
               
               
                 Modified Sugar And 
                 Induction Of Glycohydrolases 
               
               
                 Energy Metabolism 
                 And Glycotransferases, 
               
               
                   
                 Amylases 
               
               
                 Modified Protein And 
                 Induction Of 
               
               
                 Nitrogen Metabolism 
                 Aminotransferases, Arginase, Proteases 
               
               
                   
                 And Vegetative 
               
               
                   
                 Storage Proteins, Aromatic 
               
               
                   
                 Amino Acid Synthesis 
               
               
                 Secondary Metabolite 
                 Aromatic Amino Acid 
                 Keith, B et al. 1991 PNAS 88: 
               
               
                 Induction 
                 Synthesis And Secondary 
                 8821-8825 
               
               
                   
                 Metabolites 
               
               
                   
               
            
           
         
       
     
     Other biological activities that can be modulated by wound responsive genes and their products are listed in the Reference tables. Assays for detecting such biological activities are described in the Protein Domain table. 
     The MA_diff table reports the changes in transcript levels of various wound responsive genes in the aerial parts of a plant, 1 and 6 hours after the plants were wounded with forceps. The comparison was made with aerial tissues from unwounded plants. 
     The data from this time course reveal a number of types of wound responsive genes and gene products, including “early responders,” and “delayed responders.” Profiles of the individual wounding responsive genes are shown in the Table below together with examples of the kinds of associated biological activities that are modulated when the activities of one or more such genes vary in plants. 
     
       
         
           
               
               
               
               
             
               
                   
               
               
                   
                   
                   
                 EXAMPLES OF 
               
               
                 TRANSCRIPT 
                 TYPES OF 
                 PHYSIOLOGICAL 
                 BIOCHEMICAL 
               
               
                 LEVELS 
                 GENES 
                 CONSEQUENCES 
                 ACTIVITY 
               
               
                   
               
             
            
               
                 Up Regulated 
                 Early Responders 
                 Induction Of Key 
                 Transcription Factors 
               
               
                 Transcripts 
                 To Wounding 
                 Signaling Pathways 
                 Kinases And 
               
               
                 (Level At 1 h ≈ 6 h) 
                   
                 Within And Between 
                 Phosphatases 
               
               
                 Or 
                   
                 Cells 
                 Jasmonic 
               
               
                 (Level At 1 h &gt; 6 h) 
                   
                 Modulation Of 
                 Acid, Salicylic Acid 
               
               
                   
                   
                 Wounding And Stress 
                 And Nitric Oxide 
               
               
                   
                   
                 Induced Signal 
                 Pathway Proteins. 
               
               
                   
                   
                 Transduction Pathways 
                 Glycohydrolases 
               
               
                   
                   
                 Specific Gene 
                 Dehydrins 
               
               
                   
                   
                 Transcription Initiation 
                 Rnases 
               
               
                   
                   
                 Induction Of Repair 
                 Metabolic Enzymes 
               
               
                   
                   
                 Processes Or Cell Death 
                 Nodulins 
               
               
                   
                   
                 Reorientation Of 
                 Cell Division And 
               
               
                   
                   
                 Metabolism, Including 
                 Cell Wall Proteins 
               
               
                   
                   
                 Management Of Active 
                 Cold Response 
               
               
                   
                   
                 Oxygen 
                 Proteins 
               
               
                   
                   
                 Movement Of Wound 
                 Lipoxygenase 
               
               
                   
                   
                 Induced Signals Through 
                 Jacalin 
               
               
                   
                   
                 Plant 
                 Proteins To Detoxify 
               
               
                   
                   
                 Synthesis Of 
                 Active Oxygen 
               
               
                   
                   
                 Phytoalexins And 
                 Species 
               
               
                   
                   
                 Secondary Metabolites 
                 Systemin 
               
               
                   
                   
                   
                 Biosynthetic 
               
               
                   
                   
                   
                 Enzymes 
               
               
                 Up Related 
                 Delayed 
                 Maintenance Of 
                 Transcription Factors 
               
               
                 Transcripts 
                 Responders 
                 Defence Pathways 
                 Kinases And 
               
               
                 (Level At 1 h &lt; 6 h) 
                 Genes Involved In 
                 Maintenance Of 
                 Phosphatases 
               
               
                   
                 Wounding 
                 Reorientated Metabolism 
                 Jasmonic 
               
               
                   
                 Response At 
                 Maintenance Of Wound 
                 Acid, Salicylic Acid 
               
               
                   
                 Distant Sites From 
                 Response 
                 And Nitric Oxide 
               
               
                   
                 Wound. 
                 Programmed Cell Death 
                 Pathway Proteins 
               
               
                   
                 Genes Involved In 
                 In Selected Cells 
                 Glycohydrolases 
               
               
                   
                 Maintenance Of 
                 Reorientation Of 
                 Dehydrins 
               
               
                   
                 Wounding 
                 Metabolism 
                 Rnases 
               
               
                   
                 Response 
                 Movement Of Wound 
                 Metabolic Enzymes 
               
               
                   
                   
                 Induced Signals Through 
                 Nodulins 
               
               
                   
                   
                 Plant 
                 Cold Response 
               
               
                   
                   
                 Synthesis Of 
                 Proteins 
               
               
                   
                   
                 Phytoalexins And 
                 Lipoxygenase 
               
               
                   
                   
                 Secondary Metabolites 
                 Jacalin 
               
               
                   
                   
                   
                 Proteins To Detoxify 
               
               
                   
                   
                   
                 Active Oxygen 
               
               
                   
                   
                   
                 Species 
               
               
                   
                   
                   
                 Cell Division And 
               
               
                   
                   
                   
                 Cell Wall Proteins 
               
               
                   
                   
                   
                 Systemin 
               
               
                   
                   
                   
                 Biosynthetic 
               
               
                   
                   
                   
                 Enzymes 
               
               
                 Down-Regulated 
                 Early 
                 Negative Regulation Of 
                 Transcription Factors 
               
               
                 Transcripts 
                 Responder 
                 Wounding Response 
                 Change In Protein 
               
               
                 (Level At 1 h ≈ 6 h) 
                 Repressors Of 
                 Pathways Released 
                 Structure By 
               
               
                 Or 
                 Wounding 
                 Changes In Pathways 
                 Phosphory-Laton 
               
               
                 (Level At 6 Hr &gt; 1 h) 
                 Response 
                 And Processes Operating 
                 (Kinases) Or 
               
               
                   
                 State 
                 In Cells 
                 Dephos-Phorylation 
               
               
                   
                 Genes With 
                   
                 (Phosphatases) 
               
               
                   
                 Discontinued 
                   
                 Change In Chromatin 
               
               
                   
                 Expression Or 
                   
                 Structure And Or 
               
               
                   
                 UnsTable 
                   
                 Dna Topology 
               
               
                   
                 mRNA 
                   
                 Local Changes In 
               
               
                   
                 Following 
                   
                 Regulatory Proteins, 
               
               
                   
                 Wounding 
                   
                 Metabolic Enzymes, 
               
               
                   
                   
                   
                 Transporters Etc. 
               
               
                 Down-Regulated 
                 Delayed 
                 Negative Regulation Of 
                 Transcription 
               
               
                 Transcripts 
                 Repressors Of 
                 Wounding Response 
                 Factors, 
               
               
                 (Level At 1 hr &gt; 6 h) 
                 Wounding 
                 Pathways Released 
                 Phosphatases, 
               
               
                   
                 Response State 
                 Change In Pathways And 
                 Kinases 
               
               
                   
                 Genes With 
                 Process Operating In 
                 Changes In Protein 
               
               
                   
                 Discontinued 
                 Cells 
                 Complex Structures 
               
               
                   
                 Expression Or 
                 Programmed Cell Death 
                 Chromatin 
               
               
                   
                 UnsTable mRNA 
                   
                 Restructuring 
               
               
                   
                 Following 
                   
                 Proteins 
               
               
                   
                 Wounding 
                   
                 Local Changes In 
               
               
                   
                   
                   
                 Regulatory Proteins, 
               
               
                   
                   
                   
                 Metabolic Enzymes, 
               
               
                   
                   
                   
                 Transporters Etc. 
               
               
                   
                   
                   
                 Most Proteins In 
               
               
                   
                   
                   
                 Selected Cells 
               
               
                   
                   
                   
                 Undergoing Death 
               
               
                   
               
            
           
         
       
     
     Further, any desired sequence can be transcribed in similar temporal, tissue, or environmentally specific patterns as the wounding responsive genes when the desired sequence is operably linked to a promoter of a wounding responsive gene. 
     III.E.5. Methyl Jasmonate (Jasmonate) Responsive Genes, Gene Components and Products 
     Jasmonic acid and its derivatives, collectively referred to as jasmonates, are naturally occurring derivatives of plant lipids. These substances are synthesized from linolenic acid in a lipoxygenase-dependent biosynthetic pathway. Jasmonates are signalling molecules which have been shown to be growth regulators as well as regulators of defense and stress responses. As such, jasmonates represent a separate class of plant hormones. 
     Changes in external or internal jasmonate concentration result in modulation of the activities of many genes and gene products. Examples of such “jasmonate responsive” genes and gene products are shown in the Reference and Sequence Tables. These genes and/or products are responsible for effects on traits such as plant vigor and seed yield, especially when plants are growing in the presence of biotic or abiotic stresses. They were discovered and characterized from a much larger set of genes by experiments designed to find genes whose mRNA products changed in concentration in response to application of methyl jasmonate to plants. 
     Manipulation of one or more jasmonate responsive gene activities is useful to modulate the biological activities and/or phenotypes tested below. Jasmonate response genes and gene products can act alone or in combination. Useful combinations include jasmonate responsive genes and/or gene products with similar transcription profiles, similar biological activities, or members of the same co-regulated or functionally related biochemical pathways. Whole pathways or segments of pathways are controlled by transcription factor proteins and proteins controlling the activity of signal transduction pathways. Therefore, manipulation of such protein levels is especially useful for altering phenotypes and biochemical activities Such jasmonate responsive genes and gene products can function to either increase or dampen the phenotypes or activities below either in response to changes in jasmonate concentration or in the absence of jasmonate fluctuations. The MA_diff Table(s) reports the transcript levels of the experiment (see EXPT ID: 108568, 108569, 108555). For transcripts that had higher levels in the samples than the control, a “+” is shown. A “−” is shown for when transcript levels were reduced in root tips as compared to the control. For more experimental detail see the Example section below. 
     MeJA genes are those sequences that showed differential expression as compared to controls, namely those sequences identified in the MA_diff tables with a “+” or “−” indication. 
     MeJA Genes Identified by Cluster Analyses of Differential Expression 
     MeJA Genes Identified by Correlation to Genes that are Differentially Expressed 
     As described above, the transcription profiles of genes that act together are well correlated. Applicants not only have identified the genes that are differentially expressed in the microarray experiments, but also have identified the genes that act in concert with them. The MA_clust table indicates groups of genes that have well correlated transcription profiles and therefore participate in the same pathway or network. 
     A pathway or network of MeJA genes is any group in the MA_clust that comprises a cDNA ID that also appears in Expt ID 108568, 108569, 108555 of the MA_diff table(s). 
     MeJA Genes Identified by Correlation to Genes that Cause Physiological Consequences 
     Additionally, the differential expression data and the phenotypic observations can be merged to identify pathways or networks of MeJA genes. A group in the MA_clust is considered a MeJA pathway or network if the group comprises a cDNA ID that also appears in Knock-in or Knock-out tables that causes one or more of the phenotypes described in section above. 
     MeJA Genes Identified by Amino Acid Sequence Similarity 
     MeJA genes from other plant species typically encode polypeptides that share amino acid similarity to the sequences encoded by corn and  Arabidopsis  MeJA genes. Groups of MeJA genes are identified in the Protein Group table. In this table, any protein group that comprises a peptide ID that corresponds to a cDNA ID member of a MeJA pathway or network is a group of proteins that also exhibits MeJA functions/utilities. 
     Further, promoters of jasmonate responsive genes, as described in the Reference tables, for example, are useful to modulate transcription that is induced by jasmonate or any of the following phenotypes or biological activities below. 
     III.E.5.a. Use of Jasmonate Responsive Genes to Modulate Phenotypes: 
     Jasmonate responsive genes and their gene products can be used to alter or modulate one or more phenotypes including growth rate, whole plant (including height, flowering time, etc.), seedling, organ, coleoptile elongation, young leaves, roots, lateral roots, tuber formation, flowers, fruit, seeds, biomass; fresh and dry weight during any time in plant life, including maturation and senescence; number of flowers, number of seeds (including secondary metabolite accumulation, alkaloids, anthocyanins; paclitaxel and related taxanes, rosmarinic; seed yield (such as number, size, weight, harvest index, content and composition, e.g., amino acid, jasmonate, oil, protein, and starch); fruit yield (such as number, size, weight, harvest index, post harvest quality, content and composition e.g., amino acid, carotenoid, jasmonate, protein, starch); seed and fruit development; germination of dormant and non-dormant seeds; seed viability; seed reserve mobilization; fruit ripening (such as initiation of the reproductive cycle from a vegetative state); flower development time; insect attraction for fertilization; time to fruit maturity; senescence; fruits, fruit drop; leaves; stress and disease responses; drought; wounding; UV damage; and insect, fungus, virus, or worm damage. 
     Further, any desired sequence can be transcribed in similar temporal, tissue, or environmentally specific patterns as the jasmonate responsive genes when the desired sequence is operably linked to a promoter of a jasmonate responsive gene. 
     To improve any of the phenotype(s) above, activities of one or more of the jasmonate responsive genes or gene products can be modulated and the plants can be tested by screening for the desired trait. Specifically, the gene, mRNA levels, or protein levels can be altered in a plant utilizing the procedures described herein and the phenotypes can be assayed, for example, in accordance to citations described below. 
     III.E.5.b. Use of Jasmonate-Responsive Genes to Modulate Biochemical Activities: 
     The activities of one or more of the jasmonate responsive genes can be modulated to change biochemical or metabolic activities and/or pathways such as those noted below. Such biological activities are documented and can be measured according to the citations included in the Table below: 
     
       
         
           
               
               
               
             
               
                   
               
               
                   
                 BIOCHEMICAL OR 
                   
               
               
                   
                 METABOLIC 
               
               
                   
                 ACTIVITIES AND/OR 
                 CITATIONS INCLUDING 
               
               
                 PROCESS 
                 PATHWAYS 
                 ASSAYS 
               
               
                   
               
             
            
               
                 Turnover of proteins 
                 Induction of various 
                 This study. Standard 
               
               
                   
                 proteases, ubiquitin and 
                 biochemical assays. 
               
               
                   
                 proteosome components 
               
               
                   
                 and turnover of RNA 
               
               
                   
                 polymerases and 
               
               
                   
                 translation initiation factors 
               
               
                   
                 Reduction in many 
               
               
                   
                 ribosomal proteins 
               
               
                 Activation of nitrogen 
                 Induction of glutamine 
                 Crawford (1995) Plant Cell 
               
               
                 metabolism 
                 synthetase, many 
                 7, 859-868 
               
               
                   
                 aminotransferases, 
                 This study. Standard 
               
               
                   
                 vegetative storage proteins 
                 biochemical assays. 
               
               
                 Lipid turnover 
                 Induction of various 
                 This study. Standard 
               
               
                   
                 lipases, desaturases, and 
                 biochemical assays. 
               
               
                   
                 reduction of lipid transfer 
               
               
                   
                 protein mRNAs 
               
               
                 Sugar metabolism 
                 Induction of sugar 
                 This study. Standard 
               
               
                   
                 transporters, UDP 
                 biochemical assays. 
               
               
                   
                 glucosyltransferases, other 
               
               
                   
                 transferases 
               
               
                 Glycolysis and central 
                 Induction of glycolytic 
                 This study. Standard 
               
               
                 carbon metabolism 
                 related enzymes. Example, 
                 biochemical assays. 
               
               
                   
                 glucose 6-phosphate 
               
               
                   
                 dehydrogenase, 
               
               
                   
                 glyceraldehyde-3- 
               
               
                   
                 phosphate dehydrogenase, 
               
               
                   
                 phosphoglycerate kinase, 
               
               
                   
                 phosphoglucomutase ATP 
               
               
                   
                 synthase 
               
               
                 Chlorosis 
                 Degradation of 
                 Tsuchiya et al. (1999) Proc. 
               
               
                   
                 Chlorophyll 
                 Natl. Acad. Sci. USA 
               
               
                   
                   
                 96: 15362-15367 
               
               
                   
                 Inhibition of 
                 Reinbothe et al. (1993) J. 
               
               
                   
                 Photosynthesis Related 
                 Biol. Chem. 268, 10606-10611 
               
               
                   
                 Proteins 
               
               
                 Carbon Assimilation and 
                 Induction of chlorophyll ab 
                 Reinbothe et al. (1993) J. 
               
               
                 turnover 
                 binding protein precursor 
                 Biol. Chem. 268, 10606-10611 
               
               
                 Jasmonate metabolism 
                 Induction of lipid 
                 This study. Standard 
               
               
                   
                 biosynthesis, myrosinase 
                 biochemical assays. 
               
               
                   
                 and jacalin 
               
               
                 Jasmonate mediated signal 
                 Receptor binding 
                 Cho and Pai (2000) Mol 
               
               
                 transduction 
                   
                 Cells 10, 317-324 
               
               
                   
                 Protein kinases 
                 Lee et al. (1998) Mol. Gen. 
               
               
                   
                   
                 Genet. 259, 516-522 
               
               
                   
                   
                 Seo et al. (1999) Plant Cell 
               
               
                   
                   
                 11, 289-298 
               
               
                   
                   
                 Yoon et al. (1999) Plant Mol. 
               
               
                   
                   
                 Biol. 39, 991-1001 
               
               
                   
                 Ubiquitination of 
                 Xie et al. (1998) Science 280, 
               
               
                   
                 Repressor Proteins 
                 1091-1094 
               
               
                   
                 Calcium Flux regulators 
                 Bergey and Ryan (1999) 
               
               
                   
                   
                 Plant Mol. Biol. 40, 815-823 
               
               
                   
                 Transcription Activators. 
                 Xiang et al. (1996) Plant 
               
               
                   
                 Example-induction of 
                 Mol. Biol. 32, 415-426 
               
               
                   
                 various zinc finger, myb 
                 Menke et al. (1999) EMBO J. 
               
               
                   
                 and AP-2 related factors 
                 18, 4455-4463 
               
               
                 Response to Cell 
                 Lipid Peroxidation 
                 Dubery et al. (2000) Mol. 
               
               
                 Membrane Damage 
                   
                 Cell Biol. Res. Commun. 3, 
               
               
                   
                   
                 105-110 
               
               
                 Cell Elongation 
                 Inhibition of incorporation 
                 Burnett et al. (1993) Plant 
               
               
                   
                 of Glucose into Cell Wall 
                 Physiol. 103, 41-48 
               
               
                   
                 Saccharides 
               
               
                 Cell Organization and 
                 Reductions in 
                 Ishikawa et al. (1994) Plant 
               
               
                 Division 
                 tropomyosin related 
                 Mol. Biol. 26, 403-414 
               
               
                   
                 proteins and certain cyclins 
               
               
                   
                 Induction of actins and 
               
               
                   
                 tubulins 
               
               
                 Cell Wall Turnover and 
                 Induction of cell wall 
                 Creelman et al. (1992) Proc. 
               
               
                 modulation 
                 proteins, glycine-rich 
                 Natl. Acad. Sci. USA 89, 
               
               
                   
                 proteins, annexins, pectate 
                 4938-4941 
               
               
                   
                 lyase and pectin esterases 
                 Garcia-Muniz et al. (1998) 
               
               
                   
                 Reductions in various 
                 Plant Mol. Biol. 38, 623-632 
               
               
                   
                 dehydrins and expansins 
                 Norman et al (1999) Mol. 
               
               
                   
                   
                 Plant Microbe Interact. 12, 
               
               
                   
                   
                 640-644 
               
               
                 Stress, Disease, and 
                 Induction of antifungal 
                 Hildmann et al. (1992) Plant 
               
               
                 Pathogen Resistance 
                 proteins, wounding 
                 Cell 4, 1157-1170 
               
               
                   
                 responsive proteins, 
                 Reinbothe et al. (1994) Proc. 
               
               
                   
                 dehydrins, heat shock type 
                 Natl. Acad. Sci. USA 91, 
               
               
                   
                 proteins and elicitor 
                 7012-7016 
               
               
                   
                 response proteins 
                 Moons et al. (1997) Plant 
               
               
                   
                   
                 Cell 9, 2243-2259 
               
               
                   
                   
                 Richard et al. (2000) Plant 
               
               
                   
                   
                 Mol. Biol. 43, 1-10 
               
               
                   
                   
                 Van Wees et al. (2000) Proc. 
               
               
                   
                   
                 Natl. Acad. Sci. USA 97, 
               
               
                   
                   
                 8711-8716 
               
               
                   
                 Phytoalexin Biosynthesis 
                 Creelman et al. (1992) Proc. 
               
               
                   
                   
                 Natl. Acad. Sci. USA 89, 
               
               
                   
                   
                 4938-4941 
               
               
                   
                   
                 Choi et al. (1994) Proc. Natl. 
               
               
                   
                   
                 Acad. Sci. USA 91, 2329-2333 
               
               
                   
                 Biosynthesis of phenolics 
                 Doares et al., (1995) Proc. 
               
               
                   
                   
                 Natl. Acad. Sci. USA 92, 
               
               
                   
                   
                 4095-5098 
               
               
                   
                 Production of Protease 
                 Botella et al. (1996) Plant 
               
               
                   
                 Inhibitors 
                 Physiol 112, 1201-1210 
               
               
                   
                 Defense Gene 
                 Mason et al. (1993) Plant 
               
               
                   
                 Transcription in Response 
                 Cell 5, 241-251 
               
               
                   
                 to UV 
                 Schaller et al. (2000) Planta 
               
               
                   
                   
                 210, 979-984 
               
               
                 Secondary Metabolite 
                 Fruit Cartenoid 
                 Czapski and Saniewski 
               
               
                 biosynthesis 
                 Composition 
                 (1992) J. Plant Physol. 139, 
               
               
                   
                   
                 265-268 
               
               
                   
                 Palitaxel and Related 
                 Yukimune et al. (1996) 
               
               
                   
                 Taxanes 
                 Nature Biotech. 14, 1129-1132 
               
               
                   
                 Alkaloids 
                 Aerts et al. (1994) Plant J. 4, 
               
               
                   
                   
                 635-643 
               
               
                   
                   
                 Geerlings et al. (2000) J. 
               
               
                   
                   
                 Biol. Chem. 275, 3051-3056 
               
               
                   
                 Anthocyanins 
                 Franceschi et al. (1991) Proc. 
               
               
                   
                   
                 Natl. Acad. Sci. USA 83, 
               
               
                   
                   
                 6745-6749 
               
               
                   
                 Rosmarinic 
                 Mizukami et al., (1993) Plant 
               
               
                   
                   
                 Cell Reprod. 12, 706-709 
               
               
                   
                 Activation of Ethylene- 
                 Czapski and Saniewski 
               
               
                   
                 forming Enzyme and 
                 (1992) J. Plant Physiol. 139, 
               
               
                   
                 Production of Ethylene 
                 265-268 
               
               
                   
               
            
           
         
       
     
     Other biological activities that can be modulated by the jasmonate responsive genes and their products are listed in the Reference Tables. Assays for detecting such biological activities are described in the Domain section of the Reference Tables. 
     Jasmonate responsive genes are characteristically differentially transcribed in response to fluctuating jasmonate levels or concentrations, whether internal or external to an organism or cell. The MA_diff table(s) report(s) the changes in transcript levels of various jasmonate responsive genes in the aerial parts of a seedling at 1 and 6 hours after being sprayed with SILWET L-77® solution enriched with methyl jasmonate as compared to seedlings sprayed with SILWET L-77® alone. 
     The data from this time course reveal a number of types of jasmonate responsive genes and gene products, including “early responders” and “delayed responders”. Profiles of the individual kinds of jasmonate responsive genes are shown in the Table below, together with examples of the kinds of associated biological activities that are modulated when the activities of such genes vary. 
                                         GENE   FUNCTIONAL   TYPE OF   EXAMPLES OF       EXPRESSION   CATEGORY OF   BIOLOGICAL   BIOCHEMICAL       LEVELS   GENE   ACTIVITY   ACTIVITY                  Upregulated   Early Responders to   Binding and   Transcription Factors       genes   Jasmonate   Perception of   Transporters       (Level at 1 hour       Jasmonate   Kinases, Phosphatases,       ≅ 6 hours).       Transduction of   Leucine-rich Repeat       (Level at 1 hour &gt;       Jasmonate signal   Proteins (LRRs), GTP-       6 hours)       tranduction response   binding proteins (G-               pathways   proteins), calcium-               Initiation of Specific   binding proteins and               Gene Transcription to   calcium responsive               reorientate   proteins               metabolism   Proteases, lipases,                   glutamine synthetase                   (GS), arginase,                   aminotransferases,                   glycosyltransferases,                   sugar transporters, cell                   wall proteins, methyl                   transferases, glycolytic                   enzymes.       Upregulated   Delayed Jasmonate   Maintenance of   Enzymes of methyl       genes   Responders   Metabolism under   jasmonate-induced       (Level at 1 hour &lt;       high Jasmonate   pathways, including       6 hours)       Jasmonate signal   dehydrin, phytoalexin,               Tranduction Response   phenolic, carotenoid,               Pathways   alkaloid and               Gene Transcription to   anthocyanin               Reorientate   biosynthesis.               Metabolism   Transcription factors,               Gene Transcription to   Transporters, Kinases               Maintain Reorientated   and phosphatases               Metabolism   Proteases, Lipases,                   Glutaminae                   Synthetase, Arginase,                   Aminotransferases,                   Lipid Peroxidases,                   Glycosyltransferases,                   Sugar transporters,                   Cell Wall Proteins,                   Glycolytic Enzymes,                   Chlorophyll Binding                   Proteins                   Transcription factors,                   kinases, phosphatases,                   LRRs, G-proteins               Reorient Cell   Actins, Tubulins,               Division and Cell   Myosins Cyclins,               Development   Cyclin-dependent                   Kinases (CDPKs)                   Glycosyl Transferases,                   Glycosyl hydrolases,                   Expansins, Extensins,                   O-Methyl                   Transferases                   Arabinogalactan-                   proteins (AGPs),                   Enzymes of Lipid                   Biosynthesis, Cutinase       Down regulated   Early responders of   Relese of Suppression   Transcription Factors,       transcripts   Jasmonate   of Jasmonate Induced   Kinases, Phosphatases,       (level at 1 hour =   Genes with   Pathways   LRRs, G-Proteins,       6 hours)   discontinued   Reorientation of   Chromatin       (level at 6 hours &gt;   expression or   metabolism   Restructuring proteins,       1 hour)   unsTable mRNA       Ribosomal proteins,           following Jasmonate       Translation Factors,           uptake       Histones, RNA                   polymerases, Pectin                   esterase, Lipid transfer                   proteins       Down regulated   Genes with   Negative Regulation   Transcription factors       transcripts   Discontinued   of Jasmonate Induced   Kinases, Phosphatases       (level at 1 hour &gt;   expression or   Pathways Released.   Chromatin       6 hours)   UnsTable mRNA   Reorientation of   Restructuring Proteins,           Following Jasmonate   metabolism   LRRs, G-proteins           uptake       Ribosomal proteins,                   Translation Factors,                   Histones                   RNA Polymerases,                   Cyclins                   Pectin esterase, Lipid                   Transfer Proteins                    
Use of Promoters of Jasmonate Responsive Genes
 
     Promoters of Jasmonate responsive genes are useful for transcription of any desired polynucleotide or plant or non-plant origin. Further, any desired sequence can be transcribed in a similar temporal, tissue, or environmentally specific patterns as the Jasmonate responsive genes where the desired sequence is operably linked to a promoter of a Jasmonate responsive gene. The protein product of such a polynucleotide is usually synthesized in the same cells, in response to the same stimuli as the protein product of the gene from which the promoter was derived. Such promoter are also useful to produce antisense mRNAs to down-regulate the product of proteins, or to produce sense mRNAs to down-regulate mRNAs via sense suppression. 
     III.E.6. Reactive Oxygen Responsive Genes, Gene Components and H2O2 Products 
     Often growth and yield are limited by the ability of a plant to tolerate stress conditions, including pathogen attack, wounding, extreme temperatures, and various other factors. To combat such conditions, plant cells deploy a battery of inducible defense responses, including triggering an oxidative burst. The burst of reactive oxygen intermediates occurs in time, place and strength to suggest it plays a key role in either pathogen elimination and/or subsequent signaling of downstream defense functions. For example, H 2 O 2  can play a key role in the pathogen resistance response, including initiating the hypersensitive response (HR). HR is correlated with the onset of systemic acquired resistance (SAR) to secondary infection in distal tissues and organs. 
     Changes in reactive oxygen, such as H 2 O 2  or O 2   − , in the surrounding environment or in contact with a plant results in modulation of the activities of many genes and hence levels of gene products. Examples of such reactive oxygen responsive genes and gene products are shown in the Reference, Sequence, Protein Group, Protein Group Matrix, MA_diff and MA_clust tables. These genes and/or products are responsible for effects on traits such as plant vigor and seed yield. The genes were discovered and characterized from a much larger set by experiments designed to find genes whose mRNA products changed in response to application of reactive oxygen, such as H 2 O 2 , to plants. 
     Manipulation of one or more reactive oxygen responsive gene activities is useful to modulate the following biological activities and/or phenotypes listed below. Reactive oxygen responsive genes and gene products can act alone or in combination. Useful combinations include reactive oxygen responsive genes and/or gene products with similar transcription profiles, similar biological activities, or members of the same or functionally related biochemical pathways. Whole pathways or segments of pathways are controlled by transcription factor proteins and proteins controlling the activity of signal transduction pathways. Therefore, manipulation of such protein levels is especially useful for altering phenotypes and biochemical activities of plants. 
     Such reactive oxygen responsive genes and gene products can function to either increase or dampen the above phenotypes or activities either in response to changes in reactive oxygen concentration or in the absence of reactive oxygen fluctuations. The MA_diff Table(s) reports the transcript levels of the experiment (see EXPT ID: 108582, 108583, 108537, 108538, 108558, and H2O2 (relating to SMD 7523)). For transcripts that had higher levels in the samples than the control, a “+” is shown. A “−” is shown for when transcript levels were reduced in root tips as compared to the control. For more experimental detail see the Example section below. 
     Reactive Oxygen genes are those sequences that showed differential expression as compared to controls, namely those sequences identified in the MA_diff tables with a “+” or “−” indication. 
     Reactive Oxygen Genes Identified by Cluster Analyses of Differential Expression 
     Reactive Oxygen Genes Identified by Correlation to Genes that are Differentially Expressed 
     As described above, the transcription profiles of genes that act together are well correlated. Applicants not only have identified the genes that are differentially expressed in the microarray experiments, but also have identified the genes that act in concert with them. The MA_clust table indicates groups of genes that have well correlated transcription profiles and therefore participate in the same pathway or network. 
     A pathway or network of Reactive Oxygen genes is any group in the MA_clust that comprises a cDNA ID that also appears in Expt ID 108582, 108583, 108537, 108538, 108558, and H2O2 (relating to SMD 7523) of the MA_diff table(s). 
     Reactive Oxygen Genes Identified By Correlation To Genes That Cause Physiological Consequences 
     Additionally, the differential expression data and the phenotypic observations can be merged to identify pathways or networks of Reactive Oxygen genes. A group in the MA_clust is considered a Reactive Oxygen pathway or network if the group comprises a cDNA ID that also appears in Knock-in or Knock-out tables that causes one or more of the phenotypes described in section above. 
     Reactive Oxygen Genes Identified by Amino Acid Sequence Similarity 
     Reactive Oxygen genes from other plant species typically encode polypeptides that share amino acid similarity to the sequences encoded by corn and  Arabidopsis  Reactive Oxygen genes. Groups of Reactive Oxygen genes are identified in the Protein Group table. In this table, any protein group that comprises a peptide ID that corresponds to a cDNA ID member of a Reactive Oxygen pathway or network is a group of proteins that also exhibits Reactive Oxygen functions/utilities. 
     Further, promoters of reactive oxygen responsive genes, as described in the Reference tables, for example, are useful to modulate transcription that is induced by reactive oxygen or any of the following phenotypes or biological activities below. 
     III.E.6.a. Use of Reactive Oxygen Responsive Genes to Modulate Phenotypes 
     Reactive oxygen responsive genes and gene products are useful to or modulate one or more phenotypes including pathogen tolerance and/or resistance; Avr/R locus sensitive; non-host sensitive; HR; SAR (e.g., where the reactive oxygen responsive gene and products are modulated in conjuntion with any of the bacterial, fungal, virus, or other organism listed below); bacteria resistance, e.g. to  Erwinia stewartii, Pseudomonas syringae, Pseudomonas tabaci , Stuart&#39;s wilt, etc.; fungal resistance including to downy mildews such as  Scleropthora macrospora, Sclerophthora rayissiae, Sclerospora graminicola, Peronosclerospora sorghi, Peronosclerospora philippinensis, Peronosclerospora sacchari, Peronosclerospora maydis ; rusts such as  Puccinia sorphi, Puccinia polysora, Physopella zeae , etc.; other fungal diseases such as  Cercospora zeae - maydis, Colletotrichum graminicola, Fusarium monoliforme, Exserohilum turcicum, Bipolaris maydis, Phytophthora parasitica, Peronospora tabacina, Septoria , etc.; virus or viroid resistance, e.g. to tobacco or cucumber mosaic virus, ringspot virus, necrosis virus,  pelargonium  leaf curl virus, red clover mottle virus, tomato bushy stunt virus, and like viruses; insect resistance, such as to aphids e.g.  Myzus persicae ; beetles, beetle larvae; etc.; nematodes, e.g.  Meloidogyne incognita; lepidoptera , e.g.  Heliothus  spp. etc.; resistance specifically in primary or secondary leaves; stress tolerance; winter survival; cold tolerance; heavy metal tolerance, such as cadmium; physical wounding; increased organelle tolerance to redox stress, such as in mitochondria, and chloroplasts; cell death; apoptosis, including death of diseased tissue; senescence; fruit drop; biomass; fresh and dry weight during any time in plant life, such as maturation; number of flowers, seeds, branches, and/or leaves; seed yield, including number, size, weight, and/or harvest index; fruit yield, including number, size, weight, and/or harvest index; plant development; time to fruit maturity; cell wall strengthening and reinforcement; plant product quality, e.g. paper making quality); food additives; treatment of indications modulated by free radicals, and cancer 
     To regulate any of the phenotype(s) above, activities of one or more of the reactive oxygen responsive genes or gene products can be modulated and the plants can be tested by screening for the desired trait. Specifically, the gene, mRNA levels, or protein levels can be altered in a plant utilizing the procedures described herein and the phenotypes can be screened for variants as in Winkler et al. (1998) Plant Physiol 118: 743-50 and assayed, for example, in accordance to Alvarez et al., (1998) Cell 92: 773-784; Halhbrock and Scheel, (1989) Ann. Rev. Plant Physiol. Plant Mol. Biol. 40: 347-369; Lamb et al., (1997) Ann. Rev. Plant Mol. Biol. Plant Physio. 48: 251-275; Lapwood et al. (1984) Plant Pathol. 33: 13-20; Levine et al. (1996) Curr. Biol. 6: 427-437; McKersie et al., (2000) Plant Physiol. 122(4): 1427-1437; Olson and Varner (1993) Plant J. 4: 887-892; Pastore et al., (2000), FEBS Lett 470(1): 88-92; Pastori et al., (1997) Plant Physiol. 113: 411-418. Romero-Puertas et al., (1999) Free Radic. Res. 1999 31 Suppl: S25-31; Shirataki et al., Anticancer Res 20(1A): 423-426 (2000); Wu et al., (1995) Plant Cell 7: 1357-1368; 
     III.E.6.b. Use of Reactive Oxygen Responsive Genes to Modulate Biochemical Activities 
     The activities of one or more of the reactive oxygen responsive genes can be modulated to change biochemical or metabolic activities and/or pathways such as those noted below. Such biological activities are documented and can be measured according to the citations above and included in the Table below: 
     
       
         
           
               
               
               
             
               
                   
               
               
                   
                 BIOCHEMICAL OR 
                   
               
               
                   
                 METABOLIC ACTIVITIES 
                 CITATIONS INCLUDING 
               
               
                 PROCESS 
                 AND/OR PATHWAYS 
                 ASSAYS 
               
               
                   
               
             
            
               
                 Reinforcement of 
                 Modulation Of The Production Of 
                 Bradley et al. 1992. Cell 70, 
               
               
                 Cell Walls 
                 ExtracTable Proline-Rich Protein 
                 21-30 
               
               
                   
                 Modulation Of Lignification 
                 Mansouri et al. (1999) Physiol 
               
               
                   
                   
                 Plant 106: 355-362 
               
               
                 Stress, Disease, 
                 Induction Of Pathogenesis Related 
                 Chamnongpol et. al.(1998) 
               
               
                 Pathogen Resistance 
                 Proteins, Phytoalexins And Many 
                 Proc. Nat. Acad Sci USA 
               
               
                 and Wounding 
                 Defense Pathways. 
                 12; 95: 5818-23. 
               
               
                   
                 Induction Of Detoxifying 
                 Davis et al. (1993) 
               
               
                   
                 Enzymes Such As Glutathione S- 
                 Phytochemistry 32: 607-611. 
               
               
                   
                 Transferase And Ascorbate 
                 Chen et. al. Plant J. (1996) 
               
               
                   
                 Peroxidase 
                 10: 955-966 
               
               
                   
                 Disease Resistance 
                 Gadea et. al. (1999) Mol Gen 
               
               
                   
                   
                 Genet 262: 212-219 
               
               
                   
                   
                 Wu et. al. (1995) Plant Cell 7: 
               
               
                   
                   
                 1357-68 
               
               
                   
                 Reactive Oxygen Generation 
                 Orozco-Cardenas and Ryan 
               
               
                   
                 Following Wounding And 
                 (1999) Proc. Nat. Acad. Sci. 
               
               
                   
                 Changes In Physical Pressure 
                 USA 25; 96: 6553-7. 
               
               
                   
                   
                 Yahraus et al. (1995) Plant 
               
               
                   
                   
                 Physiol. 109: 1259-1266 
               
               
                   
                 Modulation Of Genes Involved In 
                 LEGENDRE ET AL. (1993) 
               
               
                   
                 Wound Repair And Cell Division 
                 PLANT PHYSIOL. 102: 233-240 
               
               
                   
                 Modulation Of Nitric Oxide 
                 DELLEDONNE ET AL. 
               
               
                   
                 Signaling 
                 (1998) NATURE 394: 585-588 
               
               
                   
                 Salicyclic Acid Accumulation And 
                 DURNER AND KLESSIG 
               
               
                   
                 Signaling 
                 (1996) J. BIOL. CHEM. 
               
               
                   
                   
                 271: 28492-501 
               
               
                 Programmed Cell 
                 Induction Of Cell Death Pathway 
                 LEVINE ET AL. (1996) 
               
               
                 Death 
                 Genes 
                 CURR. BIOL. 6: 427-437. 
               
               
                   
                   
                 REYNOLDS ET. AL.(1998) 
               
               
                   
                   
                 BIOCHEM. J. 330: 115-20 
               
               
                   
               
            
           
         
       
     
     Other biological activities that can be modulated by the reactive oxygen responsive genes and their products are listed in the Reference tables. Assays for detecting such biological activities are described in the Protein Domain table. 
     Reactive oxygen responsive genes are characteristically differentially transcribed in response to fluctuating reactive oxygen levels or concentrations, whether internal or external to an organism or cell. The MA_diff table reports the changes in transcript levels of various reactive oxygen responsive genes in the aerial parts of a plant at 1 and 6 hours after the plant was sprayed with Silwett L-77 solution enriched with hydrogen peroxide as compared to plants sprayed with Silwett L-77 alone. 
     The data from this time course reveal a number of types of reactive oxygen responsive genes and gene products, including “early responders,” and “delayed responders”. Profiles of individual reactive oxygen responsive genes are shown in the Table below together with examples of which associated biological activities are modulated when the activities of one or more such genes vary in plants. 
     
       
         
           
               
               
               
               
             
               
                   
               
               
                   
                   
                   
                 EXAMPLES OF 
               
               
                 GENE 
                 FUNCTIONAL 
                   
                 BIOCHEMICAL 
               
               
                 EXPRESSION 
                 CATEGORY OF 
                 PHYSIOLOGICAL 
                 ACTIVITY OF 
               
               
                 LEVELS 
                 GENE 
                 CONSequence 
                 GENE PRODUCTS 
               
               
                   
               
             
            
               
                 Upregulated 
                 Early Responders 
                 Perceiving 
                 Transcription Factors 
               
               
                 transcripts 
                 To 
                 Reactive Oxygen 
                 Kinases And Phosphatases 
               
               
                 (Higher at 1 h 
                 Reactive Oxygen 
                   
                 Transporters 
               
               
                 Than 6 h) 
                   
                 Reactive Oxygen 
                 Glutathione S-Transferase 
               
               
                 (Level at 1 h ≅ 
                   
                 Response 
                 Heat Shock Proteins 
               
               
                 6 h) 
                   
                 Transduction 
                 Salicylic Acid Response 
               
               
                   
                   
                 Pathways 
                 Pathway Proteins 
               
               
                   
                   
                   
                 Jasmonic Acid Pathway 
               
               
                   
                   
                 Initiating Specific 
                 Proteins 
               
               
                   
                   
                 Gene Transcription 
                 Dehydrins 
               
               
                   
                   
                   
                 Peroxidases 
               
               
                   
                   
                   
                 Catalase 
               
               
                   
                   
                   
                 Proteases 
               
               
                   
                   
                   
                 Pathogen Response Proteins 
               
               
                   
                   
                   
                 Ca 2+ Channel Blockers 
               
               
                   
                   
                   
                 Phenylalanine Ammonia 
               
               
                   
                   
                   
                 Lyase 
               
               
                 Upregulated 
                 Delayed Reactive 
                 Maintenance Of 
                 Transcription Factors 
               
               
                 transcripts 
                 Oxygen 
                 Defence Pathways 
                 Kinases And Phosphatases 
               
               
                 (Lower at 1 h 
                 Responders 
                 To Control Active 
                 Reactive Oxygen 
               
               
                 Than 6 h) 
                   
                 Oxygen 
                 Scavenging Enzymes 
               
               
                   
                   
                   
                 Cell Wall And Cell 
               
               
                   
                   
                   
                 Division/Growth Promoting 
               
               
                   
                   
                 Activation Of Cell 
                 Pathway Enzymes 
               
               
                   
                   
                 Death Pathways In 
                 Pathogen Response 
               
               
                   
                   
                 Specific Cells 
                 Proteins 
               
               
                   
                   
                   
                 Proteins Of Defence 
               
               
                   
                   
                   
                 Pathways 
               
               
                   
                   
                   
                 Proteases, Cellulases, 
               
               
                   
                   
                   
                 Nucleases And Other 
               
               
                   
                   
                   
                 Degrading Enzymes. 
               
               
                   
                   
                   
                 Membrane Proteins 
               
               
                   
                   
                   
                 Mitochondrial And 
               
               
                   
                   
                   
                 Chloroplast Energy Related 
               
               
                   
                   
                   
                 Proteins 
               
               
                 Downregulated 
                 Early Responder 
                 Negative 
                 Transcription Factors 
               
               
                 transcripts 
                 Repressors Of 
                 Regulation Of 
                 Kinases And Phosphatases 
               
               
                 Level at 1 h ≅ 6 h 
                 Reactive Oxygen 
                 Reactive Oxygen- 
                 Chromatin Remodelling 
               
               
                 Level at 6 h &gt; 1 h. 
                 Response 
                 Inducible Pathways 
                 Proteins 
               
               
                   
                 Pathways 
                 Released 
               
               
                   
                 Genes Of 
               
               
                   
                 Pathways That 
                 Reduction In 
                 Metabolic Enzymes In 
               
               
                   
                 Are Minimized In 
                 Activities Of 
                 Affected Cells 
               
               
                   
                 Response To 
                 Pathways Not 
                 Membrane Proteins And 
               
               
                   
                 Reactive Oxygen 
                 Maintained Under 
                 Cell Wall Proteins 
               
               
                 Down Regulated 
                 Delayed 
                 High Reactive 
                 Transcription Factors 
               
               
                 Transcripts 
                 Responder 
                 Oxygen 
                 Kinases And Phosphatases 
               
               
                 (Level at1 h &gt; 6 h 
                 Repressors Of 
                 Negative 
                 Chromatin Remodelling 
               
               
                   
                 Reactive Oxygen 
                 Regulation Of 
                 Proteins 
               
               
                   
                 Response 
                 Reactive Oxygen 
               
               
                   
                 Pathways 
                 Inducible Pathways 
                 Metabolic Enzymes In 
               
               
                   
                   
                 Released 
                 Affected Cells 
               
               
                   
                 Genes Of 
                   
                 Membrane Proteins And 
               
               
                   
                 Pathways That 
                 Reduction In 
                 Cell Wall Proteins 
               
               
                   
                 Are Minimised In 
                 Activities Of 
               
               
                   
                 Response To 
                 Pathways Not 
                 Many Proteins In Cells 
               
               
                   
                 Reactive Oxygen 
                 Maintained Under 
                 Undergoing Cell Death Or In 
               
               
                   
                   
                 Reactive Oxygen 
                 Damaged Cells 
               
               
                   
                   
                 Programmed Cell 
               
               
                   
                   
                 Death 
               
               
                   
               
            
           
         
       
     
     Further, promoters of reactive oxygen responsive genes, as described in the Reference tables, for example, are useful to modulate transcription that is induced by reactive oxygen or any of the following phenotypes or biological activities below. 
     III.E.7. Salicylic Acid Responsive Genes, Gene Components and Products 
     Plant defense responses can be divided into two groups: constitutive and induced. Salicylic acid (SA) is a signaling molecule necessary for activation of the plant induced defense system known as systemic acquired resistance or SAR. This response, which is triggered by prior exposure to avirulent pathogens, is long lasting and provides protection against a broad spectrum of pathogens. Another induced defense system is the hypersensitive response (HR). HR is far more rapid, occurs at the sites of pathogen (avirulent pathogens) entry and precedes SAR. SA is also the key signaling molecule for this defense pathway. 
     Changes in SA concentration in the surrounding environment or within a plant results in modulation of many genes and gene products. Examples of such SA responsive genes and gene products are shown in the Reference, Sequence, Protein Group, Protein Group Matrix, MA_diff and MA_clust tables. These genes and/or products are responsible for effects on traits such as plant vigor and seed yield. They were discovered and characterized from a much larger set by experiments designed to find genes whose mRNA products changed in response to SA treatment. 
     While SA responsive polynucleotides and gene products can act alone, combinations of these polynucleotides also affect growth and development. Useful combinations include different SA responsive polynucleotides and/or gene products that have similar transcription profiles or similar biological activities, and members of the same or similar biochemical pathways. In addition, the combination of SA responsive polynucleotides and/or gene product with another environmentally responsive polynucleotide is also useful because of the interactions that exist between hormone-regulated pathways, stress and pathogen induced pathways, nutritional pathways and development. Here, in addition to polynucleotides having similar transcription profiles and/or biological activities, useful combinations include polynucleotides that may have different transcription profiles but which participate in common and overlapping pathways. 
     Such SA responsive genes and gene products can function to either increase or dampen the above phenotypes or activities either in response to changes in SA concentration or in the absence of SA fluctuations. The MA_diff Table(s) reports the transcript levels of the experiment (see EXPT ID: 108586, 108587, 108515, 108552, 108471, 108472, 108469, 108470, 107953, 107960, 108443, 108440, 108441, 108475, 108476). For transcripts that had higher levels in the samples than the control, a “+” is shown. A “−” is shown for when transcript levels were reduced in root tips as compared to the control. For more experimental detail see the Example section below. 
     SA genes are those sequences that showed differential expression as compared to controls, namely those sequences identified in the MA_diff tables with a “+” or “−” indication. 
     SA Genes Identified by Cluster Analyses of Differential Expression 
     SA Genes Identified by Correlation to Genes that are Differentially Expressed 
     As described above, the transcription profiles of genes that act together are well correlated. Applicants not only have identified the genes that are differentially expressed in the microarray experiments, but also have identified the genes that act in concert with them. The MA_clust table indicates groups of genes that have well correlated transcription profiles and therefore participate in the same pathway or network. 
     A pathway or network of SA genes is any group in the MA_clust that comprises a cDNA ID that also appears in Expt ID 108586, 108587, 108515, 108552, 108471, 108472, 108469, 108470, 107953, 107960, 108443, 108440, 108441, 108475, 108476 of the MA_diff table(s). 
     SA Genes Identified by Correlation to Genes that Cause Physiological Consequences 
     Additionally, the differential expression data and the phenotypic observations can be merged to identify pathways or networks of SA genes. A group in the MA_clust is considered a SA pathway or network if the group comprises a cDNA ID that also appears in Knock-in or Knock-out tables that causes one or more of the phenotypes described in section above. 
     SA Genes Identified by Amino Acid Sequence Similarity 
     SA genes from other plant species typically encode polypeptides that share amino acid similarity to the sequences encoded by corn and  Arabidopsis  SA genes. Groups of SA genes are identified in the Protein Group table. In this table, any protein group that comprises a peptide ID that corresponds to a cDNA ID member of a SA pathway or network is a group of proteins that also exhibits SA functions/utilities. 
     Further, promoters of SA responsive genes, as described in the Reference tables, for example, are useful to modulate transcription that is induced by SA or any of the following phenotypes or biological activities below. 
     III.E.7.a. Use of Salicylic Acid-Responsive Genes to Modulate Phenotypes 
     SA responsive genes and gene products are useful to or modulate one or more phenotypes including pathogen tolerance and/or resistance; Avr/R locus Interactions; non-host interactions; HR; SAR, e.g., SA responsive genes and/or products in conjuction with any of the organisms listed below; resistance to bacteria e.g. to  Erwinia stewartii, Pseudomonas syringae, Pseudomonas tabaci , Stuart&#39;s wilt, etc.; resistance to fungi e.g. to Downy mildews such as  Scleropthora macrospora, Sclerophthora rayissiae, Sclerospora graminicola, Peronosclerospora sorghi, Peronosclerospora philippinensis, Peronosclerospora sacchari, Peronosclerospora maydis;  rusts such As  Puccinia sorphi, Puccinia polysora, Physopella zeae , etc.; and to other fungal diseases e.g.  Cercospora zeae - maydis, Colletotrichum graminicola, Fusarium monoliforme, Exserohilum turcicum, Bipolaris maydis, Phytophthora parasitica, Peronospora tabacina, Septoria , etc.; resistance to viruses or viroids e.g., to Tobacco or Cucumber Mosaic Virus, Ringspot Virus, Necrosis Virus,  Pelargonium  Leaf Curl Virus, Red Clover Mottle Virus, Tomato Bushy Stunt Virus, and like viruses; resistance to insects, such as to aphids e.g.  Myzus persicae ; to beetles and beetle larvae; to lepidoptera larvae e.g.  Heliothus  etc.; resistance to nematodes, e.g.  Meloidogyne incognita  etc.; local resistance in primary (infected) or secondary (uninfected) leaves; stress tolerance; winter survival; cold tolerance; salt tolerance; heavy metal tolerance, such as cadmium; tolerance to physical wounding; increased organelle tolerance to redox stress (such as in mitochondria, and chloroplasts); cell death; programmed cell death, including death of diseased tissue and during senescence); fruit drop; biomass; fresh and dry weight during any time in plant life, such as maturation; number of flowers, seeds, branches, and/or leaves; seed yield, including number, size, weight, and/or harvest index; fruit yield, including number, size, weight, and/or harvest index; plant development; time to fruit maturity; cell wall strengthening and reinforcement; plant product quality; e.g. paper making quality); food additives; treatment of indications modulated by free radicals; and cancer. 
     To regulate any of the desired phenotype(s) above, activities of one or more of the SA responsive genes or gene products can be modulated and the plants tested by screening for the desired trait. Specifically, the gene, mRNA levels, or protein levels can be altered in a plant utilizing the procedures described herein and the phenotypes can be assayed. As an example, a plant can be transformed according to Bechtold and Pelletier (1998, Methods. Mol. Biol. 82:259-266) and/or screened for variants as in Winkler et al. (1998) Plant Physiol 118: 743-50 and visually inspected for the desired phenotype or metabolically and/or functionally assayed according to Zhao et al. (1998, Plant Cell 10:359-70) and Alvarez et al. (1998, Cell 92: 733-84). 
     III.E.7.b. Use of Salicylic Acid-Responsive Genes to Modulate Biochemical Activities 
     The activities of one or more of the SA responsive genes can be modulated to change biochemical or metabolic activities and/or pathways such as those noted below. Such biological activities can be measured according to the citations included in the Table below: 
     
       
         
           
               
               
               
             
               
                   
               
               
                   
                 BIOCHEMICAL OR 
                   
               
               
                   
                 METABOLIC 
               
               
                   
                 ACTIVITIES 
                 CITATION INCLUDING 
               
               
                 PROCESS 
                 AND/OR PATHWAYS 
                 ASSAYS 
               
               
                   
               
             
            
               
                 Protection 
                 Systemic Acquired 
                 Alvarez et al. (1998) Cell 
               
               
                 From 
                 Resistance (SAR) 
                 92: 733-84 
               
               
                 Microbial 
                 Phytoalexin Biosynthesis 
                 Lapwood et al. (1984) Plant 
               
               
                 Pathogens 
                 PR Protein Biosynthesis 
                 Pathol. 33: 13-20 
               
               
                   
                 Local Resistance 
                 Davis et al. (1993) 
               
               
                   
                 Wound Response 
                 Phytochemistry 32: 607-11 
               
               
                   
                   
                 Yahraus et al. (1995) Plant 
               
               
                   
                   
                 Physiol. 109: 1259-66 
               
               
                 Cell 
                 Modulation Of Reactive 
                 Alvarez et al. (1998) Cell 
               
               
                 Signaling 
                 Oxygen Signaling 
                 92: 773-784 
               
               
                   
                 Modulation Of No 
                 Delledonne et al. (1998) 
               
               
                   
                 Signaling 
                 Nature 394: 585-588 
               
               
                 Growth And 
                 Lignification 
                 Redman et al. (1999) Plant 
               
               
                 Development 
                   
                 Physiol. 119: 795-804 
               
               
                   
               
            
           
         
       
     
     Other biological activities that can be modulated by the SA responsive genes and gene products are listed in the Reference tables. Assays for detecting such biological activities are described in the Protein Domain table. 
     Salicylic acid responsive genes are characteristically differentially transcribed in response to fluctuating SA levels or concentrations, whether internal or external to an organism or cell. The MA_diff table reports the changes in transcript levels of various SA responsive genes in entire seedlings at 1 and 6 hours after the seedling was sprayed with a Hoagland&#39;s solution enriched with SA as compared to seedlings sprayed with Hoagland&#39;s solution only. 
     The data from this time course can be used to identify a number of types of SA responsive genes and gene products, including “early responders” and “delayed responders.” Profiles of these different SA responsive genes are shown in the Table below together with examples of the kinds of associated biological activities. 
     
       
         
           
               
               
               
               
             
               
                   
               
               
                   
                   
                   
                 EXAMPLES OF 
               
               
                 GENE 
                 FUNCTIONAL 
                   
                 BIOCHEMICAL 
               
               
                 EXPRESSION 
                 CATEGORY 
                 PHYSIOLOGICAL 
                 ACTIVITIES OF GENE 
               
               
                 LEVELS 
                 OF GENE 
                 CONSEQUENCES 
                 PRODUCTS 
               
               
                   
               
             
            
               
                 Upregulated Genes 
                 Early 
                 SA Perception 
                 Transcription Factors 
               
               
                 (Level At 1 h ≅ 6 h) 
                 Responders To 
                 SA Uptake 
                 Transporters, Kinases, 
               
               
                 Or 
                 SA 
                 Modulation Of SA 
                 Phosphatases, G- 
               
               
                 (Level At 1 h &gt; 6 h) 
                   
                 Response Transduction 
                 Proteins, LRR, DNA 
               
               
                   
                   
                 Pathways 
                 Remodelling Proteins 
               
               
                 Upregulated Genes 
                 Delayed 
                 Specific Defensegene 
                 Proteases, PRProteins, 
               
               
                 (Level At 1 h &lt; 6 h) 
                 Responders To 
                 Transcription Initiation 
                 Cellulases, Chitinases, 
               
               
                   
                 SA 
                 (E.G. Pr Genes, Pal 
                 Cutinases, Other 
               
               
                   
                   
                   
                 Degrading Enzymes, Pal, 
               
               
                   
                   
                   
                 Proteins Of Defense 
               
               
                   
                   
                   
                 Pathways, Cell Wall 
               
               
                   
                   
                   
                 Proteins 
               
               
                   
                   
                   
                 Epoxide Hydrolases, 
               
               
                   
                   
                   
                 Methyl Transferases 
               
               
                 Downregulated 
                 Early 
                 Negative Regulation 
                 Transcription factors, 
               
               
                 (Level At 1 h ≅ 6 h) 
                 Responder 
                 Of SA Inducible 
                 kinases, phosphatases, G- 
               
               
                 Or 
                 Repressors To 
                 Pathways Released 
                 proteins, LRR, 
               
               
                 (Level At 6 h &gt; 1 h) 
                 SA 
                   
                 transporters, calcium 
               
               
                   
                 Genes With 
                   
                 binding proteins, 
               
               
                   
                 Discontinued 
                   
                 chromatin remodelling 
               
               
                   
                 Expression Or 
                   
                 protein 
               
               
                   
                 UnsTable 
               
               
                   
                 mRNA In The 
               
               
                   
                 Presence Of SA 
               
               
                 Down-Regulated 
                 Delayed 
                 Negative Regulation Of 
                 Transcription Factors, 
               
               
                 Transcripts 
                 Responders To 
                 SA Inducible Pathways 
                 Kinases, Phosphatases, 
               
               
                 (Level At 1 h &gt; 6 h) 
                 SA Metabolism 
                 Released 
                 G-Proteins, LRR, 
               
               
                   
                 Genes With 
                   
                 Transporters, Calcium 
               
               
                   
                 Discontinued 
                   
                 Binding Proteins, 
               
               
                   
                 Expression Or 
                   
                 Chromatin Remodelling 
               
               
                   
                 UnsTable 
                   
                 Protein 
               
               
                   
                 mRNA In The 
               
               
                   
                 Presence Of SA 
               
               
                   
               
            
           
         
       
     
     Further, any desired sequence can be transcribed in similar temporal, tissue, or environmentally specific patterns as the SA responsive genes when the desired sequence is operably linked to a promoter of a SA responsive gene. 
     III.E.8. Nitric Oxide Responsive Genes, Gene Components and Products 
     The rate-limiting element in plant growth and yield is often its ability to tolerate suboptimal or stress conditions, including pathogen attack conditions, wounding and the presence of various other factors. To combat such conditions, plant cells deploy a battery of inducible defense responses, including synergistic interactions between nitric oxide (NO), reactive oxygen intermediates (ROS), and salicylic acid (SA). NO has been shown to play a critical role in the activation of innate immune and inflammatory responses in animals. At least part of this mammalian signaling pathway is present in plants, where NO is known to potentiate the hypersensitive response (HR). In addition, NO is a stimulator molecule in plant photomorphogenesis. 
     Changes in nitric oxide concentration in the internal or surrounding environment, or in contact with a plant, results in modulation of many genes and gene products. Examples of such nitric oxide responsive genes and gene products are shown in the Reference and Sequence Tables. These genes and/or products are responsible for effects on traits such as plant vigor and seed yield. They were discovered and characterized from a much larger set by experiments designed to find genes whose mRNA products changed in response to nitric oxide treatment. 
     While nitric oxide responsive polynucleotides and gene products can act alone, combinations of these polynucleotides also affect growth and development. Useful combinations include different nitric oxide responsive polynucleotides and/or gene products that have similar transcription profiles or similar biological activities, and members of the same or similar biochemical pathways. Whole pathways or segments of pathways are controlled by transcription factor proteins and proteins controlling the activity of signal transduction pathways. Therefore, manipulation of the levels of such proteins is especially useful for altering phenotypes and biochemical activities of plants. In addition, the combination of a nitric oxide responsive polynucleotide and/or gene product with other environmentally responsive polynucleotides is also useful because of the interactions that exist between hormone-regulated pathways, stress pathways, pathogen stimulated pathways, nutritional pathways and development. Here, in addition to polynucleotides having similar transcription profiles and/or biological activities, useful combinations include polynucleotides that may have different transcription profiles but which participate in common or overlapping pathways. The MA_diff Table(s) reports the transcript levels of the experiment (see EXPT ID: 108584, 108585, 108526, 108527, 108559). For transcripts that had higher levels in the samples than the control, a “+” is shown. A “−” is shown for when transcript levels were reduced in root tips as compared to the control. For more experimental detail see the Example section below. 
     NO genes are those sequences that showed differential expression as compared to controls, namely those sequences identified in the MA_diff tables with a “+” or “−” indication. 
     NO Genes Identified by Cluster Analyses of Differential Expression 
     NO Genes Identified by Correlation to Genes that are Differentially Expressed 
     As described above, the transcription profiles of genes that act together are well correlated. Applicants not only have identified the genes that are differentially expressed in the microarray experiments, but also have identified the genes that act in concert with them. The MA_clust table indicates groups of genes that have well correlated transcription profiles and therefore participate in the same pathway or network. 
     A pathway or network of NO genes is any group in the MA_clust that comprises a cDNA ID that also appears in Expt ID 108584, 108585, 108526, 108527, 108559 of the MA_diff table(s). 
     NO Genes Identified by Correlation to Genes that Cause Physiological Consequences 
     Additionally, the differential expression data and the phenotypic observations can be merged to identify pathways or networks of NO genes. A group in the MA_clust is considered a NO pathway or network if the group comprises a cDNA ID that also appears in Knock-in or Knock-out tables that causes one or more of the phenotypes described in section above. 
     NO Genes Identified by Amino Acid Sequence Similarity 
     NO genes from other plant species typically encode polypeptides that share amino acid similarity to the sequences encoded by corn and  Arabidopsis  NO genes. Groups of NO genes are identified in the Protein Group table. In this table, any protein group that comprises a peptide ID that corresponds to a cDNA ID member of a NO pathway or network is a group of proteins that also exhibits NO functions/utilities. 
     Such nitric oxide responsive genes and gene products can function either to increase or dampen the above phenotypes or activities either in response to changes in nitric oxide concentration or in the absence of nitric oxide fluctuations. Further, promoters of nitric oxide responsive genes, as described in the Reference tables, for example, are useful to modulate transcription that is induced by nitric oxide or any of the following phenotypes or biological activities below. 
     III.E.8.a. Use of Nitric Oxide-Responsive Genes to Modulate Phenotypes: 
     Nitric oxide responsive genes and gene products are useful to or modulate one or more phenotypes including Stress Responses, Mediation of response to stresses, Disease resistance, Growth, Roots, Stems, Leaves, Cells, Promotes leaf cell elongation, Biomass; Fresh and Dry Weight during any time in plant life, such as at maturation; Size and/or Weight; Flowers, Seeds, Branches, Leaves, Roots, Development, Seed Development, Dormancy; Control rate and timing of germination, Prolongs seed storage and viability; and Senescence. 
     Further, any desired sequence can be transcribed in similar temporal, tissue, or environmentally specific patterns as the nitric responsive genes when the desired sequence is operably linked to a promoter of a nitric responsive gene. 
     To regulate any of the desired phenotype(s) above, activities of one or more of the nitric oxide responsive genes or gene products can be modulated and the plants tested by screening for the desired trait. Specifically, the gene, mRNA levels, or protein levels can be altered in a plant utilizing the procedures described herein and the phenotypes can be assayed. As an example, a plant can be transformed according to Bechtold and Pelletier (1998) Methods. Mol. Biol. 82: 259-266 and/or screened for variants as described in Winkler et al. (1998) Plant Physiol. 118: 743-50 and visually inspected for the desired phenotype. Alternatively, plants can be metabolically and/or functionally assayed according to Beligni and Lamattina (2000) Planta 210: 215-21), Lapwood et al (1984) Plant Pathol 33: 13-20, and/or Brown and Botstein (1999) Nature Genet. 21: 33-37. 
     III.E.8.b. Use of Nitric Oxide-Responsive Genes to Modulate Biochemical Activities: 
     The activities of one or more of the nitric oxide responsive genes can be modulated to change biochemical or metabolic activities and/or pathways such as those noted below. Such biological activities can be measured according to the citations included in the Table below: 
     
       
         
           
               
               
               
             
               
                   
               
               
                   
                 BIOCHEMICAL OR 
                   
               
               
                   
                 METABOLIC 
               
               
                   
                 ACTIVITIES 
                 CITATIONS INCLUDING 
               
               
                 PROCESS 
                 AND/OR PATHWAYS 
                 ASSAYS 
               
               
                   
               
             
            
               
                 Stress 
                 Programmed Cell Death 
                 Levine et al (1996) Curr. 
               
               
                 Response 
                   
                 Biol 6: 427-37 
               
               
                   
                   
                 Sellins and Cohen (1991) 
               
               
                   
                   
                 Radiat. Res. 126: 88-95 
               
               
                   
                 Reactive Oxygen based 
                 Kumar and Klessig (2000) 
               
               
                   
                 Defence Pathways 
                 Mol. Plant Microbe 
               
               
                   
                   
                 Interact. 13: 347-351 
               
               
                 Disease 
                 Microbial Pathogen 
                 Lapwood et al (1984) Plant 
               
               
                 Resistance 
                 resistance pathways 
                 Pathol 33: 13-20 
               
               
                   
                   
                 Kumar and Klessig (2000) 
               
               
                   
                   
                 Mol. Plant microbe 
               
               
                   
                   
                 interact. 13: 347-351 
               
               
                   
                   
                 Klessig et. al. (2000) Proc. 
               
               
                   
                   
                 Nat. Acad. Sci USA 97: 
               
               
                   
                   
                 8849-8855 
               
               
                   
                   
                 Delledonna et al(1998) 
               
               
                   
                   
                 Nature 394: 585-588 
               
               
                   
                 Programmed Cell Death 
                 Levine et al (1996) Curr. 
               
               
                   
                   
                 Biol 6: 427-437 
               
               
                   
                   
                 Sellins and Cohen (1991) 
               
               
                   
                   
                 Radiat. Res. 126: 88-95 
               
               
                   
                 Cellular Protectant Gene 
                 Brown and Botstein (1999) 
               
               
                   
                 expression 
                 Nat Genet 21: 33-37 
               
               
                   
                 Phytoalexin Biosynthesis 
                 Davis et al. (1993) 
               
               
                   
                   
                 Phytochemistry 32: 
               
               
                   
                   
                 607-611 
               
               
                 Signal 
                 Regulation of hydrogen 
                 Wu et al. (1995) Plant Cell 
               
               
                 Transduction 
                 peroxide signaling 
                 7, 1357-1368 
               
               
                 Reorientation 
                 Induction of ribosomal 
                 This study. Standard 
               
               
                 of nitrogen 
                 proteins, asparagine 
                 assays for detection of 
               
               
                 metabolism 
                 synthesis, proteases, 
                 changes 
               
               
                   
                 Rnases 
               
               
                 Reorientation 
                 Induction of sugar 
                 This study. Standard 
               
               
                 of sugar and 
                 transporters, ATPases, 
                 assays for detection of 
               
               
                 energy 
                 glycohydrolases, and 
                 changes 
               
               
                 metabolism 
                 glycolytic enzymes, 
               
               
                   
                 for example 
               
               
                   
               
            
           
         
       
     
     Other biological activities that can be modulated by the NO responsive genes and gene products are listed in the Reference Tables. Assays for detecting such biological activities are described in the Protein Domain table. 
     NO responsive genes are characteristically differentially transcribed in response to fluctuating NO levels or concentrations, whether internal or external to an organism or cell. The MA_diff table(s) report(s) the changes in transcript levels of various NO responsive genes in aerial tissues at 1 and 6 hours after a plant was sprayed with a Silwett L-77 solution enriched with 5 mM sodium nitroprusside, which is an NO donor. These changes are in comparison with plants sprayed with Silwett L-77 solution only. 
     The data from this time course can be used to identify a number of types of NO responsive genes and gene products, including “early responders” and “delayed responders” Profiles of these different nitric oxide responsive genes are shown in the Table below together with examples of the kinds of associated biological activities. 
                                         GENE   FUNCTIONAL       EXAMPLES OF       EXPRESSION   CATEGORY OF   PHYSIOLOGICAL   BIOCHEMICAL       LEVEL   GENE   CONSEQUENCES   ACTIVITY                  Upregulated genes   Early responder   NO Perception   Transcription Factors       (level at 1 hour ≅ 6   repressors to NO   NO Uptake       hours)       Modulation of NO   Transporters       (level at 1 hour &gt; 6       Response Transduction   Pathogen responsive       hours)       Pathways   proteins, salicylic and                   jasmonate pathway                   proteins               Specific Gene   Proteins to provide               Transcription Initiation   defence against active               of Pathways to   oxygen e.g. glutathione               Optimize NO Response   transferase, ascorbate               Pathways   free radical reductase,                   ascorbate peroxidase,                   nitrilase, heat shock                   proteins                   Proteins to reorient                   metabolism                   e.g. proteases, Rnases,                   proteasomes,                   asparagine synthetase,                   glycohydrolases,                   transporters                   Proteins to inhibit                   transport of nitric oxide                   Degradation enzymes       Upregulated   Delayed NO   Maintenance of   NO Metabolic       transcripts   responders   metabolism in presence   Pathway enzymes       (level at 1 hour &lt; 6       of High NO   Pathogen responsive       hours)       Maintenace of disease   proteins, salicylic and               defence pathways   jasmonate pathway                   proteins               Maintenance of   Proteins to provide               pathways against   defence against active               reactive oxygen   oxygen e.g. glutathione               production   transferase, ascorbate                   free radical reductase,                   ascorbate peroxidase,                   nitrilase, heat shock                   proteins               Maintenance of   Proteins to reorient               different metabolic   and sustain metabolism               programs   e.g. proteases, Rnases,                   proteasomes, asparagine                   synthetase, glycohydrolases,                   transporters,                   Proteins to inhibit                   transport of NO               Selective cell death   Degradation enzymes       Down Regulated   Early responders of   Negative regulation of   Transcription factors       Transcripts   NO utilization   NO utilization   Kinases and       (level at 1 hours ≅ 6   pathways   pathways released   phosphatases       hours)           Chromatin       (level at 6 hours &gt; 1           restructuring proteins       hour)   Genes with   Reorientation of   Transcription           discontinued   metabolism   factors, metabolic           expression or       enzymes, kinases and           unsTable mRNA       phosphatases,           following nitric oxide       transporters, ribosomal           uptake       proteins               Programmed cell death   Most proteins in cells                   undergoing cell death       Down Regulated   Delayed responder   Negative regulation of   Transcription factors       Transcripts   repressors of NO   NO utilization   Kinases and       (level at 1 hour &gt; 6   stress metabolism   pathways released   phosphatases       hours)           Chromatin                   restructuring proteins           Genes with   Reorientation of   Transcription           discontinued   metabolism   factors, metabolic           expression or       enzymes, kinases and           unsTable       phosphatases,           mRNA following       transporters, ribosomal           nitric oxide uptake       proteins.               Programmed cell death   Most proteins in cells                   undergoing                   programmed cell death                    
Use of Promoters of No Responsive Genes
 
     Promoters of NO responsive genes are useful for transcription of any desired polynucleotide or plant or non-plant origin. Further, any desired sequence can be transcribed in a similar temporal, tissue, or environmentally specific patterns as the NO responsive genes where the desired sequence is operably linked to a promoter of a NO responsive gene. The protein product of such a polynucleotide is usually synthesized in the same cells, in response to the same stimuli as the protein product of the gene from which the promoter was derived. Such promoter are also useful to produce antisense mRNAs to down-regulate the product of proteins, or to produce sense mRNAs to down-regulate mRNAs via sense suppression. 
     III.9. Osmotic Stress Responsive Genes, Gene Components and Products 
     The ability to endure and recover from osmotic and salt related stress is a major determinant of the geographical distribution and productivity of agricultural crops. Osmotic stress is a major component of stress imposed by saline soil and water deficit. Decreases in yield and crop failure frequently occur as a result of aberrant or transient environmental stress conditions even in areas considered suitable for the cultivation of a given species or cultivar. Only modest increases in the osmotic and salt tolerance of a crop species would have a dramatic impact on agricultural productivity. The development of genotypes with increased osmotic tolerance would provide a more reliable means to minimize crop losses and diminish the use of energy-costly practices to modify the soil environment. 
     Changes in the osmotic concentration of the surrounding environment or within a plant results in modulation of many genes and gene products. Examples of such osmotic stress responsive genes and gene products, including salt responsive genes, are shown in the Reference, Sequence, Protein Group, Protein Group Matrix, MA_diff and MA_clust tables. These genes and/or products are responsible for effects on traits such as plant vigor and seed yield. 
     While osmotic and/or salt stress responsive polynucleotides and gene products can act alone, combinations of these polynucleotides also affect growth and development. Useful combinations include different osmotic stress responsive polynucleotides and/or gene products that have similar transcription profiles or similar biological activities, and members of the same or similar biochemical pathways. In addition, the combination of an osmotic stress responsive polynucleotide and/or gene product with another environmentally responsive polynucleotide is also useful because of the interactions that exist between hormone-regulated pathways, stress pathways, nutritional pathways and development. Here, in addition to polynucleotides having similar transcription profiles and/or biological activities, useful combinations include polynucleotides that may have different transcription profiles but which participate in a common pathway. 
     Such osmotic and/or salt stress responsive genes and gene products can function to either increase or dampen the above phenotypes or activities either in response to changes in osmotic concentration or in the absence of osmotic fluctuations. The MA_diff Table(s) reports the transcript levels of the experiment (see EXPT ID: 108570, 108571, 108541, 108542, 108553, 108539, 108540). For transcripts that had higher levels in the samples than the control, a “+” is shown. A “−” is shown for when transcript levels were reduced in root tips as compared to the control. For more experimental detail see the Example section below. 
     Osmotic Stress genes are those sequences that showed differential expression as compared to controls, namely those sequences identified in the MA_diff tables with a “+” or “−” indication. 
     Osmotic Stress Genes Identified by Cluster Analyses of Differential Expression 
     Osmotic Stress Genes Identified by Correlation to Genes that are Differentially Expressed 
     As described above, the transcription profiles of genes that act together are well correlated. Applicants not only have identified the genes that are differentially expressed in the microarray experiments, but also have identified the genes that act in concert with them. The MA_clust table indicates groups of genes that have well correlated transcription profiles and therefore participate in the same pathway or network. 
     A pathway or network of Osmotic Stress genes is any group in the MA_clust that comprises a cDNA ID that also appears in Expt ID 108570, 108571, 108541, 108542, 108553, 108539, 108540 of the MA_diff table(s). 
     Osmotic Stress Genes Identified by Correlation to Genes that Cause Physiological Consequences 
     Additionally, the differential expression data and the phenotypic observations can be merged to identify pathways or networks of Osmotic Stress genes. A group in the MA_clust is considered a Osmotic Stress pathway or network if the group comprises a cDNA ID that also appears in Knock-in or Knock-out tables that causes one or more of the phenotypes described in section above. 
     Osmotic Stress Genes Identified by Amino Acid Sequence Similarity 
     Osmotic Stress genes from other plant species typically encode polypeptides that share amino acid similarity to the sequences encoded by corn and  Arabidopsis  Osmotic Stress genes. Groups of Osmotic Stress genes are identified in the Protein Group table. In this table, any protein group that comprises a peptide ID that corresponds to a cDNA ID member of a Osmotic Stress pathway or network is a group of proteins that also exhibits Osmotic Stress functions/utilities. 
     Further, promoters of osmotic stress responsive genes, as described in the Reference tables, for example, are useful to modulate transcription that is induced by osmotic stress or any of the following phenotypes or biological activities below. 
     III.E.9.a. Use of Osmotic Stress Responsive Genes to Modulate Phenotypes 
     Osmotic stress responsive genes and gene products are useful to or modulate one or more phenotypes including growth; roots; stems; leaves; development (such as cell growth by DNA synthesis and cell division, seed development (with regard to desiccation tolerance and dormancy, such as control rate of germination and prolongs seed storage and viability and senescence); stress responses; desiccation; drought; and salt. 
     To regulate any of the phenotype(s) above, activities of one or more of the osmotic stress responsive genes or gene products can be modulated and the plants tested by screening for the desired trait. Specifically, the gene, mRNA levels, or protein levels can be altered in a plant utilizing the procedures described herein and the phenotypes can be assayed. As an example, a plant can be transformed according to Bechtold and Pelletier (1998, Methods. Mol. Biol. 82:259-266) and/or screened for variants as in Winkler et al. (1998) Plant Physiol 118: 743-50 and visually inspected for the desired phenotype or metabolically and/or functionally assayed according to de Castro (1998, Phytochemistry 47: 689-694), Xu (1998, J Exp Bot 49: 573-582), Ausubel et al. (In: Current Protocols in Molecular Biology (1999) Volume 1, chapter 4, eds. Ausubel, Brent, Kingston, Moore, Seidman, Smith and Struhl, New York, N.Y.) and De Castro et al. (2000, Plant Physiol 122: 327-36) 
     III.E.9.b. Use of Osmotic Stress Responsive Genes to Modulate Biochemical Activities 
     The activities of one or more of the osmotic stress responsive genes can be modulated to change biochemical or metabolic activities and/or pathways such as those noted below. Such biological activities can be measured according to the citations included in the Table below: 
     
       
         
           
               
               
               
             
               
                   
               
               
                   
                 BIOCHEMICAL OR 
                   
               
               
                   
                 METABOLIC 
               
               
                   
                 ACTIVITIES 
                 CITATIONS INCLUDING 
               
               
                 PROCESS 
                 AND/OR PATHWAYS 
                 ASSAYS 
               
               
                   
               
             
            
               
                 Cell Growth And 
                 Regulation Of Osmolyte 
                 Yoshu et al. (1995) The 
               
               
                 Differentiation 
                 Synthesis 
                 Plant Journal 7: 751-60 
               
               
                   
                 Regulation Of Glycolate Pathway 
                 Streb et al. (1993) 
               
               
                   
                 And Photoinhibition Of 
                 Physiologia Plantarum. 
               
               
                   
                 Photosystem II In Response To 
                 88: 590-598 
               
               
                   
                 Stress 
               
               
                 Gene Regulation 
                 Transcriptional Regulation Of 
                 Current Protocols in 
               
               
                   
                 Osmotic Stress Induced Proteins 
                 Molecular Biology/edited 
               
               
                   
                 Through DNA Binding Proteins 
                 by Frederick M. Ausubel . . . 
               
               
                   
                   
                 [et al.]. New York: 
               
               
                   
                   
                 Published by Greene Pub. 
               
               
                   
                   
                 Associates and Wiley- 
               
               
                   
                   
                 Interscience: J. Wiley, 
               
               
                   
                   
                 c1987 
               
               
                   
                 Transcriptional Regulation Of 
                 Jonak (1996) Proceedings 
               
               
                   
                 Osmotic Stress Induced Proteins 
                 of the National Academy 
               
               
                   
                 Through Protein Phosphorylation 
                 of Sciences of the United 
               
               
                   
                 And Dephosphorylation 
                 States of America, 93: 
               
               
                   
                   
                 11274-11279; 
               
               
                   
                   
                 Monroy, A. et al., (1998) 
               
               
                   
                   
                 Analytical Biochemistry 
               
               
                   
                   
                 265: 183-185; 
               
               
                   
                 Regulation Of Osmotic Stress 
                 McCright (1998) IN: 
               
               
                   
                 Induced Gene Protein 
                 Methods in Molecular 
               
               
                   
                 Accumulation By Protein Protein 
                 Biology; Protein 
               
               
                   
                 Intereaction Between Osmotic 
                 phosphatase protocols; 
               
               
                   
                 Stress Regulated Genes And 
                 Ludlow (1998) Humana 
               
               
                   
                 Protein Phosphatase 2C 
                 Press Inc.; Suite 808, 999 
               
               
                   
                   
                 Riverview Drive, Totowa, 
               
               
                   
                   
                 New Jersey 
               
               
                   
                   
                 07512, USA.: 263-277. 
               
               
                   
                 Transcriptional Regulation Of 
                 Luo and Dean (1999) 
               
               
                   
                 Heat Induced Genes Through 
                 Journal of the National 
               
               
                   
                 Chromatin Remodeling 
                 Cancer Institute 91: 1288- 
               
               
                   
                   
                 1294; Chromatin protocols 
               
               
                   
                   
                 (1999) edited by Peter B. 
               
               
                   
                   
                 Becker. Totowa, N.J.: 
               
               
                   
                   
                 Humana Press 
               
               
                   
                 Activity Of Abcisic Acid 
                 Gubler et al. (1999) Plant 
               
               
                   
                 Regulated DNA Binding Proteins 
                 Journal 17: 1-9 
               
               
                   
                 Accumulation Of RNA Binding 
                 Sato (1995) 
               
               
                   
                 Proteins That Regulate Osmotic 
                 Nucleic Acids Research 
               
               
                   
                 Stress 
                 23: 2161-2167. 
               
               
                 Stress Response 
                 Synthesis And Metabolism Of 
                 Minocha et al. (1999) 
               
               
                   
                 Osmoprotectants Such As 
                 Plant Physiol and Biochem 
               
               
                   
                 Betaine, Proline And Trehalase 
                 37: 597-603 
               
               
                   
                 Regulation Of Sugar Transporters 
                 Dejardin et al. (1999) 
               
               
                   
                   
                 Biochem J; 344 Pt 2: 503-9 
               
               
                   
                 Regulation Of Vacuolar 
                 Gaxiola et al. (1999) 
               
               
                   
                 Sodium/Proton Antiport Activity 
                 PNAS USA 96: 1480- 
               
               
                   
                 And The Detoxification Of 
                 1485 
               
               
                   
                 Cations 
               
               
                   
                 Regulation Of Intracellular Na+ 
                 Espinoza-Ruiz et al. 
               
               
                   
                 And Li+ Ion Concentrations 
                 (1999) The Plant Journal 
               
               
                   
                   
                 20: 529-539 
               
               
                   
                 Regulation Of Universal Stress 
                 Freestone et al. (1997) 
               
               
                   
                 Protein Homologue Activity By 
                 Journal of Molecular 
               
               
                   
                 Phosphorylation And 
                 Biology, v. 274: 318-324 
               
               
                   
                 Dephosphorylation. 
               
               
                   
                 Regulation/Maintenance Of 
                 Walker (1996) Humana 
               
               
                   
                 Protein Stability During Thermal 
                 Press Inc. Suite 808, 999 
               
               
                   
                 Stress 
                 Riverview Drive, Totowa, 
               
               
                   
                   
                 New Jersey 07512, USA 
               
               
                   
                 Regulation Of Protein 
                 Vierstra (1996) Plant 
               
               
                   
                 Degradation During Thermal 
                 Molecular Biology, 
               
               
                   
                 Stress. 
                 32: 275-302. 
               
               
                   
                   
                 Vierstra and Callis (1999) 
               
               
                   
                   
                 Plant Molecular Biology, 
               
               
                   
                   
                 41: 435-442 
               
               
                 Signal Transduction 
                 Activation Of Stress Response 
                 Xinong et al. (1999) The 
               
               
                   
                 Genes 
                 Plant Journal 19: 569-578 
               
               
                   
                 Salt Tolerance 
                 Piao (1999) Plant Physiol 
               
               
                   
                   
                 19: 1527-1534 
               
               
                   
                 Calcium Mediated Stress 
                 Subbaiah et al. (1994) 
               
               
                   
                 Response 
                 Plant Physiology 105: 
               
               
                   
                   
                 369-376 
               
               
                   
                   
                 Kudla et al. (1999) PNAS 
               
               
                   
                   
                 USA 96: 4718-4723 
               
               
                   
               
            
           
         
       
     
     Other biological activities that can be modulated by the osmotic stress responsive genes and gene products are listed in the Reference tables. Assays for detecting such biological activities are described in the Protein Domain table. 
     Osmotic stress responsive genes are characteristically differentially transcribed in response to fluctuating osmotic stress levels or concentrations, whether internal or external to an organism or cell. MA_diff table reports the changes in transcript levels of various osmotic stress responsive genes in aerial tissues of plants at 1 and 6 hours after the plants were sprayed with Hoagland&#39;s solution containing 20% PEG as compared to aerial tissues from plants sprayed with Hoagland&#39;s solution only. 
     The data from this time course can be used to identify a number of types of osmotic stress responsive genes and gene products, including “early responding,” “sustained osmotic stress responders,” “repressors of osmotic stress pathways” and “osmotic stress responders.” Profiles of these different osmotic stress responsive genes are shown in the Table below together with examples of the kinds of associated biological activities. 
     
       
         
           
               
               
               
               
             
               
                   
               
               
                   
                   
                   
                 EXAMPLES OF 
               
               
                 GENE 
                 FUNCTIONAL 
                   
                 BIOCHEMICAL 
               
               
                 EXPRESSION 
                 CATEGORY 
                 PHYSIOLOGICAL 
                 ACTIVITIES OF 
               
               
                 LEVELS 
                 OF GENES 
                 CONSEQUENCES 
                 GENE PRODUCTS 
               
               
                   
               
             
            
               
                 Up Regulated 
                 Early Responders 
                 Osmotic Stress 
                 Transcription 
               
               
                 Transcripts 
                 To Osmotic 
                 Perception 
                 Factors 
               
               
                 (Level At 1 Hour ≅ 
                 Stress 
                 Osmolyte Uptake 
                 Transcription 
               
               
                 6 Hours) 
                 Universal Stress 
                 Modulation Of 
                 Coactivators 
               
               
                 (Level At 1 Hour &gt; 
                 Response Genes 
                 Osmotic Stress 
                 Membrane 
               
               
                 6 Hours) 
                 Osmotic Stress 
                 Response Signal 
                 Transporters 
               
               
                   
                 Responders 
                 Transduction Pathways 
                 Proline 
               
               
                   
                 Abscisic Acid 
                 Specific Gene 
                 Biosynthesis 
               
               
                   
                 Biosynthesis And 
                 Transcription 
                 Selective Inhibition 
               
               
                   
                 Perception 
                 Initiation 
                 Of Osmolyte 
               
               
                   
                   
                 Specific Gene 
                 Transport 
               
               
                   
                   
                 Transcription 
                 Protein 
               
               
                   
                   
                 Repression 
                 Ubiquitination 
               
               
                   
                   
                 Translation Activation 
                 Protein 
               
               
                   
                   
                 Translation 
                 Degradation 
               
               
                   
                   
                 Repression 
                 Rna Binding 
               
               
                   
                   
                 Repression Of 
                 Proteins 
               
               
                   
                   
                 “Normal State” 
                 Modification Of 
               
               
                   
                   
                 Pathways To Optimize 
                 Protein Activity By 
               
               
                   
                   
                 Osmotic Stress 
                 Phosphatases, 
               
               
                   
                   
                 Response 
                 Kinases 
               
               
                   
                   
                 Activation Of Stress 
                 Synthesis And Or 
               
               
                   
                   
                 Signaling Pathways 
                 Activation Of 
               
               
                   
                   
                 Up Regulation Of 
                 Oxide Hydrolases, 
               
               
                   
                   
                 Abscisic Acid 
                 Suoeroxidedismutase, 
               
               
                   
                   
                 Biosynthesis Pathway 
                 Iron Ascorbate 
               
               
                   
                   
                 Protein Accumulation 
                 Peroxidase 
               
               
                   
                   
                 And Activity 
                 Activation Of 
               
               
                   
                   
                 Scavenging Reactive 
                 Signaling Pathway 
               
               
                   
                   
                 Oxygen Species 
                 By Calcium 
               
               
                   
                   
                 Modification Of Cell 
                 Binding Proteins, 
               
               
                   
                   
                 Wall Composition 
                 Modification Of 
               
               
                   
                   
                 Up-Regulation Of 
                 Protein Activity By 
               
               
                   
                   
                 Universal Stress 
                 Protein-Protein 
               
               
                   
                   
                 Response Protein 
                 Interaction 
               
               
                   
                   
                 Accumulation 
                 Change In 
               
               
                   
                   
                   
                 Chromatin 
               
               
                   
                   
                   
                 Structure And/Or 
               
               
                   
                   
                   
                 Localized Dna 
               
               
                   
                   
                   
                 Topology 
               
               
                   
                   
                   
                 Modification Of 
               
               
                   
                   
                   
                 Pre-Existing 
               
               
                   
                   
                   
                 Translation Factors 
               
               
                   
                   
                   
                 By Phosphorylation 
               
               
                   
                   
                   
                 (Kinases) Or 
               
               
                   
                   
                   
                 Dephosphorylation 
               
               
                   
                   
                   
                 (Phosphatases) 
               
               
                   
                   
                   
                 Synthesis Of New 
               
               
                   
                   
                   
                 Translation Factors 
               
               
                   
                   
                   
                 Abscisic Acid 
               
               
                   
                   
                   
                 Biosynthesis 
               
               
                 Up Regulated 
                 Sustained 
                 Osmolyte Adjustment 
                 Osmotic Stress 
               
               
                 Transcripts 
                 Osmotic Stress 
                 And Adaptation 
                 Metabolic 
               
               
                 (Level At 1 Hr &lt; 6 Hr) 
                 Responders 
                 Photosynthetic 
                 Pathways 
               
               
                   
                 Repressor Of 
                 Activity Modification 
                 Sugar Biosynthetic 
               
               
                   
                 Osmotic Stress 
                 Activation Of 
                 Pathways 
               
               
                   
                 Pathways 
                 “Normal State” 
                 Sugar Transporters 
               
               
                   
                 Abscisic Acid 
                 Biosynthesis Genes 
                 Transcription 
               
               
                   
                 Perception, 
                 Negative Regulation 
                 Factors 
               
               
                   
                 Biosynthesis And 
                 Of Osmotic Stress 
                 Transcription 
               
               
                   
                 Regulation 
                 Pathways 
                 Coactivators 
               
               
                   
                   
                 Negative Regulation 
                 Membrane 
               
               
                   
                   
                 Of Abscisic Acid 
                 Transporters 
               
               
                   
                   
                 Biosynthesis 
                 Abscisic Acid 
               
               
                   
                   
                 Acivation Of Abscisic 
                 Biosynthesis 
               
               
                   
                   
                 Acid Degradation 
               
               
                   
                   
                 Pathway 
               
               
                   
                   
                 Cell Wall 
               
               
                   
                   
                 Composition 
               
               
                   
                   
                 Modification 
               
               
                 Down-Regulated 
                 Early Responder 
                 Metabolic Repression 
                 Transcription 
               
               
                 Transcripts 
                 Repressors Of 
                 Specific Gene 
                 Factors 
               
               
                 (Level At 1 Hr ≈ 6 Hr) 
                 “Normal” State Of 
                 Transcription 
                 Transcription 
               
               
                 (Level At 6 Hr &gt; 1 Hr) 
                 Metabolism 
                 Initiation 
                 Coactivators 
               
               
                   
                 Negative Regulators 
                 Specific Gene 
                 Protein 
               
               
                   
                 Of Abscisic Acid 
                 Transcription 
                 Degradation 
               
               
                   
                 Biosynthesis And 
                 Repression 
                 Rna Binding 
               
               
                   
                 Perception. 
                 Translation Activation 
                 Proteins 
               
               
                   
                 Positive Regulators 
                 Translation 
                 Modification Of 
               
               
                   
                 Of “Normal State” 
                 Repression 
                 Protein Activity By 
               
               
                   
                 Metabolic Pathways. 
                 Abscisic Acid 
                 Phosphatases, 
               
               
                   
                   
                 Degradation 
                 Kinases 
               
               
                   
                   
                 Protein Degradation 
                 Activation Of 
               
               
                   
                   
                   
                 Signaling Pathway 
               
               
                   
                   
                   
                 By Calcium 
               
               
                   
                   
                   
                 Binding Proteins, 
               
               
                   
                   
                   
                 Modification Of 
               
               
                   
                   
                   
                 Protein Activity By 
               
               
                   
                   
                   
                 Protein-Protein 
               
               
                   
                   
                   
                 Interaction 
               
               
                   
                   
                   
                 Change In 
               
               
                   
                   
                   
                 Chromatin 
               
               
                   
                   
                   
                 Structure And/Or 
               
               
                   
                   
                   
                 Localized Dna 
               
               
                   
                   
                   
                 Topology 
               
               
                   
                   
                   
                 Modification Of 
               
               
                   
                   
                   
                 Pre-Existing 
               
               
                   
                   
                   
                 Translation Factors 
               
               
                   
                   
                   
                 By Phosphorylation 
               
               
                   
                   
                   
                 (Kinases) Or 
               
               
                   
                   
                   
                 Dephosphorylation 
               
               
                   
                   
                   
                 (Phosphatases) 
               
               
                   
                   
                   
                 Synthesis Of New 
               
               
                   
                   
                   
                 Translation Factors 
               
               
                 Down-Regulated 
                 Repressors Of 
                 Osmotic Stress 
                 Transcription 
               
               
                 Transcripts 
                 “Normal” State Of 
                 Adaptation 
                 Factors 
               
               
                 (Level At 1 Hr &gt; 6 Hr) 
                 Metabolism 
                 Negative Regulation 
                 Transcription 
               
               
                   
                 Genes With 
                 Of Abscisic Acid 
                 Coactivators 
               
               
                   
                 Discontinued 
                 Biosynthesis 
                 Protein 
               
               
                   
                 Expression Or 
                 Negative Regulation 
                 Degradation 
               
               
                   
                 UnsTable mRNA In 
                 Of Osmotic Stress 
                 Rna Binding 
               
               
                   
                 Presence Of Osmotic 
                 Response Pathways 
                 Proteins 
               
               
                   
                 Stress 
                 Genes 
                 Modification Of 
               
               
                   
                 Repressor Of 
                 Osmolyte Synthesis 
                 Protein Activity By 
               
               
                   
                 Osmotic Stress 
                 And Osmolyte 
                 Phosphatases, 
               
               
                   
                 Pathways 
                 Cellular Partitioning 
                 Kinases 
               
               
                   
                 Repressors Of 
                 Readjustment 
                 Activation Of 
               
               
                   
                 Abscisic Acid 
                 Activation Of 
                 Signaling Pathway 
               
               
                   
                 Biosynthesis, 
                 “Normal State” 
                 By Calcium 
               
               
                   
                 Perception And 
                 Metabolic Pathways 
                 Binding Proteins, 
               
               
                   
                 Regulation 
                   
                 Modification Of 
               
               
                   
                   
                   
                 Protein Activity By 
               
               
                   
                   
                   
                 Protein-Protein 
               
               
                   
                   
                   
                 Interaction 
               
               
                   
                   
                   
                 Change In 
               
               
                   
                   
                   
                 Chromatin 
               
               
                   
                   
                   
                 Structure And/Or 
               
               
                   
                   
                   
                 Localized Dna 
               
               
                   
                   
                   
                 Topology 
               
               
                   
                   
                   
                 Modification Of 
               
               
                   
                   
                   
                 Pre-Existing 
               
               
                   
                   
                   
                 Translation Factors 
               
               
                   
                   
                   
                 By Phosphorylation 
               
               
                   
                   
                   
                 (Kinases) Or 
               
               
                   
                   
                   
                 Dephosphorylation 
               
               
                   
                   
                   
                 (Phosphatases) 
               
               
                   
                   
                   
                 Synthesis Of New 
               
               
                   
                   
                   
                 Translation Factors 
               
               
                   
                   
                   
                 Sugar Biosynthetic 
               
               
                   
                   
                   
                 Pathways 
               
               
                   
                   
                   
                 Sugar Transporters 
               
               
                   
               
            
           
         
       
     
     Further, any desired sequence can be transcribed in similar temporal, tissue, or environmentally specific patterns as the osmotic stress responsive genes when the desired sequence is operably linked to a promoter of an osmotic stress responsive gene. 
     III.E.10. Aluminum Responsive Genes, Gene Components and Products 
     Aluminum is toxic to plants in soluble form (Al 3+ ). Plants grown under aluminum stress have inhibited root growth and function due to reduced cell elongation, inhibited cell division and metabolic interference. As an example, protein inactivation frequently results from displacement of the Mg2+ cofactor with aluminum. These types of consequences result in poor nutrient and water uptake. In addition, because stress perception and response occur in the root apex, aluminum exposure leads to the release of organic acids, such as citrate, from the root as the plant attempts to prevent aluminum uptake. 
     The ability to endure soluble aluminum is a major determinant of the geographical distribution and productivity of agricultural crops. Decreases in yield and crop failure frequently occur as a result of aberrant, hot conditions even in areas considered suiTable for the cultivation of a given species or cultivar. Only modest increases in the aluminum tolerance of crop species would have a dramatic impact on agricultural productivity. The development of genotypes with increased aluminum tolerance would provide a more reliable means to minimize crop losses and diminish the use of costly practices to modify the environment. 
     Microarray technology allows monitoring of gene expression levels for thousands of genes in a single experiment. This is achieved by simultaneously hybridizing two differentially labeled fluorescent cDNA pools to glass slides that contain spots of DNA (Schena et al. (1995) Science 270: 467-70). The  Arabidopsis  Functional Genomics Consortium (AFGC) has recently made public the results from such microarray experiments conducted with AFGC chips containing 10,000 non-redundant ESTs, selected from 37,000 randomly sequenced ESTs generated from mRNA of different tissues and developmental stages. 
     The sequences of the ESTs showing at least two-fold increases or decreases over the controls were identified, compared to the Ceres full-length cDNA and genomic sequence databanks, and identical Ceres clones identified. MA_diff table reports the results of this analysis, indicating those Ceres clones which are up or down regulated over controls, thereby indicating the Ceres clones which are aluminum response responsive genes. 
     The MA_diff Table(s) reports the transcript levels of the experiment (see EXPT ID: Aluminum (relating to SMD 7304, SMD 7305)). For transcripts that had higher levels in the samples than the control, a “+” is shown. A “−” is shown for when transcript levels were reduced in root tips as compared to the control. For more experimental detail see the Example section below. 
     Aluminum genes are those sequences that showed differential expression as compared to controls, namely those sequences identified in the MA_diff tables with a “+” or “−” indication. 
     Aluminum Genes Identified by Cluster Analyses of Differential Expression 
     Aluminum Genes Identified by Correlation to Genes that are Differentially Expressed 
     As described above, the transcription profiles of genes that act together are well correlated. Applicants not only have identified the genes that are differentially expressed in the microarray experiments, but also have identified the genes that act in concert with them. The MA_clust table indicates groups of genes that have well correlated transcription profiles and therefore participate in the same pathway or network. 
     A pathway or network of Aluminum genes is any group in the MA_clust that comprises a cDNA ID that also appears in Expt ID Aluminum (relating to SMD 7304, SMD 7305) of the MA_diff table(s). 
     Aluminum Genes Identified by Correlation to Genes that Cause Physiological Consequences 
     Additionally, the differential expression data and the phenotypic observations can be merged to identify pathways or networks of Aluminum genes. A group in the MA_clust is considered a Aluminum pathway or network if the group comprises a cDNA ID that also appears in Knock-in or Knock-out tables that causes one or more of the phenotypes described in section above. 
     Aluminum Genes Identified by Amino Acid Sequence Similarity 
     Aluminum genes from other plant species typically encode polypeptides that share amino acid similarity to the sequences encoded by corn and  Arabidopsis  Aluminum genes. Groups of Aluminum genes are identified in the Protein Group table. In this table, any protein group that comprises a peptide ID that corresponds to a cDNA ID member of a Aluminum pathway or network is a group of proteins that also exhibits Aluminum functions/utilities. 
     III.E.10.a. Use of Aluminum Response Genes to Modulate Phenotypes 
     Changes in aluminum concentrations in a plant&#39;s surrounding environment results in modulation of many genes and gene products. Examples of such aluminum response genes and gene products are shown in the Reference and Sequence Tables. These genes and/or products are responsible for effects on traits such as plant vigor and seed yield. 
     While aluminum responsive polynucleotides and gene products can act alone, combinations of these polynucleotides also affect growth and development. Useful combinations include different aluminum responsive polynucleotides and/or gene products that have similar transcription profiles or similar biological activities, and members of the same or similar biochemical pathways. In addition, the combination of a aluminum responsive polynucleotide and/or gene product with another environmentally responsive polynucleotide is also useful because of the interactions that exist between hormone-regulated pathways, stress pathways, nutritional pathways and development. Here, in addition to polynucleotides having similar transcription profiles and/or biological activities, useful combinations include polynucleotides that may have different transcription profiles but which participate in a common pathway. 
     Such aluminum responsive genes and gene products can function to either increase or dampen the above phenotypes or activities either
         in response to changes in aluminum concentration or   in the absence of aluminum fluctuations.       

     More specifically, aluminum responsive genes and gene products are useful to or modulate one or more phenotypes including growth; roots (such as inhibition of root elongation); stems; leaves; whole plant; development (such as cell growth, elongation, and division) and mediates response to oxidative stress, calcium-mediated defense, antioxidant defense and pathogenesis. 
     To produce the desired phenotype(s) above, one or more of the aluminum response genes or gene products can be tested by screening for the desired trait. Specifically, the gene, mRNA levels, or protein levels can be altered in a plant utilizing the procedures described herein and the phenotypes can be assayed. As an example, a plant can be transformed according to Bechtold and Pelletier (1998, Methods. Mol. Biol. 82:259-266) and visually inspected for the desired phenotype or metabolically and/or functionally assayed according to Li and Fleming (1999, FEBS Lett 461: 1-5), Delhaize et al. (1999, J Biol Chem 274: 7082-8), Sigimoto and Sakamoto (1997, Genes Genet Syst 72: 311-6), Esaki et al. (2000, Plant Physiol 122: 657-65), Leonard and Gerber (1988, Mutat Res 196: 247-57), Baisakhi et al. (2000, Mutat Res 465: 1-9), Ma (2000, Plant Cell Physiol 41: 383-90) and Koyama et al. (1999, Plant Cell 40: 482-8) 
     Alternatively, the activities of one or more of the aluminum responsive genes can be modulated to change biochemical or metabolic activities and/or pathways such as those noted below. Such biological activities can be measured according to the citations included in the Table below: 
     
       
         
           
               
               
               
             
               
                   
               
               
                   
                 BIOCHEMICAL OR 
                   
               
               
                   
                 METABOLIC 
               
               
                 GENERAL 
                 ACTIVITIES 
               
               
                 CATEGORY 
                 AND/OR PATHWAYS 
                 ASSAY 
               
               
                   
               
             
            
               
                 Cell Growth and 
                 Phospholipase D (PLD) 
                 Toda et al. (1999) 
               
               
                 Development 
                 activity 
                 Biosci Biotechnol 
               
               
                   
                   
                 Biochem 63: 210-212 
               
               
                   
                 Regulation of 
               
               
                   
                 Phosphtidylserine 
               
               
                   
                 Synthase (PSS) 
               
               
                   
                 Cell wall strengthening 
                 Hamel et al. (1998) 
               
               
                   
                   
                 Planta 205: 531-38 
               
               
                 Stress Response 
                 Regulation of oxidative 
                 Esaki et al. (2000) 
               
               
                   
                 stress 
                 Plant Physiol 122: 
               
               
                   
                   
                 657-655 
               
               
                   
                 Regulation of 
                 Baisakhi et al. 
               
               
                   
                 antioxidant defense and 
                 (2000) Mutat Res 
               
               
                   
                 DNA repair 
                 465: 1-9 
               
               
                   
                 Secretion of Organic 
                 Koyama et al. 
               
               
                   
                 Acids (e.g. maleate, 
                 (1999) Plant Cell 
               
               
                   
                 citrate) from root apex 
                 40: 482-8 
               
               
                   
                 Ca2+ mediated 
                 Plieth et al. (1999) 
               
               
                   
                 Defense Responses 
                 Plant J 18: 634-50 
               
               
                   
                 Against Low pH 
               
               
                 Signaling 
                 H+ transport 
                 Degenhardt et al. 
               
               
                   
                   
                 (1988) Plant Physil 
               
               
                   
                   
                 117: 19-27 
               
               
                   
                 Auxin transport 
                 Rashotte et al. 
               
               
                   
                   
                 (2000) Plant 
               
               
                   
                   
                 Physiol 122: 481-90 
               
               
                   
               
            
           
         
       
     
     Other biological activities that can be modulated by aluminum response genes and their products are listed in the REFERENCE Table. Assays for detecting such biological activities are described in the Protein Domain table. 
                                                     EXAMPLES OF       TRANSCRIPT       PHYSIOLOGICAL   BIOCHEMICAL       LEVELS   TYPE OF GENES   CONSEQUENCES   ACTIVITY                  Up regulated   responders to   Aluminum   Transporters       transcripts   aluminum   perception   Metabolic enzymes           application   Aluminum uptake   Change in cell               and transport   membrane structure               Aluminum   and potential               metabolism   Kinases and               Synthesis of   phosphatases               secondary   Transcription               metabolites and/or   activators               proteins   Change in chromatin               Modulation of   structure and/or               aluminum   localized DNA               response   topology               transduction               pathways               Specific gene               transcription               initiation       Down-regulated   responder to   Negative   Transcription factors       transcripts   aluminum   regulation of   Change in protein           repressors of   aluminum   structure by           aluminum state of   pathways   phosphorylation           metabolism   Changes in   (kinases) or           Genes with   pathways and   dephosphorylation           discontinued   processes   (phosphatases)           expression or   operating in cells   Change in chromatin           unsTable mRNA in   Changes in other   structure and/or DNA           presence of aluminum   metabolisms than   topology               aluminum   Stability of factors for                   protein synthesis and                   degradation                   Metabolic enzymes                    
Use of Promoters of Aluminum Responsive Genes
 
     Promoters of Aluminum responsive genes are useful for transcription of any desired polynucleotide or plant or non-plant origin. Further, any desired sequence can be transcribed in a similar temporal, tissue, or environmentally specific patterns as the Aluminum responsive genes where the desired sequence is operably linked to a promoter of a Aluminum responsive gene. The protein product of such a polynucleotide is usually synthesized in the same cells, in response to the same stimuli as the protein product of the gene from which the promoter was derived. Such promoter are also useful to produce antisense mRNAs to down-regulate the product of proteins, or to produce sense mRNAs to down-regulate mRNAs via sense suppression. 
     III.E.11. Cadmium Responsive Genes, Gene Components and Products 
     Cadmium (Cd) has both toxic and non-toxic effects on plants. Plants exposed to non-toxic concentrations of cadmium are blocked for viral disease due to the inhibition of systemic movement of the virus. Surprisingly, higher, toxic levels of Cd do not inhibit viral systemic movement, suggesting that cellular factors that interfere with the viral movement are triggered by non-toxic Cd concentrations but repressed in high Cd concentrations. Furthermore, exposure to non-toxic Cd levels appears to reverse posttranslational gene silencing, an inherent plant defense mechanism. Consequently, exploring the effects of Cd exposure has potential for advances in plant disease control in addition to soil bio-remediation and the improvement of plant performance in agriculture. 
     Changes in cadmium concentrations in a plant&#39;s surrounding environment results in modulation of many genes and gene products. Microarray technology allows monitoring of gene expression levels for thousands of genes in a single experiment. This is achieved by simultaneously hybridizing two differentially labeled fluorescent cDNA pools to glass slides that contain spots of DNA (Schena et al. (1995) Science 270: 467-70). The US  Arabidopsis  Functional Genomics Consortium (AFGC) has recently made public the results from such microarray experiments conducted with AFGC chips containing some 10,000 non-redundant ESTs, selected from about 37,000 randomly sequenced ESTs generated from mRNA of different tissues and developmental stages. 
     The sequences of the ESTs showing at least two-fold increases or decreases in plants treated with 10 μM cadmium compared with untreated plants were identified, compared to the Ceres full length cDNA and genomic sequence databanks, and the equivalent Ceres clones identified. The MA_diff table(s) report(s) the results of this analysis, indicating those Ceres clones which are up or down regulated over controls, thereby indicating the Ceres clones which represent cadmium responsive genes. 
     Examples of such cadmium responsive genes and gene products are shown in the Reference and Sequence Tables. These genes and/or products are responsible for effects on traits such as plant vigor and seed yield. 
     While cadmium responsive polynucleotides and gene products can act alone, combinations of these polynucleotides also affect growth and development. Useful combinations include different cadmium responsive polynucleotides and/or gene products that have similar transcription profiles or similar biological activities, and members of the same or similar biochemical pathways. Whole pathways or segments of pathways are controlled by transcription factor proteins and proteins controlling the activity of signal transduction pathways. Therefore, manipulation of such protein levels is especially useful for altering phenotypes and biochemical activities of plants. In addition, the combination of a cadmium responsive polynucleotide and/or gene product with other environmentally responsive polynucleotides is also useful because of the interactions that exist between, for example, stress and pathogen induced pathways, nutritional pathways and development. Here, in addition to polynucleotides having similar transcription profiles and/or biological activities, useful combinations include polynucleotides that may have different transcription profiles but which participate in common or overlapping pathways. 
     The MA_diff Table(s) reports the transcript levels of the experiment (see EXPT ID: Cadium (relating to SMD 7427, SMD 7428)). For transcripts that had higher levels in the samples than the control, a “+” is shown. A “−” is shown for when transcript levels were reduced in root tips as compared to the control. For more experimental detail see the Example section below. 
     Cadium genes are those sequences that showed differential expression as compared to controls, namely those sequences identified in the MA_diff tables with a “+” or “−” indication. 
     Cadium Genes Identified by Cluster Analyses of Differential Expression 
     Cadium Genes Identified by Correlation to Genes that are Differentially Expressed 
     As described above, the transcription profiles of genes that act together are well correlated. Applicants not only have identified the genes that are differentially expressed in the microarray experiments, but also have identified the genes that act in concert with them. The MA_clust table indicates groups of genes that have well correlated transcription profiles and therefore participate in the same pathway or network. 
     A pathway or network of Cadium genes is any group in the MA_clust that comprises a cDNA ID that also appears in Expt ID Cadium (relating to SMD 7427, SMD 7428) of the MA_diff table(s). 
     Cadium Genes Identified by Correlation to Genes that Cause Physiological Consequences 
     Additionally, the differential expression data and the phenotypic observations can be merged to identify pathways or networks of Cadium genes. A group in the MA_clust is considered a Cadium pathway or network if the group comprises a cDNA ID that also appears in Knock-in or Knock-out tables that causes one or more of the phenotypes described in section above. 
     Cadium Genes Identified by Amino Acid Sequence Similarity 
     Cadium genes from other plant species typically encode polypeptides that share amino acid similarity to the sequences encoded by corn and  Arabidopsis  Cadium genes. Groups of Cadium genes are identified in the Protein Group table. In this table, any protein group that comprises a peptide ID that corresponds to a cDNA ID member of a Cadium pathway or network is a group of proteins that also exhibits Cadium functions/utilities. 
     Such cadmium responsive genes and gene products can function to either increase or dampen phenotypes or activities either in response to changes in cadmium concentration or in the absence of cadmium fluctuations. Further, promoters of cadmium responsive genes, as described in the Reference tables, for example, are useful to modulate transcription that is induced by cadmium or any of the following phenotypes or biological activities below. 
     III.E.11.a. Use of Cadmium Responsive Genes, Gene Components and Products to Modulate Phenotypes 
     Cadmium responsive genes and gene products are useful to or modulate one or more phenotypes including growth, roots, initiation and maintenance of cell division, stems, leaves, development, mitochondria, post-embryonic root meristem development, senescence, stress response, modulation of jasmonic acid and other stress control pathways, metabolic detoxification, heavy metals, plant and seed yield; and fruit yield. 
     Further, any desired sequence can be transcribed in similar temporal, tissue, or environmentally specific patterns as the cadmium responsive genes when the desired sequence is operably linked to a promoter of a cadmium responsive gene. 
     To regulate any of the phenotype(s) above, activities of one or more of the cadmium responsive genes or gene products can be modulated and tested by screening for the desired trait. Specifically, the gene, mRNA levels, or protein levels can be altered in a plant utilizing the procedures described herein and the phenotypes can be assayed. As an example, a plant can be transformed according to Bechtold and Pelletier (1998) Methods. Mol. Biol. 82:259-266) and/or screened for variants as in Winkler et al. (1998) Plant Physiol 118: 743-50 and visually inspected for the desired phenotype or metabolically and/or functionally assayed according to Ghoshroy et al. (1998, Plant J 13: 591-602), Citovsky et al. (1998, Plant J 16: 13-20), Clemens et al. (1999, EMBO J 18: 3325-33), Chen et al. (2000, Chemosphere 41: 229-34), Xian and Oliver (1998, Plant Cell 10: 1539-90), Romero-Peurtas et al. (1999, Free Rad Res 31: S25-31), Gaur and Noraho (1995, Biomed Environ Sci 8: 202-10), Thomine et al. (2000, PNAS USA 97: 4991-6), Howden et al. (1995, Plant Physiol 107: 1067-73), Kesseler and Brand (1994, Eur J Biochem 225: 907-22) and Vernoux et al. (2000, Plant Cell 12: 97-110). 
     III.E.10.b. Use of Cadmium-Responsive Genes, Gene Components and Products to Modulate Biochemical Activities 
     The activities of one or more of the cadmium responsive genes can be modulated to change biochemical or metabolic activities and/or pathways such as those noted below. Such biological activities can be measured according to the citations included in the Table below: 
     
       
         
           
               
               
               
             
               
                   
               
               
                   
                 BIOCHEMICAL OR 
                   
               
               
                   
                 METABOLIC 
                   
               
               
                   
                 ACTIVITIES AND/OR 
                 CITATIONS INCLUDING 
               
               
                 PROCESS 
                 PATHWAYS 
                 ASSAYS 
               
               
                   
               
             
            
               
                 Growth,  
                 Root Growth 
                 Thomine et al. (2000) PNAS 
               
               
                 Differentiation 
                 Initiation and maintenance  
                 USA 97: 4991-6 
               
               
                 and  
                 of cell division 
                 Vernoux et al. (2000) Plant  
               
               
                 Development 
                 Resistance to Cadmium- 
                 Cell 12: 97-110 
               
               
                   
                 inhibition of root growth 
                   
               
               
                 Metabolism 
                 Cadmium sensing 
                 Howden et al. (1995) Plant 
               
               
                   
                   
                 Physiol 107: 1067-73 
               
               
                   
                 Cadmium uptake and 
                 Gaur and Noraho (1995)  
               
               
                   
                 transport 
                 Biomed Environ Sci 8: 202- 
               
               
                   
                   
                 10 
               
               
                   
                 Decreased cadmium 
                 Thomine et al. (2000) PNAS 
               
               
                   
                 transport 
                 USA 97: 4991-6 
               
               
                   
                 Phytoremediation 
                   
               
               
                   
                 Inhibition of oxidative 
                 Kesseler and Brand (1994)  
               
               
                   
                 phophorylation 
                 Eur. Biochem 225: 907-22 
               
               
                 Plant Defenses 
                 Viral resistance 
                 Ghoshroy et al. (1998) Plant  
               
               
                   
                 Inhibition of systemic 
                 J 13: 591-602 
               
               
                   
                 movement of virus 
                   
               
               
                   
                 Block of viral disease 
                   
               
               
                   
                 Detoxification of heavy 
                 Clemens et al. (1999) EMBO  
               
               
                   
                 metals 
                 J 18: 3325-33 
               
               
                   
                 Enhanced stress resistance 
                 Romero-Peurtas et al. (1999) 
               
               
                   
                   
                 Free Rad Res 31: S25-31 
               
               
                   
                 Cadmium resistance 
                 Xiang and Oliver (1998)  
               
               
                   
                 via modulation of jasmonic 
                 Plant Cell 10: 1539-90 
               
               
                   
                 acid signaling pathway 
                   
               
               
                 Signaling 
                 Relief of post-translational 
                 Citovsky et al. (1998) Plant J  
               
               
                   
                 gene silencing 
                 16: 13-20 
               
               
                   
               
            
           
         
       
     
     Other biological activities that can be modulated by the cadmium responsive genes and gene products are listed in the Reference tables. Assays for detecting such biological activities are described in the Protein Domain table. 
     Cadmium responsive genes are characteristically differentially transcribed in response to fluctuating cadmium levels or concentrations, whether internal or external to an organism or cell. The MA_diff table(s) report(s) the changes in transcript levels of various cadmium responsive genes following treatment with 10 μM cadmium, relative to untreated plants. Profiles of some cadmium responsive genes are shown in the Table below together with examples of the kinds of associated biological activities. 
                                                     EXAMPLES OF       TRANSCRIPT   TYPE OF   PHYSIOLOGICAL   BIOCHEMICAL       LEVELS   GENES   CONSEQUENCES   ACTIVITY                  Up regulated   Responders    Cadmium perception   Transporters       transcripts   to cadmium   Cadmium uptake and   Metabolic enzymes           Application   transport   Change in cell            Genes    Cadmium metabolism   membrane structure            induced   Synthesis of    and potential            by cadmium   secondary metabolites    Kinases and                and/or proteins   Phosphatases                Modulation of   Transcription                cadmium response   activators                transduction pathways   Change in                Specific gene   chromatin structure                transcription initiation   and/or localized               Genes involved in   DNA topology               inhibiting systemic   RNA binding                movement of plant   proteins               viral RNA                   Genes involved in                    post translational                    gene silencing           Down-   Responders    Negative regulation of   Transcription        regulated   to cadmium   cadmium pathways   factors       transcripts   Genes    released   Change in            repressed   Changes in pathways   protein structure           by cadmium   and processes    by phosphorylation           Genes with   operating in cells   (kinases) or           discontinued   Changes in    Dephosphoryaltion           expression    metabolism other than    (phosphatases)           or unsTable    cadmium pathways   Change in            mRNA in    Genes involved in   chromatin structure           presence of   facilitating systemic   and/or DNA           cadmium   movement of plant   topology               viral RNA   Factors for protein               Genes involved in   synthesis and               promoting post   degradation               translational gene   Metabolic enzymes               silencing   RNA binding                   proteins                    
Use of Promoters of Cadmium Responsive Genes
 
     Promoters of Cadmium responsive genes are useful for transcription of any desired polynucleotide or plant or non-plant origin. Further, any desired sequence can be transcribed in a similar temporal, tissue, or environmentally specific patterns as the Cadmium responsive genes where the desired sequence is operably linked to a promoter of a Cadmium responsive gene. The protein product of such a polynucleotide is usually synthesized in the same cells, in response to the same stimuli as the protein product of the gene from which the promoter was derived. Such promoter are also useful to produce antisense mRNAs to down-regulate the product of proteins, or to produce sense mRNAs to down-regulate mRNAs via sense suppression. 
     111.12. Disease Responsive Genes, Gene Components and Products 
     Often growth and yield are limited by the ability of a plant to tolerate stress conditions, including pathogen attack. To combat such conditions, plant cells deploy a battery of inducible defense responses, including the triggering of an oxidative burst and the transcription of pathogenesis-related protein (PR protein) genes. These responses depend on the recognition of a microbial avirulence gene product (avr) by a plant resistance gene product (R), and a series of downstream signaling events leading to transcription-independent and transcription-dependent disease resistance responses. Reactive oxygen species (ROS) such as H 2 O 2  and NO from the oxidative burst plays a signaling role, including initiation of the hypersensitive response (HR) and induction of systemic acquired resistance (SAR) to secondary infection by unrelated pathogens. PR proteins are able to degrade the cell walls of invading microorganisms, and phytoalexins are directly microbicidal. 
     The presence of an avirulent pathogen and/or changes in the concentrations of O 2   − , H 2 O 2  and NO in the environment surrounding a plant cell modulate the activities of many genes and, therefore, the levels of many gene products. Examples of tobacco mosaic virus (TMV) responsive genes and gene products, many of them operating through an ROS signaling system, are shown in The Reference and Sequence Tables. These genes and/or products are responsible for effects on traits such as plant vigor and seed yield. The genes were discovered and characterized from a much larger set by experiments designed to find genes whose mRNA products changed in response to application of TMV to plants. 
     Microarray technology allows monitoring of gene expression levels for thousands of genes in a single experiment. This is achieved by hybridizing labeled fluorescent cDNA pools to glass slides that contain spots of DNA (Schena et al. (1995) Science 270: 467-70). The US  Arabidopsis  Functional Genomics Consortium (AFGC) has recently made public the results from such microarray experiments conducted with AFGC chips containing some 10,000 non-redundant ESTs, selected from about 37,000 randomly sequenced ESTs generated from mRNA of different tissues and developmental stages. 
     The sequences of the ESTs showing at least two-fold increases or decreases in response to TMV infection over the non infected controls were identified, compared to the Ceres full length cDNA and genomic sequence databanks, and equivalent Ceres clones identified. The MA_diff table(s) report(s) the results of this analysis, indicating those Ceres clones which are up or down regulated over controls, thereby indicating the Ceres clones which represent disease responsive genes. 
     Manipulation of one or more disease responsive gene activities is useful to modulate the biological processes and/or phenotypes listed below. Disease responsive genes and gene products can act alone or in combination. Useful combinations include disease responsive genes and/or gene products with similar transcription profiles, similar biological activities, or members of the same or functionally related biochemical pathways. Whole pathways or segments of pathways are controlled by transcription factor proteins and proteins controlling the activity of signal transduction pathways. Therefore, manipulation of such protein levels is especially useful for altering phenotypes and biochemical activities of plants. 
     Such disease responsive genes and gene products can function to either increase or dampen the above phenotypes or activities either in response to changes in active oxygen concentration or in the absence of active oxygen fluctuations. The MA_diff Table(s) reports the transcript levels of the experiment (see EXPT ID: Disease (relating to SMD 7342, SMD 7343)). For transcripts that had higher levels in the samples than the control, a “+” is shown. A “−” is shown for when transcript levels were reduced in root tips as compared to the control. For more experimental detail see the Example section below. 
     Disease genes are those sequences that showed differential expression as compared to controls, namely those sequences identified in the MA_diff tables with a “+” or “−” indication. 
     Disease Genes Identified by Cluster Analyses of Differential Expression 
     Disease Genes Identified by Correlation to Genes that are Differentially Expressed 
     As described above, the transcription profiles of genes that act together are well correlated. Applicants not only have identified the genes that are differentially expressed in the microarray experiments, but also have identified the genes that act in concert with them. The MA_clust table indicates groups of genes that have well correlated transcription profiles and therefore participate in the same pathway or network. 
     A pathway or network of Disease genes is any group in the MA_clust that comprises a cDNA ID that also appears in Expt ID Disease (relating to SMD 7342, SMD 7343) of the MA_diff table(s). 
     Disease Genes Identified by Correlation to Genes that Cause Physiological Consequences 
     Additionally, the differential expression data and the phenotypic observations can be merged to identify pathways or networks of Disease genes. A group in the MA_clust is considered a Disease pathway or network if the group comprises a cDNA ID that also appears in Knock-in or Knock-out tables that causes one or more of the phenotypes described in section above. 
     Disease Genes Identified by Amino Acid Sequence Similarity 
     Disease genes from other plant species typically encode polypeptides that share amino acid similarity to the sequences encoded by corn and  Arabidopsis  Disease genes. Groups of Disease genes are identified in the Protein Group table. In this table, any protein group that comprises a peptide ID that corresponds to a cDNA ID member of a Disease pathway or network is a group of proteins that also exhibits Disease functions/utilities. 
     Further, promoters of disease responsive genes, as described in the Reference tables, for example, are useful to modulate transcription that is induced by disease or any of the following phenotypes or biological activities below. Further, any desired sequence can be transcribed in similar temporal, tissue, or environmentally specific patterns as the disease responsive genes when the desired sequence is operably linked to a promoter of a disease responsive gene. 
     III.E.12.a. Use of Disease Responsive Genes, Gene Components and Products to Modulate Phenotypes 
     Disease responsive genes and gene products are useful to or modulate one or more phenotypes including pathogen tolerance and/or resistance; Avr/R locus interactions; non-host interactions; HR; SAR; resistance to bacteria e.g. to  Erwinia stewartii, Pseudomonas syringae, Pseudomonas tabaci , Stuart&#39;s wilt, etc.; resistance to fungi, e.g. to downy mildews such as  Scleropthora macrospora, Sclerophthora rayissiae, Sclerospora graminicola, Peronosclerospora sorghi, Peronosclerospora philippinensis, Peronosclerospora sacchari, Peronosclerospora maydis ; rusts such as  Puccinia sorphi, Puccinia polysora, Physopella zeae , etc.; and to other fungal diseases e.g.  Cercospora zeae - maydis, Colletotrichum graminicola, Fusarium monoliforme, Exserohilum turcicum, Bipolaris maydis, Phytophthora parasitica, Peronospora tabacina, Septoria , etc.; resistance to viruses or viroids e.g. to tobacco or cucumber mosaic virus, ringspot virus, necrosis virus,  pelargonium  leaf curl virus, red clover mottle virus, tomato bushy stunt virus, and like viruses; rrResistance to insects, such as to aphids e.g.  Myzus persicae ; to beetles and beetle larvae; to lepidoptera larvae, e.g.  Heliothus  etc.; resistance to Nematodes, e.g.  Meloidogyne incognita  etc.; local resistance in primary (infected) or secondary (uninfected) leaves; stress tolerance; winter survival; cold tolerance; salt tolerance; heavy metal tolerance, such as cadmium; tolerance to physical wounding; increased organelle tolerance to redox stress, such as in mitochondria, and chloroplasts; cell death; programmed cell death, including death of diseased tissue and during senescence; fruit drop; biomass; fresh and dry weight during any time in plant life, such as maturation; number of flowers, seeds, branches, and/or leaves; seed yield, including number, size, weight, and/or harvest index; fruit yield, including number, size, weight, and/or harvest index; plant development; time to fruit maturity; cell wall strengthening and reinforcement; plant product quality; paper making quality; food additives; treatment of indications modulated by free radicals; cancer; kinds of low molecular weight compounds such as phytoalexins; abundance of low molecular weight compounds such as phytoalexins; other phenotypes based on gene silencing. 
     To regulate any of the phenotype(s) above, activities of one or more of the disease responsive genes or gene products can be modulated and the plants can be tested by screening for the desired trait. Specifically, the gene, mRNA levels, or protein levels can be altered in a plant utilizing the procedures described herein and the phenotypes can be screened for variants as in Winkler et al. (1998) Plant Physiol 118: 743-50 and assayed, for example, in accordance to Alvarez et al., (1998) Cell 92: 773-784; Halhbrock and Scheel, (1989) Ann. Rev. Plant Physiol. Plant Mol. Biol. 40: 347-369; Lamb et al., (1997) Ann. Rev. Plant Mol. Biol. Plant Physiol. 48: 251-275; Lapwood et al. (1984) Plant Pathol. 33: 13-20; Levine et al. (1996) Curr. Biol. 6: 427-437; McKersie et al., (2000) Plant Physiol. 122: 1427-1437; Olson and Varner (1993) Plant J. 4: 887-892; Pastore et al., (2000), FEBS Lett 470: 88-92; Pastori et al., (1997) Plant Physiol. 113: 411-418; Romero-Puertas et al., (1999) Free Radic. Res. 1999 31 Suppl: S25-31; Shirataki et al., Anticancer Res 20: 423-426 (2000); Wu et al., (1995) Plant Cell 7: 1357-1368. 
     III.E.12.b. Use of Disease Responsive Genes, Gene Components and Products to Modulate Biochemical Activities 
     The activities of one or more of the disease responsive genes can be modulated to change biochemical or metabolic activities and/or pathways such as those noted below. Such biological activities are documented and can be measured according to the citations above and included in the Table below: 
     
       
         
           
               
               
               
             
               
                   
               
               
                   
                 BIOCHEMICAL OR 
                   
               
               
                   
                 METABOLIC 
                   
               
               
                   
                 ACTIVITIES AND/OR 
                 CITATIONS INCLUDING 
               
               
                 PROCESS 
                 PATHWAYS 
                 ASSAYS 
               
               
                   
               
             
            
               
                 Resistance to Pathogens 
                 Induction of ROS signaling 
                 Wu et.al.(1995) Plant Cell 7: 
               
               
                   
                 pathways 
                 1357-68 
               
               
                   
                 Modulation of nitric oxide 
                 Delledonne et al. (1998) Nature 
               
               
                   
                 signaling 
                 394: 585-588 
               
               
                   
                 Induction of PR proteins, 
                 Chamnongpol et.al.(1998) Proc. 
               
               
                   
                 phytoalexins, and defense 
                 Nat.Acad Sci USA 12; 95: 5818- 
               
               
                   
                 pathways 
                 23. 
               
               
                   
                   
                 Davis et al. (1993) 
               
               
                   
                   
                 Phytochemistry 32: 607-611 
               
               
                   
                 Induction of cellular 
                 Chen et.al. Plant J. (1996) 
               
               
                   
                 protectant genes such as 
                 10: 955-966 
               
               
                   
                 glutathione S-transferase 
                 Gadea et.al.(1999) Mol Gen 
               
               
                   
                 (GST) and ascorbate 
                 Genet 262:212-219 
               
               
                   
                 peroxidase 
                 Wu et.al.(1995) Plant Cell 7: 
               
               
                   
                   
                 1357-68 
               
               
                   
                 ROS levels following 
                 Orozco-Cardenas and Ryan 
               
               
                   
                 wounding and changes in 
                 (1999) Proc.Nat. Acad. Sci. USA 
               
               
                   
                 physical pressure 
                 25; 96: 6553-7. 
               
               
                   
                   
                 Yahraus et al. (1995) Plant 
               
               
                   
                   
                 Physiol. 109: 1259-1266 
               
               
                   
                 Salicyclic acid levels and 
                 Durner and Klessig (1996) 
               
               
                   
                 signaling 
                 J. Biol. Chem. 271: 28492-501 
               
               
                 Responses to Wounding 
                 Expression of genes Involved 
                 Legendre et al. (1993) Plant 
               
               
                   
                 in wound repair and cell 
                 Physiol. 102: 233-240 
               
               
                   
                 division 
                   
               
               
                 Responses to Environmental 
                 Expression of genes involved 
                 Shi et al. (2000) Proc. Natl. Acad. 
               
               
                 Stress 
                 in responses to drought, cold,  
                 Sci. USA 97: 6896-6901 
               
               
                   
                 salt, heavy metals 
                   
               
               
                 Reinforcement of Cell Walls 
                 Modulation of the Production 
                 Bradley et al. (1992) Cell 70, 21- 
               
               
                   
                 of ExtracTable Proline-Rich 
                 30 
               
               
                   
                 Protein 
                   
               
               
                   
                 Modulation of Lignification 
                 Mansouri et al. (1999) Physiol. 
               
               
                   
                   
                 Plant 106: 355-362 
               
               
                 Programmed Cell Death 
                 Induction of PCD activating 
                 Levine et al. (1996) Curr. Biol. 6: 
               
               
                   
                 genes 
                 427-437. Reynolds et.al. (1998) 
               
               
                   
                   
                 Biochem. J. 330: 115-20 
               
               
                   
                 Suppression of PCD 
                 Pennell and Lamb (1997) Plant 
               
               
                   
                 suppressing genes 
                 Cell 9, 1157-1168 
               
               
                   
               
            
           
         
       
     
     Other biological activities that can be modulated by the disease responsive genes and their products are listed in the Reference Table. Assays for detecting such biological activities are described in the Protein Domain table. 
     Disease responsive genes are characteristically differentially transcribed in response to fluctuating levels of disease. The MA_diff table(s)report(s) the changes in transcript levels of various disease responsive genes in the aerial parts of a plant 3 days after the plant was sprayed with a suspension of TMV relative to control plants sprayed with water. 
     The data from this experiment reveal a number of types of disease responsive genes and gene products, including “early responders,” and “delayed responders”. Profiles of individual disease responsive genes are shown in the Table below with examples of which associated biological activities are modulated when the activities of one or more such genes vary in plants. 
     
       
         
           
               
               
               
               
             
               
                   
               
               
                   
                   
                   
                 EXAMPLES OF 
               
               
                 GENE 
                 FUNCTIONAL 
                   
                 BIOCHEMICAL 
               
               
                 EXPRESSION 
                 CATEGORY 
                 PHYSIOLOGICAL 
                 ACTIVITY 
               
               
                 LEVELS 
                 OF GENE 
                 CONSequence 
                 OF GENE PRODUCTS 
               
               
                   
               
             
            
               
                 Upregulated 
                 Early Responders 
                 ROS Perception and 
                 Transcription factors, 
               
               
                 transcripts 
                 to Pathogens 
                 Response 
                 kinases, phosphatases, GTP- 
               
               
                   
                   
                   
                 binding proteins (G- 
               
               
                   
                   
                   
                 proteins), leucine rich repeat 
               
               
                   
                   
                   
                 proteins (LRRs), 
               
               
                   
                   
                   
                 transporters, calcium 
               
               
                   
                   
                   
                 binding proteins, chromatin 
               
               
                   
                   
                   
                 remodeling proteins 
               
               
                   
                   
                 Initiation of Gene 
                 Glutathione S-transferase 
               
               
                   
                   
                 Transcription 
                 (GST), 
               
               
                   
                   
                   
                 heat shock proteins, 
               
               
                   
                   
                   
                 salicylic acid (SA) response 
               
               
                   
                   
                   
                 pathway proteins, jasmonate 
               
               
                   
                   
                   
                 response pathway proteins, 
               
               
                   
                   
                   
                 dehydrins, peroxidases, 
               
               
                   
                   
                   
                 catalases 
               
               
                   
                 Delayed 
                 Initiation of Defence 
                 Proteases, pathogen 
               
               
                   
                 Responders to 
                 Gene Transcription 
                 response (PR) proteins, 
               
               
                   
                 Pathogens 
                   
                 cellulases, chitinases, 
               
               
                   
                   
                   
                 cutinases, glucanases, other 
               
               
                   
                   
                   
                 degrading enzymes, calcium 
               
               
                   
                   
                   
                 channel blockers, 
               
               
                   
                   
                   
                 phenylalanine ammonia 
               
               
                   
                   
                   
                 lyase, proteins of defense 
               
               
                   
                   
                   
                 pathways, cell wall proteins 
               
               
                   
                   
                   
                 incuding proline rich 
               
               
                   
                   
                   
                 proteins and glycine rich 
               
               
                   
                   
                   
                 proteins, epoxide hydrolase, 
               
               
                   
                   
                   
                 methyl transferases 
               
               
                   
                   
                 Activation of cell death 
                 Transcription factors 
               
               
                   
                   
                 pathways 
                 kinases, phosphatases, DNA 
               
               
                   
                   
                   
                 surveillance proteins, p53, 
               
               
                   
                   
                   
                 proteases, endonucleases, 
               
               
                   
                   
                   
                 GTP-binding proteins (G- 
               
               
                   
                   
                   
                 proteins), leucine rich repeat 
               
               
                   
                   
                   
                 proteins (LRRs), 
               
               
                   
                   
                   
                 transporters, calcium 
               
               
                   
                   
                   
                 binding proteins, 
               
               
                   
                   
                   
                 mitochondrial and 
               
               
                   
                   
                   
                 chloroplast energy related 
               
               
                   
                   
                   
                 proteins, ribosome 
               
               
                   
                   
                   
                 inactivating proteins 
               
               
                   
                   
                 Initiation of Cellular 
                 Reactive oxygen scavenging 
               
               
                   
                   
                 Protectant Gene 
                 enzymes, GST, catalase, 
               
               
                   
                   
                 Transcription 
                 peroxidase, ascorbate 
               
               
                   
                   
                   
                 oxidase 
               
               
                 Downregulated 
                 Early responders 
                 Negative regulation of 
                 Transcription factors, 
               
               
                 transcripts 
                 to pathogens 
                 pathogen inducible 
                 kinases, phosphatases, GTP- 
               
               
                   
                   
                 pathways released 
                 binding proteins (G- 
               
               
                   
                   
                   
                 proteins), leucine rich repeat 
               
               
                   
                   
                   
                 proteins (LRRs), 
               
               
                   
                   
                   
                 transporters, calcium 
               
               
                   
                   
                   
                 binding proteins, chromatin 
               
               
                   
                   
                   
                 remodelling proteins 
               
               
                   
                 Genes repressed 
                 Negative regulation of 
                 Transcription factors, 
               
               
                   
                 by TMV 
                 ROS inducible 
                 kinases, phosphatases, GTP- 
               
               
                   
                   
                 pathways released 
                 binding proteins (G- 
               
               
                   
                   
                   
                 proteins), leucine rich repeat 
               
               
                   
                   
                   
                 proteins (LRRs), 
               
               
                   
                   
                   
                 transporters, calcium 
               
               
                   
                   
                   
                 binding proteins, chromatin 
               
               
                   
                   
                   
                 remodelling proteins 
               
               
                   
                 Delayed 
                 Negative regulation of 
                 Transcription factors, 
               
               
                   
                 Responders to 
                 pathogen inducible 
                 kinases, phosphatases, GTP- 
               
               
                   
                 Pathogens 
                 pathways released 
                 binding proteins (G- 
               
               
                   
                   
                   
                 proteins), leucine rich repeat 
               
               
                   
                   
                   
                 proteins (LRRs), 
               
               
                   
                   
                   
                 transporters, calcium 
               
               
                   
                   
                   
                 binding proteins, chromatin 
               
               
                   
                   
                   
                 remodelling proteins 
               
               
                   
                 Genes repressed 
                 Negative regulation of 
                 Transcription factors, 
               
               
                   
                 by TMV 
                 genes suppressing 
                 kinases, phosphatases, GTP- 
               
               
                   
                   
                 programmed cell death 
                 binding proteins (G- 
               
               
                   
                   
                 released 
                 proteins), leucine rich repeat 
               
               
                   
                   
                   
                 proteins (LRRs), 
               
               
                   
                   
                   
                 transporters, calcium 
               
               
                   
                   
                   
                 binding proteins, chromatin 
               
               
                   
                   
                   
                 remodelling proteins 
               
               
                   
               
            
           
         
       
     
     Use of Promoters of Disease Responsive Genes 
     Promoters of Disease responsive genes are useful for transcription of any desired polynucleotide or plant or non-plant origin. Further, any desired sequence can be transcribed in a similar temporal, tissue, or environmentally specific patterns as the Disease responsive genes where the desired sequence is operably linked to a promoter of a Disease responsive gene. The protein product of such a polynucleotide is usually synthesized in the same cells, in response to the same stimuli as the protein product of the gene from which the promoter was derived. Such promoter are also useful to produce antisense mRNAs to down-regulate the product of proteins, or to produce sense mRNAs to down-regulate mRNAs via sense suppression. 
     II.E.13. Defense (LOL2) Responsive Genes, Gene Components and Products 
     Often growth and yield are limited by the ability of a plant to tolerate stress conditions, including pathogen attack. To combat such conditions, plant cells deploy a battery of inducible defense responses, including the triggering of an oxidative burst and the transcription of pathogenesis-related protein (PR protein) genes. Reactive oxygen species (ROS) such as H 2 O 2  and NO from the oxidative burst play a signaling role, including initiation of the hypersensitive response (HR) and induction of systemic acquired resistance (SAR) to secondary infection by unrelated pathogens. Some PR proteins are able to degrade the cell walls of invading microorganisms, and phytoalexins are directly microbicidal. Other defense related pathways are regulated by salicylic acid (SA) or methyl jasmonate (MeJ). 
     These responses depend on the recognition of a microbial avirulence gene product (avr) by a plant resistance gene product (R), and a series of downstream signaling events leading to transcription-independent and transcription-dependent disease resistance responses. Current models suggest that R-gene-encoded receptors specifically interact with pathogen-encoded ligands to trigger a signal transduction cascade. Several components include ndr1 and eds1 loci. NDR1, EDS1, PR1, as well as PDF 1.2, a MeJ regulated gene and Nim1, a SA regulated gene, are differentially regulated in plants with mutations in the LOL2 gene. 
     LOL2 shares a novel zinc finger motif with LSD1, a negative regulator of cell death and defense response. Due to an alternative splice site the LOL2 gene encodes two different proteins, one of which contains an additional, putative DNA binding motif. Northern analysis demonstrated that LOL2 transcripts containing the additional DNA binding motif are predominantly upregulated after treatment with both virulent and avirulent  Pseudomonas syringae  pv maculicola strains. Modulation in this gene can also confer enhanced resistance to virulent and avirulent  Peronospora parasitica  isolates 
     Examples of LOL2 responsive genes and gene products are shown in the Reference, Sequence, Protein Group, Protein Group Matrix, MA_diff and MA_clust tables. These genes and/or products are responsible for effects on traits such as plant vigor, disease resistance, and seed yield. The genes were discovered and characterized from a much larger set by microarray experiments designed to find genes whose mRNA products changed when the LOL2 gene was mutated in plants. 
     Microarray technology allows monitoring of gene expression levels for thousands of genes in a single experiment. This is achieved by hybridizing labeled fluorescent cDNA pools to glass slides that contain spots of DNA (Schena et al. (1995) Science 270: 467-70). The US  Arabidopsis  Functional Genomics Consortium (AFGC) has recently made public the results from such microarray experiments conducted with AFGC chips containing some about 10,000 non-redundant ESTs, selected from about 37,000 randomly sequenced ESTs generated from mRNA of different tissues and developmental stages. 
     The sequences of the ESTs showing at least two-fold increases or decreases in plants with the LOL2 mutation versus wildtype were obtained. Specifically, the plant line lol-2-2 tested, a loss of function mutation. The ESTs were compared to the Ceres full length cDNA and genomic sequence databanks, and equivalent Ceres clones identified. The MA_diff table reports the results of this analysis, indicating those Ceres clones which are up or down regulated over controls, thereby indicating the Ceres clones which represent LOL2 responsive genes. 
     Manipulation of one or more LOL2 responsive gene activities is useful to modulate the biological processes and/or phenotypes listed below. LOL2 responsive genes and gene products can act alone or in combination. Useful combinations include LOL2 responsive genes and/or gene products with similar transcription profiles, similar biological activities, or members of the same or functionally related biochemical pathways. Whole pathways or segments of pathways are controlled by transcription factor proteins and proteins controlling the activity of signal transduction pathways. Therefore, manipulation of such protein levels is especially useful for altering phenotypes and biochemical activities of plants. 
     Such LOL2 responsive genes and gene products can function to either increase or dampen the above phenotypes or activities either in response to changes in active LOL2 gene or in the absence. The MA_diff Table(s) reports the transcript levels of the experiment (see EXPT ID: lol2 (relating to SMD 8031, SMD 8032)). For transcripts that had higher levels in the samples than the control, a “+” is shown. A “−” is shown for when transcript levels were reduced in root tips as compared to the control. For more experimental detail see the Example section below. 
     Defense genes are those sequences that showed differential expression as compared to controls, namely those sequences identified in the MA_diff tables with a “+” or “−” indication. 
     Defense Genes Identified by Cluster Analyses of Differential Expression 
     Defense Genes Identified by Correlation to Genes that are Differentially Expressed 
     As described above, the transcription profiles of genes that act together are well correlated. Applicants not only have identified the genes that are differentially expressed in the microarray experiments, but also have identified the genes that act in concert with them. The MA_clust table indicates groups of genes that have well correlated transcription profiles and therefore participate in the same pathway or network. 
     A pathway or network of Defense genes is any group in the MA_clust that comprises a cDNA ID that also appears in Expt ID lol2 (relating to SMD 8031, SMD 8032) of the MA_diff table(s). 
     Defense Genes Identified by Correlation to Genes that Cause Physiological Consequences 
     Additionally, the differential expression data and the phenotypic observations can be merged to identify pathways or networks of Defense genes. A group in the MA_clust is considered a Defense pathway or network if the group comprises a cDNA ID that also appears in Knock-in or Knock-out tables that causes one or more of the phenotypes described in section above. 
     Defense Genes Identified by Amino Acid Sequence Similarity 
     Defense genes from other plant species typically encode polypeptides that share amino acid similarity to the sequences encoded by corn and  Arabidopsis  Defense genes. Groups of Defense genes are identified in the Protein Group table. In this table, any protein group that comprises a peptide ID that corresponds to a cDNA ID member of a Defense pathway or network is a group of proteins that also exhibits Defense functions/utilities. 
     Further, promoters of LOL2 responsive genes, as described in the Reference tables, for example, are useful to modulate transcription that is induced by LOL2 responsive genes or any of the following phenotypes or biological activities below. Further, any desired sequence can be transcribed in similar temporal, tissue, or environmentally specific patterns as the LOL2 responsive genes when the desired sequence is operably linked to a promoter of a LOL2 responsive gene. 
     III.E.12.a. Use of Lo12 Responsive Genes, Gene Components and Products to Modulate Phenotypes 
     LOL2 responsive genes and gene products are useful to or modulate one or more phenotypes including pathogen tolerance and/or resistance; Avr/r locus interactions; Non-Host interactions; HR; SAR, e.g., disease responsive genes acting in conjunction with infection with any of the organisms listed below; resistance to bacteria e.g. to  Erwinia stewartii, Pseudomonas syringae, Pseudomonas tabaci , Stuart&#39;s wilt, etc.; resistance to fungi e.g. to downy mildews such as  Scleropthora macrospora, Sclerophthora rayissiae, Sclerospora graminicola, Peronosclerospora sorghi, Peronosclerospora philippinensis, Peronosclerospora sacchari, Peronosclerospora maydis ; rusts such as  Puccinia sorphi, Puccinia polysora, Physopella zeae , etc.; and to other fungal diseases e.g.  Cercospora zeae - maydis, Colletotrichum graminicola, Fusarium monoliforme, Exserohilum turcicum, Bipolaris maydis, Phytophthora parasitica, Peronospora tabacina, Septoria , etc.; resistance to viruses or viroids e.g. to tobacco or cucumber mosaic virus, ringspot virus, necrosis virus,  pelargonium  leaf curl virus, red clover mottle virus, tomato bushy stunt virus, and like viruses; resistance to insects, such as to aphids e.g.  Myzus persicae ; to beetles and beetle larvae; to lepidoptera larvae, e.g.  Heliothus  etc.; resistance to nematodes, e.g.  Meloidogyne incognita  etc.; local resistance in primary (infected) or secondary (uninfected) leaves; stress tolerance; winter survival; cold tolerance; salt tolerance, heavy metal tolerance, such as cadmium; tolerance to physical wounding; increased organelle tolerance to redox stress, such as in mitochondria, and chloroplasts; cell death; programmed cell death, including death of diseased tissue and during senescence; fruit drop; biomass; fresh and dry weight during any time in plant life, such as maturation; number of flowers, seeds, branches, and/or leaves; seed yield, including number, size, weight, and/or harvest index; fruit yield, including number, size, weight, and/or harvest index; plant development; time to fruit maturity; cell wall strengthening and reinforcement; plant product quality; paper making quality; food additives; treatment of indications modulated by free radicals; cancer; kinds of low molecular weight compounds such as phytoalexins; abundance of low molecular weight compounds such as phytoalexins; and other phenotypes based on gene silencing. 
     To regulate any of the phenotype(s) above, activities of one or more of the LOL2 responsive genes or gene products can be modulated and the plants can be tested by screening for the desired trait. Specifically, the gene, mRNA levels, or protein levels can be altered in a plant utilizing the procedures described herein and the phenotypes can be screened for variants as in Winkler et al. (1998) Plant Physiol 118: 743-50 and assayed, for example, in accordance to Alvarez et al., (1998) Cell 92: 773-784; Halhbrock and Scheel, (1989) Ann. Rev. Plant Physiol. Plant Mol. Biol. 40: 347-369; Lamb et al., (1997) Ann. Rev. Plant Mol. Biol. Plant Physiol. 48: 251-275; Lapwood et al. (1984) Plant Pathol. 33: 13-20; Levine et al. (1996) Curr. Biol. 6: 427-437; McKersie et al., (2000) Plant Physiol. 122: 1427-1437; Olson and Varner (1993) Plant J. 4: 887-892; Pastore et al., (2000), FEBS Lett 470: 88-92; Pastori et al., (1997) Plant Physiol. 113: 411-418; Romero-Puertas et al., (1999) Free Radic. Res. 1999 31 Suppl: S25-31; Shirataki et al., Anticancer Res 20: 423-426 (2000); Wu et al., (1995) Plant Cell 7: 1357-1368. 
     III.E.12.b. Use of Defense Responsive Genes to Modulate Biochemical Activities 
     The activities of one or more of the defense (LOL2) responsive genes can be modulated to change biochemical or metabolic activities and/or pathways such as those noted below. Such biological activities are documented and can be measured according to the citations above and included in the Table below: 
     
       
         
           
               
               
               
             
               
                   
               
               
                   
                 BIOCHEMICAL OR 
                   
               
               
                   
                 METABOLIC ACTIVITIES 
                 CITATIONS INCLUDING 
               
               
                 PROCESS 
                 AND/OR PATHWAYS 
                 ASSAYS 
               
               
                   
               
             
            
               
                 Resistance To Pathogens 
                 Induction Of ROS Signaling 
                 Wu et.al.(1995) Plant Cell 7: 
               
               
                   
                 Pathways 
                 1357-68 
               
               
                   
                 Modulation Of Nitric Oxide 
                 Delledonne et al. (1998) Nature 
               
               
                   
                 Signaling 
                 394: 585-588 
               
               
                   
                 Induction Of PR Proteins, 
                 Chamnongpol et.al.(1998) Proc. 
               
               
                   
                 Phytoalexins, And Defense 
                 Nat.Acad Sci USA 12; 95: 5818-23. 
               
               
                   
                 Pathways 
                 Davis et al. (1993) Phytochemistry 
               
               
                   
                   
                 32: 607-611 
               
               
                   
                 Induction Of Cellular 
                 Chen et.al. Plant J. (1996) 10: 955- 
               
               
                   
                 Protectant Genes Such As 
                 966 
               
               
                   
                 Glutathione S-Transferase 
                 Gadea et.al.(1999) Mol Gen Genet 
               
               
                   
                 (GST) And Ascorbate 
                 262: 212-219 
               
               
                   
                 Peroxidase 
                 Wu et.al.(1995) Plant Cell 7: 
               
               
                   
                   
                 1357-68 
               
               
                   
                 ROS Levels Following 
                 Orozco-Cardenas and Ryan (1999) 
               
               
                   
                 Wounding And Changes In 
                 Proc.Nat. Acad. Sci. USA 
               
               
                   
                 Physical Pressure 
                 25; 96: 6553-7. 
               
               
                   
                   
                 Yahraus et al. (1995) Plant 
               
               
                   
                   
                 Physiol. 109: 1259-1266 
               
               
                   
                 Salicyclic Acid Levels And 
                 Durner and Klessig (1996) 
               
               
                   
                 Signaling 
                 J.Biol.Chem. 271: 28492-501 
               
               
                 Responses To Wounding 
                 Expression Of Genes Involved 
                 Legendre et al. (1993) Plant 
               
               
                   
                 In Wound Repair And Cell 
                 Physiol. 102: 233-240 
               
               
                   
                 Division 
                   
               
               
                 Responses To 
                 Expression Of Genes Involved 
                 Shi et al. (2000) Proc. Natl. Acad. 
               
               
                 Environmental Stress 
                 In Responses To Drought, 
                 Sci. USA 97: 6896-6901 
               
               
                   
                 Cold, Salt, Heavy Metals 
                   
               
               
                 Reinforcement Of Cell 
                 Modulation Of The Production 
                 Bradley et al. (1992) Cell 70, 21- 
               
               
                 Walls 
                 Of ExtracTable Proline-Rich 
                 30 
               
               
                   
                 Protein 
                   
               
               
                   
                 Modulation Of Lignification 
                 Mansouri et al. (1999) Physiol. 
               
               
                   
                   
                 Plant 106: 355-362 
               
               
                 Programmed Cell Death 
                 Induction Of Pcd Activating 
                 Levine et al. (1996) Curr. Biol. 6: 
               
               
                   
                 Genes 
                 427-437. Reynolds et.al. (1998) 
               
               
                   
                   
                 Biochem. J. 330: 115-20 
               
               
                   
                 Suppression Of PCD 
                 Pennell and Lamb (1997) Plant 
               
               
                   
                 Suppressing Genes 
                 Cell 9, 1157-1168 
               
               
                   
               
            
           
         
       
     
     Other biological activities that can be modulated by the LOL2 responsive genes and their products are listed in the Reference tables. Assays for detecting such biological activities are described in the Protein Domain table. 
     LOL2 responsive genes are characteristically differentially transcribed in response to fluctuating levels of disease. MA_diff table reports the changes in transcript levels of various LOL2 responsive genes in the lol-2 line versus control plants. 
     The data from this experiment reveal a number of types of LOL2 responsive genes and gene products. Profiles of individual LOL2 responsive genes are shown in the Table below with examples of which associated biological activities are modulated when the activities of one or more such genes vary in plants. 
                                                     EXAMPLES OF       GENE   FUNCTIONAL       BIOCHEMICAL       EXPRESSION   CATEGORY   PHYSIOLOGICAL   ACTIVITY       LEVELS   OF GENE   CONSequence   OF GENE PRODUCTS                  Upregulated   Early Responders   ROS Perception and   Transcription factors,       transcripts   to the LOL2   Response   kinases, phosphatases, GTP-           Mutation       binding proteins (G-                   proteins), leucine rich repeat                   proteins (LRRs),                   transporters, calcium                   binding proteins, chromatin                   remodeling proteins               Initiation of Gene   Glutathione S-transferase               Transcription   (GST),                   heat shock proteins,                   salicylic acid (SA) response                   pathway proteins, jasmonate                   response pathway proteins,                   dehydrins, peroxidases,                   catalases           Delayed   Initiation of Defence   Proteases, pathogen           Responders to the   Gene Transcription   response (PR) proteins,           LOL2 Mutation       cellulases, chitinases,                   cutinases, glucanases, other                   degrading enzymes, calcium                   channel blockers,                   phenylalanine ammonia                   lyase, proteins of defense                   pathways, cell wall proteins                   incuding proline rich                   proteins and glycine rich                   proteins, epoxide hydrolase,                   methyl transferases               Activation of cell death   Transcription factors               pathways   kinases, phosphatases, DNA                   surveillance proteins, p53,                   proteases, endonucleases,                   GTP-binding proteins (G-                   proteins), leucine rich repeat                   proteins (LRRs),                   transporters, calcium                   binding proteins,                   mitochondrial and                   chloroplast energy related                   proteins, ribosome                   inactivating proteins               Initiation of Cellular   Reactive oxygen scavenging               Protectant Gene   enzymes, GST, catalase,               Transcription   peroxidase, ascorbate                   oxidase       Downregulated   Early Responders   Negative regulation of   Transcription factors,       transcripts   to the LOL2   LOL2 Mutation   kinases, phosphatases, GTP-           Mutation   inducible pathways   binding proteins (G-               released   proteins), leucine rich repeat                   proteins (LRRs),                   transporters, calcium                   binding proteins, chromatin                   remodelling proteins           Genes Repressed   Negative regulation of   Transcription factors,           by the LOL2   ROS inducible   kinases, phosphatases, GTP-           Mutation   pathways released   binding proteins (G-                   proteins), leucine rich repeat                   proteins (LRRs),                   transporters, calcium                   binding proteins, chromatin                   remodelling proteins           Delayed   Negative regulation of   Transcription factors,           Responders to the   LOL2 Mutation   kinases, phosphatases, GTP-           LOL2 Mutation   inducible pathways   binding proteins (G-               released   proteins), leucine rich repeat                   proteins (LRRs),                   transporters, calcium                   binding proteins, chromatin                   remodelling proteins           Genes Repressed   Negative Regulation Of   Transcription Factors,           By The LOL2   Genes Suppressing   Kinases, Phosphatases,           Mutation   Programmed Cell   GTP-Binding Proteins (G-               Death Released   Proteins), Leucine Rich                   Repeat Proteins (Lrrs),                   Transporters, Calcium                   Binding Proteins,                   Chromatin Remodelling                   Proteins                    
Use of Promoters of Defense Responsive Genes
 
     Promoters of Defense responsive genes are useful for transcription of any desired polynucleotide or plant or non-plant origin. Further, any desired sequence can be transcribed in a similar temporal, tissue, or environmentally specific patterns as the Defense responsive genes where the desired sequence is operably linked to a promoter of a Defense responsive gene. The protein product of such a polynucleotide is usually synthesized in the same cells, in response to the same stimuli as the protein product of the gene from which the promoter was derived. Such promoter are also useful to produce antisense mRNAs to down-regulate the product of proteins, or to produce sense mRNAs to down-regulate mRNAs via sense suppression. 
     III.E.14. Iron Responsive Genes, Gene Components and Products 
     Iron (Fe) deficiency in humans is the most prevalent nutritional problem worldwide today. Increasing iron availability via diet is a sustainable malnutrition solution for many of the world&#39;s nations. One-third of the world&#39;s soils, however, are iron deficient. Consequently, to form a food-based solution to iron malnutrition, we need a better understanding of iron uptake, storage and utilization by plants. Furthermore, exposure to non-toxic Fe levels appears to affect inherent plant defense mechanisms. Consequently, exploring the effects of Fe exposure has potential for advances in plant disease resistance in addition to human nutrition. 
     Microarray technology allows monitoring of gene expression levels for thousands of genes in a single experiment. This is achieved by simultaneously hybridizing two differentially labeled fluorescent FeNA pools to glass slides that contain spots of DNA (Schena et al. (1995) Science 270: 467-70). The  Arabidopsis  Functional Genomics Consortium (AFGC) has recently made public the results from such microarray experiments conducted with AFGC chips containing 10,000 non-redundant ESTs, selected from 37,000 randomly sequenced ESTs generated from mRNA of different tissues and developmental stages. 
     The sequences of the ESTs showing at least two-fold increases or decreases over the controls were identified, compared to the Ceres full length FeNA and genomic sequence databanks, and identical Ceres clones identified. MA_diff table reports the results of this analysis, indicating those Ceres clones that are up or down regulated over controls, thereby indicating the Ceres clones which are iron responsive genes. 
     The MA_diff Table(s) reports the transcript levels of the experiment (see EXPT ID: Iron (relating to SMD 7114, SMD 7115, SMD 7125)). For transcripts that had higher levels in the samples than the control, a “+” is shown. A “−” is shown for when transcript levels were reduced in root tips as compared to the control. For more experimental detail see the Example section below. 
     Iron genes are those sequences that showed differential expression as compared to controls, namely those sequences identified in the MA Jiff tables with a “+” or “−” indication. 
     Iron Genes Identified by Cluster Analyses of Differential Expression 
     Iron Genes Identified by Correlation to Genes that are Differentially Expressed 
     As described above, the transcription profiles of genes that act together are well correlated. Applicants not only have identified the genes that are differentially expressed in the microarray experiments, but also have identified the genes that act in concert with them. The MA_clust table indicates groups of genes that have well correlated transcription profiles and therefore participate in the same pathway or network. 
     A pathway or network of Iron genes is any group in the MA_clust that comprises a cDNA ID that also appears in Expt ID Iron (relating to SMD 7114, SMD 7115, SMD 7125) of the MA_diff table(s). 
     Iron Genes Identified by Correlation to Genes that Cause Physiological Consequences 
     Additionally, the differential expression data and the phenotypic observations can be merged to identify pathways or networks of Iron genes. A group in the MA_clust is considered a Iron pathway or network if the group comprises a cDNA ID that also appears in Knock-in or Knock-out tables that causes one or more of the phenotypes described in section above. 
     Iron Genes Identified by Amino Acid Sequence Similarity 
     Iron genes from other plant species typically encode polypeptides that share amino acid similarity to the sequences encoded by corn and  Arabidopsis  Iron genes. Groups of Iron genes are identified in the Protein Group table. In this table, any protein group that comprises a peptide ID that corresponds to a cDNA ID member of a Iron pathway or network is a group of proteins that also exhibits Iron functions/utilities. 
     III.E.14.a. Use of Iron Responsive Genes to Modulate Phenotypes 
     Iron responsive genes and gene products are useful to or modulate one or more phenotypes including growth; roots; root hair formation; stems, leaves; development; senescence; plant nutrition; uptake and assimilation of organic compounds; uptake and assimilation of inorganic compounds; animal (including human) nutrition; improved dietary mineral nutrition; stress response metabolic detoxification; and heavy metals. 
     To improve any of the phenotype(s) above, activities of one or more of the iron responsive genes or gene products can be modulated and tested by screening for the desired trait. Specifically, the gene, mRNA levels, or protein levels can be altered in a plant utilizing the procedures described herein and the phenotypes can be assayed. As an example, a plant can be transformed according to Bechtold and Pelletier (1998, Methods. Mol. Biol. 82:259-266) and visually inspected for the desired phenotype or metabolically and/or functionally assayed according to Schmidt et al. (2000, Plant Physiol 122:1109-18), Meagher (2000) Current Opinion in Plant Biology 3: 153-62), Deak (1999, Nature Biotechnology (1999, Nature Biotechnology 17: 192-96), Wei and Theil (2000, J. Biol Chem 275: 17488-93) and Vansuyt et al. (1997, FEBS Letters 410: 195-200). 
     III.E.14.b. Use of Iron-Responsive Genes, Gene Components and Products to Modulate Biochemical Activities 
     The activities of one or more of the iron responsive genes can be modulated to change biochemical or metabolic activities and/or pathways such as those noted below. Such biological activities can be measured according to the citations included in the Table below: 
     
       
         
           
               
               
               
             
               
                   
               
               
                   
                 BIOCHEMICAL OR 
                   
               
               
                   
                 METABOLIC 
                 CITATIONS 
               
               
                   
                 ACTIVITIES AND/OR 
                 INCLUDING 
               
               
                 PROCESS 
                 PATHWAYS 
                 ASSAYS 
               
               
                   
               
             
            
               
                 Growth , Differentiation 
                 Root Growth 
                 Robinson et al. (1999) 
               
               
                 and Development 
                 Initiation of root 
                 Nature 397: 694-97 
               
               
                   
                 hairs 
                   
               
               
                 Metabolisms 
                 Iron sensing 
                 Thomine et al. (2000) 
               
               
                   
                   
                 PNAS USA 97: 4991-6 
               
               
                   
                 Iron uptake and transport 
                 Thomine et al. (2000) 
               
               
                   
                 decreased iron 
                 PNAS USA 97: 4991-6 
               
               
                   
                 transport 
                 Zhu (1999) Plant 
               
               
                   
                 phytoremediation 
                 Physiol 119: 73-79 
               
               
                 Plant Defenses 
                 Protection from oxidative 
                 Deak (1999) Nature 
               
               
                   
                 damage 
                 Biotechnology 17: 192- 
               
               
                   
                   
                 6 
               
               
                 Signaling 
                 Specific gene 
                 Brand and Perrimon 
               
               
                   
                 transcription gene 
                 (1993) Development 
               
               
                   
                 silencing 
                 118: 401-415 
               
               
                   
               
            
           
         
       
     
     Other biological activities that can be modulated by the iron responsive genes and gene products are listed in the REFERENCE Table. Assays for detecting such biological activities are described in the Protein Domain table. 
     Iron responsive genes are characteristically differentially transcribed in response to fluctuating iron levels or concentrations, whether internal or external to an organism or cell. MA_diff table reports the changes in transcript levels of various iron responsive genes. 
     The microarray comparison consists of probes prepared from root RNA of  A. thaliana  (Columbia) seedlings grown under iron-sufficient conditions and seedlings grown under iron-deficient. The data from this experiment reveal a number of types genes and gene products. Profiles of these different iron responsive genes are shown in the Table below with examples of associated biological activities. 
                                                     EXAMPLES OF       TRANSCRIPT   TYPE OF   PHYSIOLOGICAL   BIOCHEMICAL       LEVELS   GENES   CONSEQUENCES   ACTIVITY                  Up regulated   responders    Iron perception   Transporters       transcripts   to iron   Iron uptake and   Metabolic enzymes           application   transport   Change in cell               Iron metabolism   membrane structure               Synthesis of   and potential               secondary   Kinases and               metabolites   phosphatases               and/or proteins   Transcription                   activators               Modulation of   Change in                iron response   chromatin structure                transduction   and/or localized                pathways   DNA topology               Specific gene                   transcription                   initiation           Down-   responder to    Negative   Transcription        regulated   iron repressors    regulation of iron   factors       transcripts   of iron state    pathways   Change in protein           of metabolism       structure by           Genes with   Changes in   phosphorylation           discontinued   pathways and   (kinases) or           expression or   processes   dephosphoryaltion           unsTable    operating in cells   (phosphatases)           mRNA in    Changes in other   Change in            presence   metabolisms than   chromatin structure            of iron   iron   and/or DNA                    topology                   Stability of factors                   for protein                    synthesis and                    degradation                   Metabolic enzymes                    
Use of Promoters of Iron Responsive Genes
 
     Promoters of Iron responsive genes are useful for transcription of any desired polynucleotide or plant or non-plant origin. Further, any desired sequence can be transcribed in a similar temporal, tissue, or environmentally specific patterns as the Iron responsive genes where the desired sequence is operably linked to a promoter of a Iron responsive gene. The protein product of such a polynucleotide is usually synthesized in the same cells, in response to the same stimuli as the protein product of the gene from which the promoter was derived. Such promoter are also useful to produce antisense mRNAs to down-regulate the product of proteins, or to produce sense mRNAs to down-regulate mRNAs via sense suppression. 
     III.E.15. Shade Responsive Genes, Gene Components and Products 
     Plants sense the ratio of Red (R):Far Red (FR) light in their environment and respond differently to particular ratios. A low R:FR ratio, for example, enhances cell elongation and favors flowering over leaf production. The changes in R:FR ratios mimic and cause the shading response effects in plants. The response of a plant to shade in the canopy structures of agricultural crop fields influences crop yields significantly. Therefore manipulation of genes regulating the shade avoidance responses can improve crop yields. While phytochromes mediate the shade avoidance response, the down-stream factors participating in this pathway are largely unknown. One potential downstream participant, ATHB-2, is a member of the HD-Zip class of transcription factors and shows a strong and rapid response to changes in the R:FR ratio. ATHB-2 overexpressors have a thinner root mass, smaller and fewer leaves and longer hypocotyls and petioles. This elongation arises from longer epidermal and cortical cells, and a decrease in secondary vascular tissues, paralleling the changes observed in wild-type seedlings grown under conditions simulating canopy shade. On the other hand, plants with reduced ATHB-2 expression have a thick root mass and many larger leaves and shorter hypocotyls and petioles. Here, the changes in the hypocotyl result from shorter epidermal and cortical cells and increased proliferation of vascular tissue. Interestingly, application of Auxin is able to reverse the root phenotypic consequences of high ATHB-2 levels, restoring the wild-type phenotype. Consequently, given that ATHB-2 is tightly regulated by phytochrome, these data suggest that ATHB-2 may link the Auxin and phytochrome pathways in the shade avoidance response pathway. 
     Changes in R:FR ratios promote changes in gene expression. Microarray technology allows monitoring of gene expression levels for thousands of genes in a single experiment. This is achieved by hybridizing labeled fluorescent cDNA pools to glass slides that contain spots of DNA (Schena et al. (1995) Science 270: 467-70). The US  Arabidopsis  Functional Genomics Consortium (AFGC) has recently made public the results from such microarray experiments conducted with AFGC chips containing about 10,000 non-redundant ESTs, selected from about 37,000 randomly sequenced ESTs generated from mRNA of different tissues and developmental stages. 
     The sequences of the ESTs showing at least two-fold increases or decreases in plants given 4 hours of FR rich light after growth in high R:FR light compared with the controls of plants grown in high R:FR light only, were identified, compared to the Ceres full length cDNA and genomic sequence databanks, and equivalent Ceres clones identified. The MA_diff table(s) report(s) the results of this analysis, indicating those Ceres clones which are up or down regulated over controls, thereby indicating the Ceres clones which are shade avoidance responsive genes. 
     Examples of far red light induced, shade avoidance responsive genes and gene products are shown in the Reference and Sequence Tables. These genes and/or products are responsible for effects on traits such as plant vigor and seed yield. 
     While far red light, shade avoidance responsive polynucleotides and gene products can act alone, combinations of these polynucleotides also affect growth and development. Useful combinations include different shade avoidance responsive polynucleotides and/or gene products that have similar transcription profiles or similar biological activities, and members of the same or similar biochemical pathways. In addition, the combination of a shade avoidance responsive polynucleotide and/or gene product with another environmentally responsive polynucleotides is also useful because of the interactions that exist between hormone-regulated pathways, stress and pathogen induced pathways, nutritional pathways, light induced pathways and development. Here, in addition to polynucleotides having similar transcription profiles and/or biological activities, useful combinations include polynucleotides that may have different transcription profiles but which participate in common or overlapping pathways. 
     Such far red light induced shade avoidance responsive genes and gene products can function to either increase or dampen the above phenotypes or activities either in response to changes in far red light or in the absence of far red light fluctuations. The MA_diff Table(s) reports the transcript levels of the experiment (see EXPT ID: Shade (relating to SMD 8130, SMD 7230)). For transcripts that had higher levels in the samples than the control, a “+” is shown. A “−” is shown for when transcript levels were reduced in root tips as compared to the control. For more experimental detail see the Example section below. 
     Shade genes are those sequences that showed differential expression as compared to controls, namely those sequences identified in the MA_diff tables with a “+” or “−” indication. 
     Shade Genes Identified by Cluster Analyses of Differential Expression 
     Shade Genes Identified by Correlation to Genes that are Differentially Expressed 
     As described above, the transcription profiles of genes that act together are well correlated. Applicants not only have identified the genes that are differentially expressed in the microarray experiments, but also have identified the genes that act in concert with them. The MA_clust table indicates groups of genes that have well correlated transcription profiles and therefore participate in the same pathway or network. 
     A pathway or network of Shade genes is any group in the MA_clust that comprises a cDNA ID that also appears in Expt ID Shade (relating to SMD 8130, SMD 7230) of the MA_diff table(s). 
     Shade Genes Identified by Correlation to Genes that Cause Physiological Consequences 
     Additionally, the differential expression data and the phenotypic observations can be merged to identify pathways or networks of Shade genes. A group in the MA_clust is considered a Shade pathway or network if the group comprises a cDNA ID that also appears in Knock-in or Knock-out tables that causes one or more of the phenotypes described in section above. 
     Shade Genes Identified by Amino Acid Sequence Similarity 
     Shade genes from other plant species typically encode polypeptides that share amino acid similarity to the sequences encoded by corn and  Arabidopsis  Shade genes. Groups of Shade genes are identified in the Protein Group table. In this table, any protein group that comprises a peptide ID that corresponds to a cDNA ID member of a Shade pathway or network is a group of proteins that also exhibits Shade functions/utilities. 
     Further, promoters of shade avoidance responsive genes, as described in the Reference tables, for example, are useful to modulate transcription that is induced by shade avoidance or any of the following phenotypes or biological activities below. Further, any desired sequence can be transcribed in similar temporal, tissue, or environmentally specific patterns as the shade avoidance responsive genes when the desired sequence is operably linked to a promoter of a circadian (clock) responsive gene. 
     III.E.15.a. Use of Far Red Responsive, Shade Avoidance Response Genes To Modulate Phenotypes 
     High FR:R, shade avoidance responsive genes and gene products can be used to alter or modulate one or more phenotypes including growth; roots; elongation; lateral root formation; stems; elongation; expansion; leaves; expansion; carotenoid composition; development; cell; photosynthetic apparatus; efficiency; flower; flowering time; fruit; seed; dormancy; control rate and timing of germination; prolongs seed storage and viability; inhibition of hydrolytic enzyme synthesis; seed and fruit yield; senescence; abscission; leaf fall; flower longevity; differentiation; vascularization; and shade (avoidance) responses in plant architecture. 
     To regulate any of the phenotype(s) above, activities of one or more of the High FR: R light, shade avoidance responsive genes or gene products can be modulated and the plants tested by screening for the desired trait. Specifically, the gene, mRNA levels, or protein levels can be altered in a plant utilizing the procedures described herein and the phenotypes can be assayed. As an example, a plant can be transformed according to Bechtold and Pelletier (1998, Methods. Mol. Biol. 82:259-266) and/or screened for variants as in Winkler et al. (1998) Plant Physiol 118: 743-50 and visually inspected for the desired phenotype or metabolically and/or functionally assayed according to Carabelli et al. (1996, PNAS USA 93: 3530-3535), Aguirrezabal and Tardieu (1996, J Exp Bot 47: 411-20), Heyer et al. (1995, Plant Physiol 109: 53-61), Garcia-Plazaola et al. (1997, J Exp Bot 48: 1667-74), Schwanz et al. (1996, J Exp Bot 47L 1941-50), Koehne et al. (1999, Biochem Biophys Acta 1412:94-107), Melis (1984, J Cell Biochem 24: 271-85), Steindeler et al. (1999, Development 126: 4235-45), Cruz (1997, J Exp Bot 48: 15-24), Stephanou and Manetas (1997, J Exp Bot 48: 1977-85), Grammatikopoulos et al (1999, J Exp Bot 50:517-21), Krause et al. (1999, Plant Physiol 121: 1349-58), Aukerman et al. (1997, Plant Cell 9: 1317-26), Wagner et al. (1997, Plant Cell 9: 731-43), Weinig (2000) Evolution Int J Org Evolution 54: 124-26), Cocbum et al. (1996, J Exp Bot 47: 647-53), Devlin et al. (1999, Plant Physiol 119: 909-15), Devlin et al. (1998, Plant Cell 10: 1479-87), Finlayson et al. (1998, Plant Physiol 116: 17-25), Morelli and Ruberti (2000, Plant Physiol 122: 621-26), Aphalo et al. (1999, J Exp Bot 50: 1629-34), Sims et al. (1999, J Exp Bot 50: 50: 645-53) and Ballare (1999, Trends Plant Sci 4: 97-102). 
     III.E.15.b. Use of Far Red Light, Shade Avoidance Responsive Genes to Modulate Biochemical Activities 
     The activities of one or more of the far red light, shade avoidance responsive genes can be modulated to change biochemical or metabolic activities and/or pathways such as those noted below. Such biological activities can be measured according to the citations included in the Table below: 
     
       
         
           
               
               
               
             
               
                   
               
               
                   
                 BIOCHEMICAL OR 
                   
               
               
                   
                 METABOLIC 
                   
               
               
                   
                 ACTIVITIES AND/OR 
                 CITATIONS INCLUDING 
               
               
                 PROCESS 
                 PATHWAYS 
                 ASSAYS 
               
               
                   
               
             
            
               
                 Cell Growth and 
                 Cell Elongation 
                 Carabelli et al. (1996) PNAS USA 
               
               
                 Differentiation 
                   
                 93: 3530-35 
               
               
                   
                 Leaf Expansion 
                 Heyer et al. (1995) Plant Physiol 
               
               
                   
                   
                 109: 53-61 
               
               
                 Photosynthesis 
                 Development of 
                 Jagtap et al. (1998) J Exp Bot 49: 
               
               
                   
                 Photosynthetic Apparatus 
                 1715-21 
               
               
                   
                   
                 Melis (1984) J Cell Biochem 24: 
               
               
                   
                   
                 271-285 
               
               
                   
                   
                 McCain (1995) Biophys J 69: 1105- 
               
               
                   
                   
                 10 
               
               
                   
                 Carotenoid Composition 
                 Garcia-Plazaola et al (1997) J Exp 
               
               
                   
                   
                 Bot 48: 1667-74 
               
               
                 Carbon/Nitrogen 
                 Carbon and Nitrogen 
                 Cruz (1997) J Exp Bot 48: 15-24 
               
               
                 Metabolism 
                 Assimilation 
                   
               
               
                 Far red light, shade 
                   
                 Newton AL, Sharpe BK, Kwan A, 
               
               
                 avoidance response 
                   
                 Mackay JP, Crossley M. J Biol 
               
               
                 binding by transcription 
                   
                 Chem. May 19, 2000; 275(20): 15128- 
               
               
                 factors 
                   
                 34; Lopez Ribera I, Ruiz-Avila L, 
               
               
                   
                   
                 Puigdomenech P. Biochem Biophys 
               
               
                   
                   
                 Res Commun. Jul. 18, 1997; 
               
               
                   
                   
                 236(2): 510-6; de Pater S, Greco 
               
               
                   
                   
                 V, Pham K, Memelink J, Kijne J. 
               
               
                   
                   
                 Nucleic Acids Res. Dec. 1, 1996; 
               
               
                   
                   
                 24(23): 4624-31. 
               
               
                 Signaling 
                 UV Light Perception 
                 Stephanou and Manetas (1997) J 
               
               
                   
                   
                 Exp Bot 48: 1977-85 
               
               
                   
                 Far-red/Red Light 
                 Aukerman et al. (1997) Plant Cell 
               
               
                   
                 Perception 
                 9: 1317-26 
               
               
                   
                   
                 Wagner et al. (1997) Plant Cell 9: 
               
               
                   
                   
                 731-43 
               
               
                   
                 Interaction of “Shade 
                 Finlayson et al. (1998) Plant 
               
               
                   
                 Factor” with Ethylene 
                 Physiol 116: 17-25 
               
               
                   
                 Production/Transduction 
                   
               
               
                   
                 Interaction of “Shade 
                 Reed et al. (1998) Plant Physiol 
               
               
                   
                 Factor” with Auxin 
                 118: 1369-78 
               
               
                   
                 Production/Transduction 
                   
               
               
                   
                 Plant to Plant signalling 
                 Sims et al. (1999) J Exp Bot 50: 
               
               
                   
                   
                 645-53 
               
               
                   
               
            
           
         
       
     
     Other biological activities that can be modulated by shade avoidance response genes and their products are listed in the REF TABLES. Assays for detecting such biological activities are described in the Protein Domain table. 
     High FR:R, shade avoidance responsive genes are differentially transcribed in response to high FR:R ratios. The microarray comparison to reveal such genes consisted of probes prepared from RNA isolated from the aerial tissues of  A. thaliana  (Columbia) two-week old seedlings grown in high R:FR ratios compared to seedlings grown in high R:FR ratios followed by 4 hours of FR-rich light treatment. The data from this experiment reveal a number of types genes and gene products and examples of the classes of genes are given in the Table below. 
                                                     EXAMPLES OF       TRANSCRIPT   TYPE OF   PHYSIOLOGICAL   BIOCHEMICAL       LEVELS   GENES   CONSEQUENCES   ACTIVITY                  Up regulated   Responders    Far red light   Transporters       transcripts   to high   perception   Metabolic enzymes           FR:R   Metabolism   Change in cell           light ratios   affected by far red   membrane structure           Genes induced    light   and potential           by high   Synthesis of   Kinases and           FR:R light    secondary   phosphatases           ratio   metabolites and/or   Transcription               proteins   activators               Modulation of   Change in                high FR:R light   chromatin structure                ratio transduction   and/or localized                pathways   DNA topology               Specific gene   Leaf production               transcription   factors               initiation           Down-   Responders    Changes in   Transcription        regulated   to high   pathways and   factors       transcripts   FR:R light    processes   Change in protein           ratios   operating in cells   structure by           Genes repressed    Changes in   phosphorylation           by high FR:R    metabolisms other   (kinases) or           light ratio   than far red   dephosphorylation           Genes with   stimulated   (phosphatases)           discontinued   pathways   Change in            expression or       chromatin structure            unsTable        and/or DNA            mRNA during        topology           high FR:R        Stability of factors            ratio light       for protein                    synthesis and                    degradation                   Metabolic enzymes                   Cell elongation                    factors                   Flowering                    promotion factors                    
Use of Promoters of Shade Avoidance Genes
 
     Promoters of Shade Avoidance genes are useful for transcription of any desired polynucleotide or plant or non-plant origin. Further, any desired sequence can be transcribed in a similar temporal, tissue, or environmentally specific patterns as the Shade Avoidance genes where the desired sequence is operably linked to a promoter of a Shade Avoidance gene. The protein product of such a polynucleotide is usually synthesized in the same cells, in response to the same stimuli as the protein product of the gene from which the promoter was derived. Such promoter are also useful to produce antisense mRNAs to down-regulate the product of proteins, or to produce sense mRNAs to down-regulate mRNAs via sense suppression. 
     III.E.16. Sulfur Responsive Genes, Gene Components and Products 
     Sulfur is one of the important macronutrients required by plants. It is taken up from the soil solution by roots as in the form of sulfate anion which higher plants are dependent on to fulfill their nutritional sulfur requirement. After uptake from the soil, sulfate is either accumulated and stored in vacuole or it is assimilated into various organic compounds, e.g. cysteine, glutathione, methionine, etc. Thus, plants also serve as nutritional sulfur sources for animals. Sulfur can be assimilated in one of two ways: it is either incorporated as sulfate in a reaction called sulfation, or it is first reduced to sulfide, the substrate for cysteine synthesis. In plants, majority of sulfur is assimilated in reduced form. 
     Sulfur comprises a small by vital fraction of the atoms in many protein molecules. As disulfide bridges, the sulfur atoms aid in stabilizing the folded proteins, such cysteine residues. Cys is the first sulfur-containing amino acids, which in proteins form disulfide bonds that may affect the tertiary structures and enzyme activities. This redox balance is mediated by the disulfide/thiol interchange of thioredoxin or glutaredoxin using NADPH as an electron donor. Sulfur can also become sulfhydryl (SH) groups participating in the active sites of some enzymes and some enzymes require the aid of small molecules that contain sulfur. In addition, the machinery of photosynthesis includes some sulfur-containing compounds, such as ferrodoxin. Thus, sulfate assimilation plays important roles not only in the sulfur nutrition but also in the ubiquitous process that may regulate the biochemical reactions of various metabolic pathways. 
     Deficiency of sulfur leads to a marked chlorosis in younger leaves, which may become white in color. Other symptoms of sulfur deficiency also include weak stems and reduced growth. Adding sulfur fertilizer to plants can increase root development and a deeper green color of the leaves in sulfur-deficient plants. However, Sulfur is generally sufficient in soils for two reasons: it is a contaminant in potassium and other fertilizers and a product of industrial combustion. Sulfur limitation in plants is thus likely due to the limitation of the uptake and distribution of sulfate in plants. Seven cell type specific sulfate transporter genes have been isolated from  Arabidopsis . In sulfate-starved plants, expression of the high-affinity transporter, AtST1-1, is induced in root epidermis and cortex for acquisition of sulfur. The low affinity transporter, AtST2-1 (AST68), accumulates in the root vascular tissue by sulfate starvation for root-to-shoot transport of sulfate. These studies have shown that the whole-plant process of sulfate transport is coordinately regulated by the expression of these 2 sulfate transporter genes under sulfur limited conditions. Recent studies have proposed that feeding of O-acetylserine, GSH and selenate may regulate the expression of AtST1-1 and AtST2-1 (AST68) in roots either positively or negatively. However, regulatory proteins that may directly control the expression of these genes have not been identified yet. 
     It has been established that there are regulatory interactions between assimilatory sulfate and nitrate reduction in plants. The two assimilatory pathways are very similar and well coordinated; deficiency for one element was shown to repress the other pathway. The coordination between them should be taken into consideration when one tries to alter one of pathways. 
     Microarray technology allows monitoring of gene expression levels for thousands of genes in a single experiment. This is achieved by simultaneously hybridizing two differentially labeled fluorescent cDNA pools to glass slides that contain spots of DNA (Schena et al. (1995) Science 270: 467-70). The  Arabidopsis  Functional Genomics Consortium (AFGC) has recently made public the results from such microarray experiments conducted with AFGC chips containing 10,000 non-redundant ESTs, selected from 37,000 randomly sequenced ESTs generated from mRNA of different tissues and developmental stages. 
     The sequences of the ESTs showing at least two-fold increases or decreases over the controls were identified, compared to the Ceres full-length cDNA and genomic sequence databanks, and identical Ceres clones identified. MA_diff table reports the results of this analysis, indicating those Ceres clones which are up or down regulated over controls, thereby indicating the Ceres clones which are sulfur response responsive genes. 
     The MA_diff Table(s) reports the transcript levels of the experiment (see EXPT ID: Sulfur (relating to SMD 8034, SMD 8035)). For transcripts that had higher levels in the samples than the control, a “+” is shown. A “−” is shown for when transcript levels were reduced in root tips as compared to the control. For more experimental detail see the Example section below. 
     Sulfur genes are those sequences that showed differential expression as compared to controls, namely those sequences identified in the MA_diff tables with a “+” or “−” indication. 
     Sulfur Genes Identified by Cluster Analyses of Differential Expression 
     Sulfur Genes Identified by Correlation to Genes that are Differentially Expressed 
     As described above, the transcription profiles of genes that act together are well correlated. Applicants not only have identified the genes that are differentially expressed in the microarray experiments, but also have identified the genes that act in concert with them. The MA_clust table indicates groups of genes that have well correlated transcription profiles and therefore participate in the same pathway or network. 
     A pathway or network of Sulfur genes is any group in the MA_clust that comprises a cDNA ID that also appears in Expt ID Sulfur (relating to SMD 8034, SMD 8035) of the MA_diff table(s). 
     Sulfur Genes Identified by Correlation to Genes that Cause Physiological Consequences 
     Additionally, the differential expression data and the phenotypic observations can be merged to identify pathways or networks of Sulfur genes. A group in the MA_clust is considered a Sulfur pathway or network if the group comprises a cDNA ID that also appears in Knock-in or Knock-out tables that causes one or more of the phenotypes described in section above. 
     Sulfur Genes Identified by Amino Acid Sequence Similarity 
     Sulfur genes from other plant species typically encode polypeptides that share amino acid similarity to the sequences encoded by corn and  Arabidopsis  Sulfur genes. Groups of Sulfur genes are identified in the Protein Group table. In this table, any protein group that comprises a peptide ID that corresponds to a cDNA ID member of a Sulfur pathway or network is a group of proteins that also exhibits Sulfur functions/utilities. 
     III.E.16.a. Use of Sulfur Responsive Genes to Modulate Phenotypes 
     Sulfur responsive genes and gene products are useful to or modulate one or more phenotypes including growth; roots; stems; leaves; development; chloroplasts and mitochondria; fruit development; seed development; seed storage proteins; senescence; differentiation; plastid/chloroplast and mitochondria differentiation; protection against oxidative damage; regulation of enzymes via redox control by thiol groups; metabolic detoxification; photosynthesis; and carbon dioxide fixation. 
     To improve any of the phenotype(s) above, activities of one or more of the sulfur responsive genes or gene products can be modulated and tested by screening for the desired trait. Specifically, the gene, mRNA levels, or protein levels can be altered in a plant utilizing the procedures described herein and the phenotypes can be assayed. As an example, a plant can be transformed according to Bechtold and Pelletier (1998, Methods. Mol. Biol. 82:259-266) and visually inspected for the desired phenotype or metabolically and/or functionally assayed according to Saito et al. (1994, Plant Physiol. 106: 887-95), Takahashi et al (1997, Proc. Natl. Acad. Sci. USA 94: 11102-07) and Koprivova et al. (2000, Plant Physiol. 122: 737-46). 
     III.E.16.b. Use of Sulfur-Responsive Genes, Gene Components and Products to Modulate Biochemical Activities 
     The activities of one or more of the sulfur responsive genes can be modulated to change biochemical or metabolic activities and/or pathways such as those noted below. Such biological activities can be measured according to the citations included in the Table below: 
     
       
         
           
               
               
               
             
               
                   
               
               
                   
                 BIOCHEMICAL  
                   
               
               
                   
                 OR METABOLIC  
                   
               
               
                   
                 ACTIVITIES 
                 CITATIONS INCLUDING 
               
               
                 PROCESS 
                 AND/OR PATHWAYS 
                 ASSAYS 
               
               
                   
               
             
            
               
                 Growth , 
                 Root 
                 Klein and Klein (1988) Mineral 
               
               
                 Differentiation  
                 Leaf 
                 Nutrition, In CM Wilson and J 
               
               
                 and 
                 Stem 
                 Gregory, eds Fundamentals of 
               
               
                 Development 
                 Chloroplast/ 
                 Plant Science. Harper and Row 
               
               
                   
                 Mitochondria 
                 Publishers, Inc., NY, p163 
               
               
                   
                 development/ 
                 Rost et al. (1984) The  
               
               
                   
                 differentiation 
                 Absorption and Transport  
               
               
                   
                   
                 System, In R Bern, ed,  
               
               
                   
                   
                 Botany—A Brief Introduction  
               
               
                   
                   
                 to Plant Biology. John Wiley  
               
               
                   
                   
                 and Sons, NY, p96. 
               
               
                   
                   
                 Huluigue et al. (2000) Biochem 
               
               
                   
                   
                 Biophys Res Commun 271:  
               
               
                   
                   
                 380-5 
               
               
                   
                   
                 Kapazoglou et al. (2000) Eur J 
               
               
                   
                   
                 Biochem 267: 352-60 
               
               
                   
                 Seed storage protein 
                 Kim et al. (1999) 209: 282-9 
               
               
                   
                 synthesis 
                   
               
               
                 Metabolisms 
                 Sulfate uptake and  
                 Takahashi et al. (1997) Proc  
               
               
                   
                 transport 
                 Natl Acad Sci USA 94:  
               
               
                   
                   
                 11102-07 
               
               
                   
                 Cysteine Biosynthesis 
                 Saito et al. (1992) Proc Natl  
               
               
                   
                   
                 Acad Sci USA 89: 8078-82 
               
               
                   
                   
                 Hesse et al. (1999) Amino  
               
               
                   
                   
                 Acids 16: 113-31 
               
               
                   
                 Methionine biosynthesis 
                 Bourgis et al. (1999) Plant Cell  
               
               
                   
                   
                 11: 1485-98 
               
               
                   
                 Carbon dioxide fixation  
                 Buchana (1991) Arch Biochem 
               
               
                   
                 in photosynthesis 
                 Biophys 288: 1-9 
               
               
                   
                 Thioredoxin reduction 
                 Leustek and Saito (1999) Plant 
               
               
                   
                   
                 Phyiol 120: 637-43 
               
               
                   
                   
                 Mamedova et al. (1999) FEBS 
               
               
                   
                   
                 Lett 462: 421-4 
               
               
                   
                 Nitrogen metabolism 
                 Koprivova et al. (2000) Plant 
               
               
                   
                   
                 Physiol. 122: 737-46 
               
               
                   
                   
                 Yamaguchi et al. (1999) Biosci 
               
               
                   
                   
                 Biotechnol Biochem 63: 762-6 
               
               
                 Plant Defenses 
                 Reduction of oxidative 
                 May et al. (1998) J Expt Bio  
               
               
                   
                 stress—oxygen  
                 49: 649-67 
               
               
                   
                 metabolism and reactive  
                 Kreuz et al. (1996) Plant  
               
               
                   
                 oxygen species 
                 Physiol 111: 349-53 
               
               
                   
                 Detoxification of toxins, 
                 Zhao et al. (1998) Plant Cell  
               
               
                   
                 xenobiotics and heavy 
                 10: 359-70 
               
               
                   
                 metals 
                   
               
               
                   
                 Defense against  
                 Kyung and Fleming (1997) J  
               
               
                   
                 pathogens or microbes 
                 Food Prot 60: 67-71 
               
               
                   
                 Disease prevention by 
                 Fahey et al. (1997) Proc Natl  
               
               
                   
                 secondary sulfur- 
                 Acad Sci USA 94: 10367-72 
               
               
                   
                 containing compounds 
                   
               
               
                   
                 Activation of kinases  
                 Davis et al. (1999) Plant Cell  
               
               
                   
                 and phosphatases 
                 11: 1179-90 
               
               
                   
               
            
           
         
       
     
     Other biological activities that can be modulated by the sulfur responsive genes and gene products are listed in the REFERENCE Table. Assays for detecting such biological activities are described in the Protein Domain table. 
     Sulfur responsive genes are characteristically differentially transcribed in response to fluctuating sulfur levels or concentrations, whether internal or external to an organism or cell. MA_diff table reports the changes in transcript levels of various sulfur responsive genes. 
     Profiles of these different sulfur responsive genes are shown in the Table below with examples of associated biological activities. 
                                                     EXAMPLES OF       TRANSCRIPT       PHYSIOLOGICAL   BIOCHEMICAL       LEVELS   TYPE OF GENES   CONSEQUENCES   ACTIVITY                  Up regulated   Responders to sulfur   Sulfur perception   Transporters       transcripts   Application   Sulfur uptake and   Metabolic enzymes               transport   Change in cell               Sulfur metabolism   membrane structure               Synthesis of   and potential               secondary   Kinases and               metabolites and/or   phosphatases               proteins   Transcription               Modulation of   activators               sulfur response   Change in chromatin               transduction   structure and/or               pathways   localized DNA               Specific gene   topology               transcription   Redox control               initiation       Down-regulated   responder to sulfur   Negative   Transcription factors       transcripts   repressors of sulfur   regulation of   Change in protein           state of metabolism   sulfur pathways   structure by           Genes with   Changes in   phosphorylation           discontinued   pathways and   (kinases) or           expression or   processes   dephosphoryaltion           unsTable mRNA in   operating in cells   (phosphatases)           presence of sulfur   Changes in other   Change in chromatin               metabolisms than   structure and/or DNA               sulfur   topology                   Stability of factors for                   protein synthesis and                   degradation                   Metabolic enzymes                    
Use of Promoters of Sulfur Responsive Genes
 
     Promoters of Sulfur responsive genes are useful for transcription of any desired polynucleotide or plant or non-plant origin. Further, any desired sequence can be transcribed in a similar temporal, tissue, or environmentally specific patterns as the Sulfur responsive genes where the desired sequence is operably linked to a promoter of a Sulfur responsive gene. The protein product of such a polynucleotide is usually synthesized in the same cells, in response to the same stimuli as the protein product of the gene from which the promoter was derived. Such promoter are also useful to produce antisense mRNAs to down-regulate the product of proteins, or to produce sense mRNAs to down-regulate mRNAs via sense suppression. 
     III.E.17. Zinc Responsive Genes, Gene Components and Products 
     Phytoremediation of soils contaminated with toxic levels of heavy metals requires the understanding of plant metal transport and tolerance. The numerous  Arabidopsis thaliana  studies have given scientists the potential for dissection and elucidation of plant micronutrient/heavy metal uptake and accumulation pathways. It has been shown altered regulation of ZNT1, a Zn/Cd transporter, contributes to high Zn uptake. Isolation and characterization of Zn/Cd hyperaccumulation genes may allow expression in higher biomass plant species for efficient contaminated soil clean up. Identification of additional Zn transport, tolerance and nutrition-related genes involved in heavy metal accumulation will enable manipulation of increased uptake (for phytoremediation) as well as limitation of uptake or leak pathways that contribute to toxicity in crop plants. Additionally, Zn-binding ligands involved in Zn homeostasis or tolerance may be identified, as well as factors affecting the activity or expression of Zn binding transcription factors. Gene products acting in concert to effect Zn uptake, which would not have been identified in complementation experiments, including multimeric transporter proteins, could also be identified. 
     Microarray technology allows monitoring of gene expression levels for thousands of genes in a single experiment. This is achieved by simultaneously hybridizing two differentially labeled fluorescent cDNA pools to glass slides that contain spots of DNA (Schena et al. (1995) Science 270: 467-70). The  Arabidopsis  Functional Genomics Consortium (AFGC) has recently made public the results from such microarray experiments conducted with AFGC chips containing 10,000 non-redundant ESTs, selected from 37,000 randomly sequenced ESTs generated from mRNA of different tissues and developmental stages. 
     The sequences of the ESTs showing at least two-fold increases or decreases over the controls were identified, compared to the Ceres full-length cDNA and genomic sequence databanks, and identical Ceres clones identified. The Zn response information was then used in conjunction with the existing annotation to attribute biological function or utility to the full-length cDNA and corresponding genomic sequence. 
     The MA_diff Table(s) reports the transcript levels of the experiment (see EXPT ID: Zinc (relating to SMD 7310, SMD 7311)). For transcripts that had higher levels in the samples than the control, a “+” is shown. A “−” is shown for when transcript levels were reduced in root tips as compared to the control. For more experimental detail see the Example section below. 
     Zinc genes are those sequences that showed differential expression as compared to controls, namely those sequences identified in the MA_diff tables with a “+” or “−” indication. 
     Zinc Genes Identified by Cluster Analyses of Differential Expression 
     Zinc Genes Identified by Correlation to Genes that are Differentially Expressed 
     As described above, the transcription profiles of genes that act together are well correlated. Applicants not only have identified the genes that are differentially expressed in the microarray experiments, but also have identified the genes that act in concert with them. The MA_clust table indicates groups of genes that have well correlated transcription profiles and therefore participate in the same pathway or network. 
     A pathway or network of Zinc genes is any group in the MA_clust that comprises a cDNA ID that also appears in Expt ID Zinc (relating to SMD 7310, SMD 7311) of the MA_diff table(s). 
     Zinc Genes Identified by Correlation to Genes that Cause Physiological Consequences 
     Additionally, the differential expression data and the phenotypic observations can be merged to identify pathways or networks of Zinc genes. A group in the MA_clust is considered a Zinc pathway or network if the group comprises a cDNA ID that also appears in Knock-in or Knock-out tables that causes one or more of the phenotypes described in section above. 
     Zinc Genes Identified by Amino Acid Sequence Similarity 
     Zinc genes from other plant species typically encode polypeptides that share amino acid similarity to the sequences encoded by corn and  Arabidopsis  Zinc genes. Groups of Zinc genes are identified in the Protein Group table. In this table, any protein group that comprises a peptide ID that corresponds to a cDNA ID member of a Zinc pathway or network is a group of proteins that also exhibits Zinc functions/utilities. 
     III.E.17.a. Use of Zn Transport, Tolerance and Nutrition-Related Genes to Modulate Phenotypes 
     Changes in zinc concentration in the surrounding environment or in contact with a plant results in modulation of many genes and gene products. Examples of such zinc responsive genes and gene products are shown in the Reference, Sequence tables, Protein Group, Protein Group Matrix, MA_diff, and MA_clust tables. These genes and/or products are responsible for effects on traits such as plant vigor and seed yield. 
     While zinc responsive polynucleotides and gene products can act alone, combinations of these polynucleotides also affect growth and development. Useful combinations include different zinc responsive polynucleotides and/or gene products that have similar transcription profiles or similar biological activities, and members of the same or similar biochemical pathways. In addition, the combination of a zinc responsive polynucleotide and/or gene product with another environmentally responsive polynucleotide is also useful because of the interactions that exist between hormone-regulated pathways, stress pathways, nutritional pathways and development. Here, in addition to polynucleotides having similar transcription profiles and/or biological activities, useful combinations include polynucleotides that may have different transcription profiles but which participate in a common pathway. 
     Such zinc responsive genes and gene products can function to either increase or dampen the above phenotypes or activities either
         in response to changes in zinc concentration or   in the absence of zinc fluctuations.       

     Zn transport, tolerance and nutrition-related genes and gene products can be used to alter or modulate one or more phenotypes including Zn uptake; transport of Zn or other heavy metals into roots; epidermal/cortical uptake; Xylem loading; Zn compartmentation; Xylem unloading; Phloem loading; efflux from cells to apoplast; sequestration in vacuoles/subcellular compartments; Zn tolerance; chelation of Zn; transport of Zn; metabolic and transcriptional control; activity of Zn binding enzymes; and activity of Zn binding transcription factors. 
     To improve any of the phenotype(s) above, activities of one or more of the Zn transport, tolerance and nutrition-related genes or gene products can be modulated and the plants can be tested by screening for the desired trait. Specifically, the gene, mRNA levels, or protein levels can be altered in a plant utilizing the procedures described herein and the phenotypes can be assayed, for example, in accordance to Lasat M M, Pence N S, Garvin D F, Ebbs S D, Kochian L V. J Exp Bot. 2000 January; 51(342):71-9; Grotz N, Fox T, Connolly E, Park W, Guerinot M L, Eide D. Proc Natl Acad Sci USA. 1998 Jun. 9; 95(12):7220-4; Crowder M W, Maiti M K, Banovic L, Makaroff C A. FEBS Lett. 1997 Dec. 1; 418(3):351-4; Hart J J, Norvell W A, Welch R M, Sullivan L A, Kochian L V. Plant Physiol. 1998 September; 118(1):219-26. 
     III.E.17.b. Use of Zn Transport, Tolerance and Nutrition-Related Genes to Modulate Biochemical Activities 
     Alternatively, the activities of one or more of the zinc responsive genes can be modulated to change biochemical or metabolic activities and/or pathways such as those noted below. Such biological activities can be measured according to the citations included in the Table below: 
     
       
         
           
               
               
               
             
               
                   
               
               
                   
                 BIOCHEMICAL OR 
                   
               
               
                   
                 METABOLIC 
               
               
                   
                 ACTIVITIES AND/OR 
                 CITATIONS INCLUDING 
               
               
                 PROCESS 
                 PATHWAYS 
                 ASSAYS 
               
               
                   
               
             
            
               
                 Zn Uptake and 
                 Zn Influx 
                 Lasat MM, Pence NS, Garvin DF, 
               
               
                 Assimilation 
                   
                 Ebbs SD, Kochian LV. J Exp Bot. 
               
               
                   
                   
                 2000 Jan; 51(342): 71-9. 
               
               
                   
                 Zn compartmentation 
                 Hart JJ, Norvell WA, Welch RM, 
               
               
                   
                   
                 Sullivan LA, Kochian LV. Plant 
               
               
                   
                   
                 Physiol. 1998 Sep; 118(1): 219-26. 
               
               
                 Zn binding by metabolic 
                   
                 Crowder MW, Maiti MK, Banovic L, 
               
               
                 enzymes 
                   
                 Makaroff CA. FEBS Lett. 1997 
               
               
                   
                   
                 Dec 1; 418(3): 351-4; Kenzior AL, 
               
               
                   
                   
                 Folk WR. FEBS Lett. 1998 Dec 
               
               
                   
                   
                 4; 440(3): 425-9. 
               
               
                 Zn binding by 
                   
                 Newton AL, Sharpe BK, Kwan A, 
               
               
                 transcription factors 
                   
                 Mackay JP, Crossley M. J Biol 
               
               
                   
                   
                 Chem. 2000May19; 275(20): 15128-34; 
               
               
                   
                   
                 Lopez Ribera I, Ruiz-Avila L, 
               
               
                   
                   
                 Puigdomenech P. Biochem Biophys 
               
               
                   
                   
                 Res Commun. 1997 Jul 
               
               
                   
                   
                 18; 236(2): 510-6; de Pater S, Greco V, 
               
               
                   
                   
                 Pham K, Memelink J, Kijne J. 
               
               
                   
                   
                 Nucleic Acids Res. 1996 Dec 
               
               
                   
                   
                 1; 24(23): 4624-31. 
               
               
                 Synthesis of proteins to 
                   
                 Schafer HJ, Greiner S, 
               
               
                 chelate Zn and other 
                   
                 Rausch T, Haag-Kerwer A. 
               
               
                 metals 
                   
                 FEBS Lett. 1997 Mar 
               
               
                   
                   
                 10; 404(2-3): 216-20. 
               
               
                   
                   
                 Rauser WE. Cell Biochem 
               
               
                   
                   
                 Biophys. 1999; 31(1): 19-48. 
               
               
                 Synthesis of metabolites 
                   
                 Rauser WE. Cell Biochem Biophys. 
               
               
                 to chelate Zn and other 
                   
                 1999; 31(1): 19-48. 
               
               
                 metals 
               
               
                   
               
            
           
         
       
     
     Other biological activities that can be modulated by Zn transport, tolerance and nutrition-related genes and their products are listed in the Reference tables. Assays for detecting such biological activities are described in the Protein Domain table. 
     Zn transport, tolerance and nutrition-related genes are differentially transcribed in response to low Zn concentrations. The microarray comparison consists of probes prepared from root RNA of  A. thaliana  (Columbia) seedlings hydroponically grown in complete nutrient medium (control) and Zn deficient seedlings grown in —Zn nutrient medium (experimental). The data from this experiment reveal a number of types genes and gene products. MA_diff table reports the changes in transcript levels of various zinc responsive genes in entire seedlings at 1 and 6 hours after a plant was sprayed with a Hoagland&#39;s solution enriched with zinc as compared to seedlings sprayed with Hoagland&#39;s solution only. 
     The data from this time course can be used to identify a number of types of zinc responsive genes and gene products, including “early responding,” “high zinc responders,” “repressors of zinc deprivation pathways” and “zinc deprivation responders.” Profiles of these different zinc responsive genes are shown in the Table below with examples of associated biological activities. 
                                                     EXAMPLES OF       TRANSCRIPT       PHYSIOLOGICAL   BIOCHEMICAL       LEVELS   TYPE OF GENE   CONSequence   ACTIVITY                  Upregulated   Early responders to   Zinc Perception   Transcription       transcripts (level at   Zinc   Zinc Uptake   Factors       1 hour ≅ 6 hours)       Modulation of Zinc   Transporters       (level at       Response Transduction       1 hour &gt; 6 hours)       Pathways               Specific Gene               Transcription Initiation           Zinc Deprivation   Repression of Pathways   Inhibit Transport of           Responders   to Optimize Zinc   Zinc               Response Pathways   Degradation       Level at   Delayed Zinc       Zinc Metabolic       1 hour &lt; 6 hours   Responders       Pathways           Repressor of Zinc   Negative Regulation of           Deprivation Pathways   Zinc Pathways       Down Regulated   Early responder   Negative Regulators of   Suppressing Zinc       transcripts (Level   repressors of Zinc   Zinc Utilization Pathways   Requiring processes       at 1 hour ≅ 6 hours)   utilization Pathways       (Level at       6 hours &gt; 1 hour)       Level at   Genes with   Changes in pathways and       1 hour &gt; 6 hours   discontinued   processes operating I cells           expression or           unsTable mRNA           following Zinc uptake                    
Use of Promoters of Zinc Responsive Genes
 
     Promoters of Zinc responsive genes are useful for transcription of any desired polynucleotide or plant or non-plant origin. Further, any desired sequence can be transcribed in a similar temporal, tissue, or environmentally specific patterns as the Zinc responsive genes where the desired sequence is operably linked to a promoter of a Zinc responsive gene. The protein product of such a polynucleotide is usually synthesized in the same cells, in response to the same stimuli as the protein product of the gene from which the promoter was derived. Such promoter are also useful to produce antisense mRNAs to down-regulate the product of proteins, or to produce sense mRNAs to down-regulate mRNAs via sense suppression. 
     IV. Utilities of Particular Interest 
     Genes capable of modulating the phenotypes in the following table are useful produce the associated utilities in the table. Such genes can be identified by their cDNA ID number in the Knock-in and Knock-out Tables. That is, those genes noted in those Tables to have a phenotype as listed in the following column entitled “Phenotype Modulated by a Gene” are useful for the purpose identified in the corresponding position in the column entitled “Utilities”. 
     
       
         
           
               
               
             
               
                   
               
               
                 Phenotype 
                   
               
               
                 Modulated by a 
               
               
                 Gene 
                 Utilities 
               
               
                   
               
             
            
               
                   
               
            
           
           
               
               
               
            
               
                 Leaf shape 
                 Cordate 
                 decrease wind opacity, 
               
               
                   
                 Cup-shaped 
                 decrease lodging (plant fall over), 
               
               
                   
                 Curled 
                 increase biomass by making larger or 
               
               
                   
                   
                 different shaped leaves, 
               
               
                   
                 Laceolate 
                 improve the efficiency of mechanical 
               
               
                   
                   
                 harvesting, 
               
               
                   
                 Lobed 
                 decrease transpiration for better drought 
               
               
                   
                   
                 tolerance, 
               
               
                   
                 Oval 
                 changing leaf shape to collect and absorb 
               
               
                   
                   
                 water, 
               
               
                   
                 Ovate 
                 modulation of canopy structure and shading 
               
               
                   
                   
                 for altered irradiance close to the ground, 
               
               
                   
                 Serrate 
                 enhanced uptake of pesticides (herbicides, 
               
               
                   
                   
                 fungicides, etc), 
               
               
                   
                 Trident 
                 creation of ornamental leaf shapes, 
               
               
                   
                 Undulate 
                 increase resistance to pathogens by 
               
               
                   
                   
                 decreasing amount of water that collects on 
               
               
                   
                   
                 leaves, 
               
               
                   
                 Vertically Oblong 
                 change proporation of cell types in the 
               
               
                   
                   
                 leaves for enhanced photosynthesis, 
               
               
                   
                   
                 decreased transpiration, and enhanced 
               
               
                   
                 Other Shapes 
                 accumulation of desirable compounds 
               
               
                   
                   
                 including secondary metabolites in 
               
               
                   
                   
                 specialized cells, 
               
               
                   
                   
                 decrease insect feeding, 
               
               
                   
                 Long petioles 
                 decrease wind opacity, 
               
               
                   
                 Short petioles 
                 decrease lodging (plant fall over), 
               
               
                   
                   
                 increase biomass by better positioning of 
               
               
                   
                   
                 the leaf blade, 
               
               
                   
                   
                 decrease insect feeding, 
               
               
                   
                   
                 decrease transpiration for better drought 
               
               
                   
                   
                 tolerance, 
               
               
                   
                   
                 position leaves most effectively for 
               
               
                   
                   
                 photosynthetic efficiency 
               
               
                   
                 Fused 
                 ornamental applications to make distinctive 
               
               
                   
                   
                 plants, 
               
               
                 Reduced fertility 
                 Short siliques 
                 increase or decrease the number of seeds in 
               
               
                   
                   
                 a fruit, 
               
               
                   
                   
                 increasing fruit size, 
               
               
                   
                   
                 modulating fruit shape to better fit 
               
               
                   
                   
                 harvesting or packaging requirements, 
               
               
                   
                   
                 useful for controlling dehisence and seed 
               
               
                   
                   
                 scatter 
               
               
                   
                 Reduced fertility 
                 useful in hybrid breeding programs, 
               
               
                   
                 Sterility 
                 increasing fruit size, 
               
               
                   
                   
                 production of seedless fruit, 
               
               
                   
                   
                 useful as targets for gametocides, 
               
               
                   
                   
                 modulating fruit shape to better fit 
               
               
                   
                   
                 harvesting or packaging requirements, 
               
               
                   
                   
                 useful for controlling dehisence and seed 
               
               
                   
                   
                 scatter 
               
               
                   
                 Flower size 
                 useful for edible flowers 
               
               
                   
                   
                 useful for flower derived products such as 
               
               
                   
                   
                 fragrances 
               
               
                   
                   
                 useful for modulating seed size and number 
               
               
                   
                   
                 in combination with seed-specific genes 
               
               
                   
                   
                 value in the ornamental industry 
               
               
                 Stature 
                 Large 
                 increasing or decreasing plant biomass, 
               
               
                   
                 Small 
                 optimizing plant stature to increase yield 
               
               
                   
                   
                 under various diverse environmental 
               
               
                   
                   
                 conditions, e.g., when water or nutrients 
               
               
                   
                   
                 are limiting, 
               
               
                   
                 Dwarfs 
                 decreasing lodging, 
               
               
                   
                   
                 increasing fruit number and size, 
               
               
                   
                   
                 controlling shading and canopy effects 
               
               
                 Meristems 
                   
                 Change plant architecture, 
               
               
                   
                   
                 increase or decrease number of leaves as 
               
               
                   
                   
                 well as change the types of leaves to 
               
               
                   
                   
                 increase biomass, 
               
               
                   
                   
                 improve photosynthetic efficiency, 
               
               
                   
                   
                 create new varieties of ornamental plants 
               
               
                   
                   
                 with enhanced leaf design, 
               
               
                   
                   
                 preventing flowering to opimize vegetative 
               
               
                   
                   
                 growth, 
               
               
                   
                   
                 control of apical dominace, 
               
               
                   
                   
                 increase or decrease flowering time to fit 
               
               
                   
                   
                 season, water or fertilizer schedules, 
               
               
                   
                   
                 change arrangement of leaves on the stem 
               
               
                   
                   
                 (phyllotaxy) to optimize plant density, 
               
               
                   
                   
                 decrease insect feeding, 
               
               
                   
                   
                 or decrease pathogen infection, 
               
               
                   
                   
                 increase number of trichome/glandular 
               
               
                   
                   
                 trichome producing leaves 
               
               
                   
                   
                 targets for herbicides, 
               
               
                   
                   
                 generate ectopic meristems and ectopic 
               
               
                   
                   
                 growth of vegetative and floral tissues and 
               
               
                   
                   
                 seeds and fruits 
               
               
                 Stem 
                 Strong 
                 modify lignin content/composition for 
               
               
                   
                   
                 creation of harder woods or reduce 
               
               
                   
                   
                 difficulty/costs in pulping for 
               
               
                   
                 Weak 
                 paper production or increase 
               
               
                   
                   
                 digestibility of forage crops, 
               
               
                   
                   
                 decrease lodging, 
               
               
                   
                   
                 modify cell wall polysaccharides in stems 
               
               
                   
                   
                 and fruits for improved texture and 
               
               
                   
                   
                 nutrition. 
               
               
                   
                   
                 increase biomass 
               
               
                   
                 Late/Early Bolting 
                 Break the need for long vernalization of 
               
               
                   
                   
                 vernalization-dependent crops, e.g., winter 
               
               
                   
                   
                 wheat, thereby increasing yield 
               
               
                   
                   
                 decrease or increase generaton time 
               
               
                   
                   
                 increase biomass 
               
               
                 Lethals 
                 Embryo-lethal 
                 produce seedless fruit, 
               
               
                   
                   
                 use as herbicide targets 
               
               
                   
                 Embryo-defective 
                 produce seedless fruit, 
               
               
                   
                   
                 use as herbicide targets 
               
               
                   
                 Seedling 
                 use as herbicide targets, 
               
               
                   
                   
                 useful for metabolic engineering, 
               
               
                   
                 Pigment-lethals 
                 use as herbicide targets, 
               
               
                   
                   
                 increase photosynthetic efficiency 
               
               
                 Pigment 
                 Dark Green 
                 Increase nutritional value, 
               
               
                   
                   
                 enhanced photosynthesis and carbon 
               
               
                   
                   
                 dioxide combustion and therefore increase 
               
               
                   
                   
                 plant vigor and biomass, 
               
               
                   
                   
                 enhanced photosynthetic efficiency and 
               
               
                   
                   
                 therefore increase plant vigor and biomass, 
               
               
                   
                   
                 prolong vegetative development, 
               
               
                   
                   
                 enhanced protection against pathogens, 
               
               
                   
                 YGV1 
                 Useful as targets for herbicides, 
               
               
                   
                   
                 increase photosynthetic efficiency and 
               
               
                   
                   
                 therefore increase plant vigor and biomass, 
               
               
                   
                 YGV2 
                 Useful as targets for herbicides, 
               
               
                   
                   
                 control of change from embryonic to adult 
               
               
                   
                   
                 organs, 
               
               
                   
                   
                 increase metabolic efficiency, 
               
               
                   
                   
                 increase photosynthetic efficiency and 
               
               
                   
                   
                 therefore increased plant vigor and biomass, 
               
               
                   
                 YGV3 
                 Useful as targets for herbicides, 
               
               
                   
                   
                 nitrogen sensing/uptake/usage, 
               
               
                   
                   
                 increase metabolic efficiency and therefore 
               
               
                   
                   
                 increased plant vigor and biomass, 
               
               
                   
                 Interveinal chlorosis 
                 to increase photosynthetic efficiency and 
               
               
                   
                   
                 therefore increase plant vigor and biomass 
               
               
                   
                   
                 to increase or decrease nitrogen transport 
               
               
                   
                   
                 and therefore increase plant vigor and 
               
               
                   
                   
                 biomass 
               
               
                   
                   
                 use as herbicide targets 
               
               
                   
                   
                 increase metabolic efficiency, 
               
               
                 Roots 
                 Short (primary root) 
                 to access water from rainfall, 
               
               
                   
                   
                 to access rhizobia spray application, for 
               
               
                   
                   
                 anaerobic soils, 
               
               
                   
                   
                 useful to facilitate harvest of root crops, 
               
               
                   
                 Thick (primary root) 
                 useful for increasing biomass of root crops, 
               
               
                   
                   
                 for preventing plants dislodging during 
               
               
                   
                   
                 picking and harvesting, 
               
               
                   
                   
                 as root grafts, for animal feeds 
               
               
                   
                 Branching (primary root) 
                 modulation allows betters access to water, 
               
               
                   
                   
                 minerals, fertilizers, rhizobia prevent soil 
               
               
                   
                   
                 erosion, s 
               
               
                   
                   
                 increasing root biomass 
               
               
                   
                   
                 decrease root lodging, 
               
               
                   
                 Long (lateral roots) 
                 modulation allows improved access to 
               
               
                   
                   
                 water, nutrients, fertilizer, rhizobia, prevent 
               
               
                   
                   
                 soil erosion 
               
               
                   
                   
                 increase root biomass 
               
               
                   
                   
                 decrease root lodging 
               
               
                   
                   
                 modulation allows control on the depth of 
               
               
                   
                   
                 root growth in soil to access water and 
               
               
                   
                   
                 nutriennts 
               
               
                   
                   
                 modulation allows hormonal control of root 
               
               
                   
                   
                 growth and development (size) 
               
               
                   
                 Agravitropic 
                 modulation allows control on the depth of 
               
               
                   
                   
                 root growth in soil 
               
               
                   
                 Curling (primary root) 
                 modulation allows hormonal control of root 
               
               
                   
                   
                 growth and development (size) 
               
               
                   
                   
                 useful in anaerobic soils in allowing roots 
               
               
                   
                   
                 to stay close to surface 
               
               
                   
                   
                 harvesting of root crops 
               
               
                   
                 Poor germination 
               
               
                 Trichome 
                 Reduced Number 
                 Genes useful for decreasing transpiration, 
               
               
                   
                 Glabrous 
                 increased production of glandular trichomes 
               
               
                   
                   
                 for oil or other secreted chemicals of value, 
               
               
                   
                 Increased Number 
                 use as deterrent for insect herbivory and 
               
               
                   
                   
                 ovipostion 
               
               
                   
                   
                 modulation will increase resistance to UV 
               
               
                   
                   
                 light, 
               
               
                 Wax mutants 
                   
                 decrease insect herbivory and oviposition, 
               
               
                   
                   
                 compostion changes for the cosmetics 
               
               
                   
                   
                 industry, 
               
               
                   
                   
                 decrease transpiration, 
               
               
                   
                   
                 provide pathogen resistance, 
               
               
                   
                   
                 UV protection, 
               
               
                   
                   
                 modulation of leaf runoff properties and 
               
               
                   
                   
                 improved access for herbicides and 
               
               
                   
                   
                 fertilizers 
               
               
                 Cotyledons 
                   
                 modulation of seeds structure in legumes, 
               
               
                   
                   
                 increase nutritional value, 
               
               
                   
                   
                 improve seedling competion under field 
               
               
                   
                   
                 conditions, 
               
               
                 Seeds 
                 Transparent testa 
                 genes useful for metabolic engineering 
               
               
                   
                   
                 anthocyanin and flavonoid pathways 
               
               
                   
                 Light 
                 improved nutritional content 
               
               
                   
                 Dark 
               
               
                   
                   
                 decrease petal abscission 
               
               
                 Flowers 
                 Other 
                 decrease pod shattering 
               
               
                 Hypocotysl 
                 Long 
                 to improve germination rates 
               
               
                   
                   
                 to improve plant survivability 
               
               
                   
                 Short 
                 to improve germination rates 
               
               
                   
                   
                 to improve plant survivability 
               
               
                   
               
            
           
         
       
     
     V. Enhanced Foods 
     Animals require external supplies of amino acids that they cannot synthesize themselves. Also, some amino acids are required in larger quantities. The nutritional values of plants for animals and humans can thus be modified by regulating the amounts of the constituent amino acids that occur as free amino acids or in proteins. For instance, higher levels of lysine and/or methionine would enhance the nutritional value of corn seed. Applicants herein provide several methods for modulating the amino acid content:
         (1) expressing a naturally occurring protein that has a high percentage of the desired amino acid(s);   (2) expressing a modified or synthetic coding sequence that has an enhanced percentage of the desired amino acids; or   (3) expressing the protein(s) that are capable of synthesizing more of the desired amino acids.
 
A specific example is expressing proteins with enhanced, for example, methionine content, preferentially in a corn or cereal seed used for animal nutrition or in the parts of plants used for nutritional purposes.
       

     A protein is considered to have a high percentage of an amino acid if the amount of the desired amino acid is at least 1% of the total number of residues in a protein; more preferably 2% or greater. Amino acids of particular interest are tryptophan, lysine, methionine, phenylalanine, threonine leucine, valine, and isoleucine. Examples of naturally occurring proteins with a high percentage of any one of the amino acid of particular interest are listed in the Enhanced Amino Acid Table. 
     The sequence(s) encoding the selected protein(s) are operably linked to a promoter and other regulatory sequences and transformed into a plant as described below. The promoter is chosen optimally for promoting the desired level of expression of the protein in the selected organ e.g. a promoter highly functional in seeds. Modifications may be made to the sequence encoding the protein to ensure protein transport into, for example, organelles or storage bodies or its accumulation in the organ. Such modifications may include addition of signal sequences at or near the N terminus and amino acid residues to modify protein stability or appropriate glycosylation. Other modifications may be made to the transcribed nucleic acid sequence to enhance the stability or translatability of the mRNA, in order to ensure accumulation of more of the desired protein. Suitable versions of the gene construct and transgenic plants are selected on the basis of, for example, the improved amino acid content and nutritional value measured by standard biochemical tests and animal feeding trials. 
     VI. Use of Novel Genes to Facilitate Exploitation of Plants as Factories for the Synthesis of Valuable Molecules 
     Plants and their constituent cells, tissues, and organs are factories that manufacture small organic molecules such as sugars, amino acids, fatty acids, vitamins, etc., as well as macromolecules such as proteins, nucleic acids, oils/fats and carbohydrates. Plants have long been a source of pharmaceutically beneficial chemicals; particularly, the secondary metabolites and hormone-related molecules synthesized by plants. Plants can also be used as factories to produce carbohydrates or lipids that comprises a carbon backbone useful as precursors of plastics, fiber, fuel, paper, pulp, rubber, solvents, lubricants, construction materials, detergents, and other cleaning materials. Plants can also generate other compounds that are of economic value, such as dyes, flavors, and fragrances. Both the intermediates as well as the end-products of plant bio-synthetic pathways have been found useful. 
     With the polynucleotides and polypeptides of the instant invention, modification of both in-vitro and in-vivo synthesis of such products is possible. One method of increasing the amount of either the intermediates or the end-products synthesized in a cell is to increase the expression of one or more proteins in the synthesis pathway as discussed below. Another method of increasing production of an intermediate is to inhibit expression of protein(s) that synthesize the end-product from the intermediate. Levels of end-products and intermediates can also be modified by changing the levels of enzymes that specifically change or degrade them. The kinds of molecules made can be also be modified by changing the genes encoding specific enzymes performing reactions at specific steps of the biosynthetic pathway. These genes can be from the same or a different organism. The molecular structures in the biosynthetic pathways can thus be modified or diverted into different branches of a pathway to make novel end-products. 
     Novel genes comprising selected promoters and sequences encoding enzymes are transformed into the selected plant to modify the levels, composition and/or structure of, without limitation:
         Terpenoids   Alkaloids   Hormones, including brassinosteriods   Flavonoids   Steroids   Vitamins such as
           Retinol   Riboflavin   Thiamine   
           Caffeine   Morphine and other alkaloids   Peptides and amino acid synthesis   Antioxidants   Starches and lipids   Fatty acids   Fructose, mannose and other sugars   Glycerolipid   Citric acid   Lignin   Flavors   Fragrances   Essential oils   Colors or dyes   Gum   Gels   Waxes       

     The modifications are made by designing one or more novel genes per application comprising promoters, to ensure production of the enzyme(s) in the relevant cells, in the right amount, and polynucleotides encoding the relevant enzyme. The promoters and polynucleotides are the subject of this application. The novel genes are transformed into the relevant species using standard procedures. Their effects are measured by standard assays for the specific chemical/biochemical products. 
     These polynucleotides and proteins of the invention that participate in the relevant pathways and are useful for changing production of the above chemicals and biochemicals are identified in the Reference tables by their enzyme function. More specifically, proteins of the invention that have the enzymatic activity of one of the entries in the following table entitled “Emzymes Effecting Modulation of Biological Pathways” are of interest to modulate the corresponding pathways to produce precursors or final products noted above that are of industrial use. Biological activities of particular interest are listed below. 
     Other polynucleotides and proteins that regulate where, when and to what extent a pathway is active in a plant are extremely useful for modulating the synthesis and accumulation of valuable chemicals. These elements including transcription factors, proteins involved in signal transduction and other proteins in the control of gene expression are described elsewhere in this application. 
     
       
         
           
               
               
               
             
               
                   
               
               
                 Pathway 
                   
                   
               
               
                 Name 
                 Enzyme Description 
                 Comments 
               
               
                   
               
             
            
               
                 Alkaloid 
                 Morphine 6- 
                 Also acts on other alkaloids, including codeine, 
               
               
                 biosynthesis I 
                 dehydrogenase 
                 normorphine and ethylmorphine, but only very 
               
               
                   
                   
                 slowly on 7,8-saturated derivatives such as 
               
               
                   
                   
                 dihydromorphine and dihydrocodeine In the 
               
               
                   
                   
                 reverse direction, also reduces naloxone to the 
               
               
                   
                   
                 6-alpha-hydroxy analog Activated by 2- 
               
               
                   
                   
                 mercaptoethanol 
               
               
                   
                 Codeinone reductase 
                 Stereospecifically catalyses the reversible 
               
               
                   
                 (NADPH) 
                 reduction of codeinone to codeine, which is a 
               
               
                   
                   
                 direct precursor of morphine in the opium 
               
               
                   
                   
                 poppy plant,  Papaver somniferum   
               
               
                   
                 Salutaridine reductase 
                 Stereospecifically catalyses the reversible 
               
               
                   
                 (NADPH) 
                 reduction of salutaridine to salutaridinol, which 
               
               
                   
                   
                 is a direct precursor of morphinan alkaloids in 
               
               
                   
                   
                 the poppy plant, Papaver somniferum 
               
               
                   
                 (S)-stylopine synthase 
                 Catalyses an oxidative reaction that does not 
               
               
                   
                   
                 incorporate oxygen into the product Forms the 
               
               
                   
                   
                 second methylenedioxy bridge of the 
               
               
                   
                   
                 protoberberine alkaloid stylopine from 
               
               
                   
                   
                 oxidative ring closure of adjacent phenolic and 
               
               
                   
                   
                 methoxy groups of cheilanthifoline 
               
               
                   
                 (S)-cheilanthifoline 
                 Catalyses an oxidative reaction that does not 
               
               
                   
                 synthase 
                 incorporate oxygen into the product Forms the 
               
               
                   
                   
                 methylenedioxy bridge of the protoberberine 
               
               
                   
                   
                 alkaloid cheilanthifoline from oxidative ring 
               
               
                   
                   
                 closure of adjacent phenolic and methoxy 
               
               
                   
                   
                 groups of scoulerine 
               
               
                   
                 Salutaridine synthase 
                 Forms the morphinan alkaloid salutaridine by 
               
               
                   
                   
                 intramolecular phenol oxidation of reticuline 
               
               
                   
                   
                 without the incorporation of oxygen into the 
               
               
                   
                   
                 product 
               
               
                   
                 (S)-canadine synthase 
                 Catalyses an oxidative reaction that does not 
               
               
                   
                   
                 incorporate oxygen into the product Oxidation 
               
               
                   
                   
                 of the methoxyphenol group of the alkaloid 
               
               
                   
                   
                 tetrahydrocolumbamine results in the 
               
               
                   
                   
                 formation of the methylenedioxy bridge of 
               
               
                   
                   
                 canadine 
               
               
                   
                 Protopine 6- 
                 Involved in benzophenanthridine alkaloid 
               
               
                   
                 monooxygenase 
                 synthesis in higher plants 
               
               
                   
                 Dihydrosanguinarine 
                 Involved in benzophenanthridine alkaloid 
               
               
                   
                 10-monooxygenase 
                 synthesis in higher plants 
               
               
                   
                 Monophenol 
                 A group of copper proteins that also catalyse 
               
               
                   
                 monooxygenase 
                 the reaction of EC 1.10.3.1, if only 1,2- 
               
               
                   
                   
                 benzenediols are available as substrate 
               
               
                   
                 L-amino acid oxidase 
               
               
                   
                 1,2-dehydroreticulinium 
                 Stereospecifically reduces the 1,2- 
               
               
                   
                 reductase (NADPH) 
                 dehydroreticulinium ion to (R)-reticuline, 
               
               
                   
                   
                 which is a direct precursor of morphinan 
               
               
                   
                   
                 alkaloids in the poppy plant, papaver 
               
               
                   
                   
                 somniferum The enzyme does not catalyse the 
               
               
                   
                   
                 reverse reaction to any significant extent under 
               
               
                   
                   
                 physiological conditions 
               
               
                   
                 Dihydrobenzo- 
                 Also catalyzes: dihydrochelirubine + O(2) = 
               
               
                   
                 phenanthridine oxidase 
                 chelirubine + H(2)O(2) Also catalyzes: 
               
               
                   
                   
                 dihydromacarpine + O(2) = macarpine + 
               
               
                   
                   
                 H(2)O(2) Found in higher plants Produces 
               
               
                   
                   
                 oxidized forms of the benzophenanthridine 
               
               
                   
                   
                 alkaloids 
               
               
                   
                 Reticuline oxidase 
                 The product of the reaction, (S)-scoulerine, is a 
               
               
                   
                   
                 precursor of protopine, protoberberine and 
               
               
                   
                   
                 benzophenanthridine alkaloid biosynthesis in 
               
               
                   
                   
                 plants Acts on (S)-reticuline and related 
               
               
                   
                   
                 compounds, converting the N-methyl group 
               
               
                   
                   
                 into the methylene bridge (‘berberine 
               
               
                   
                   
                 bridge[PRIME]) of (S)- 
               
               
                   
                   
                 tetrahydroprotoberberines 
               
               
                   
                 3[PRIME]-hydroxy-N- 
                 Involved in isoquinoline alkaloid metabolism 
               
               
                   
                 methyl-(S)-coclaurine 
                 in plants Has also been shown to catalyse the 
               
               
                   
                 4[PRIME]-O- 
                 methylation of (R,S)-laudanosoline, (S)- 
               
               
                   
                 methyltransferase 
                 3[PRIME]-hydroxycoclaurine and (R,S)-7-O- 
               
               
                   
                   
                 methylnoraudanosoline 
               
               
                   
                 (S)-scoulerine 9-O- 
                 The product of this reaction is a precursor for 
               
               
                   
                 methyltransferase 
                 protoberberine alkaloids in plants 
               
               
                   
                 Columbamine O- 
                 The product of this reaction is a protoberberine 
               
               
                   
                 methyltransferase 
                 alkaloid that is widely distributed in the plant 
               
               
                   
                   
                 kingdom Distinct in specificity from EC 
               
               
                   
                   
                 2.1.1.88 
               
               
                   
                 10-hydroxydihydro- 
                 Part of the pathway for synthesis of 
               
               
                   
                 sanguinarine 10-O- 
                 benzophenanthridine alkaloids in plants 
               
               
                   
                 methyltransferase 
               
               
                   
                 12-hydroxydi- 
                 Part of the pathway for synthesis of 
               
               
                   
                 hydrochelirubine 12-O- 
                 benzophenanthridine alkaloid macarpine in 
               
               
                   
                 methyltransferase 
                 plants 
               
               
                   
                 (R,S)-norcoclaurine 6- 
                 Norcoclaurine is 6,7-dihydroxy-1-[(4- 
               
               
                   
                 O-methyltransferase 
                 hydroxyphenyl)methyl]-1,2,3,4- 
               
               
                   
                   
                 tetrahydroisoquinoline The enzyme will also 
               
               
                   
                   
                 catalyse the 6-O-methylation of (R,S)- 
               
               
                   
                   
                 norlaudanosoline to form 6-O-methyl- 
               
               
                   
                   
                 norlaudanosoline, but this alkaloid has not 
               
               
                   
                   
                 been found to occur in plants 
               
               
                   
                 Salutaridinol 7-O- 
                 At higher pH values the product, 7-O- 
               
               
                   
                 acetyltransferase 
                 acetylsalutaridinol, spontaneously closes the 4-&gt; 
               
               
                   
                   
                 5 oxide bridge by allylic elimination to form 
               
               
                   
                   
                 the morphine precursor thebaine From the 
               
               
                   
                   
                 opium poppy plant, Papaver somniferum 
               
               
                   
                 Aspartate 
                 Also acts on L-tyrosine, L-phenylalanine and 
               
               
                   
                 aminotransferase 
                 L-tryptophan. This activity can be formed from 
               
               
                   
                   
                 EC 2.6.1.57 by controlled proteolysis 
               
               
                   
                 Tyrosine 
                 L-phenylalanine can act instead of L-tyrosine 
               
               
                   
                 aminotransferase 
                 The mitochondrial enzyme may be identical 
               
               
                   
                   
                 with EC 2.6.1.1 The three isoenzymic forms 
               
               
                   
                   
                 are interconverted by EC 3.4.22.4 
               
               
                   
                 Aromatic amino acid 
                 L-methionine can also act as donor, more 
               
               
                   
                 transferase 
                 slowly Oxaloacetate can act as acceptor 
               
               
                   
                   
                 Controlled proteolysis converts the enzyme to 
               
               
                   
                   
                 EC 2.6.1.1 
               
               
                   
                 Tyrosine decarboxylase 
                 The bacterial enzyme also acts on 3- 
               
               
                   
                   
                 hydroxytyrosine and, more slowly, on 3- 
               
               
                   
                   
                 hydroxyphenylalanine 
               
               
                   
                 Aromatic-L-amino-acid 
                 Also acts on L-tryptophan, 5-hydroxy-L- 
               
               
                   
                 decarboxylase 
                 tryptophan and dihydroxy-L-phenylalanine 
               
               
                   
                   
                 (DOPA) 
               
               
                 Alkaloid 
                 Tropine dehydrogenase 
                 Oxidizes other tropan-3-alpha-ols, but not the 
               
               
                 biosynthesis 
                   
                 corresponding beta-derivatives 
               
               
                 II 
               
               
                   
                 Tropinone reductase 
               
               
                   
                 Hyoscyamine (6S)- 
               
               
                   
                 dioxygenase 
               
               
                   
                 6-beta- 
               
               
                   
                 hydroxyhyoscyamine 
               
               
                   
                 epoxidase 
               
               
                   
                 Amine oxidase (copper- 
                 A group of enzymes including those oxidizing 
               
               
                   
                 containing) 
                 primary amines, diamines and histamine One 
               
               
                   
                   
                 form of EC 1.3.1.15 from rat kidney also 
               
               
                   
                   
                 catalyses this reaction 
               
               
                   
                 Putrescine N- 
               
               
                   
                 methyltransferase 
               
               
                   
                 Ornithine 
               
               
                   
                 decarboxylase 
               
               
                   
                 Oxalyl-CoA 
               
               
                   
                 decarboxylase 
               
               
                   
                 Phenylalanine 
                 May also act on L-tyrosine 
               
               
                   
                 ammonia-lyase 
               
               
                 Androgen and 
                 3-beta-hydroxy- 
                 Acts on 3-beta-hydroxyandrost-5-en-17-one to 
               
               
                 estrogen 
                 delta(5)-steroid 
                 form androst-4-ene-3,17-dione and on 3-beta- 
               
               
                 metabolism 
                 dehydrogenase 
                 hydroxypregn-5-en-20-one to form 
               
               
                   
                   
                 progesterone 
               
               
                   
                 11-beta-hydroxysteroid 
               
               
                   
                 dehydrogenase 
               
               
                   
                 Estradiol 17-alpha- 
               
               
                   
                 dehydrogenase 
               
               
                   
                 3-alpha-hydroxy-5- 
               
               
                   
                 beta-androstane-17-one 
               
               
                   
                 3-alpha-dehydrogenase 
               
               
                   
                 3-alpha (17-beta)- 
                 Also acts on other 17-beta-hydroxysteroids, on 
               
               
                   
                 hydroxysteroid 
                 the 3-alpha-hydroxy group of pregnanes and 
               
               
                   
                 dehydrogenase (NAD+) 
                 bile acids, and on benzene dihydrodiol 
               
               
                   
                   
                 Different from EC 1.1.1.50 or EC 1.1.1.213 
               
               
                   
                 3-alpha-hydroxysteroid 
                 Acts on other 3-alpha-hydroxysteroids and on 
               
               
                   
                 dehydrogenase (B- 
                 9-, 11- and 15-hydroxyprostaglandin B- 
               
               
                   
                 specific) 
                 specific with respect to NAD(+) or NADP(+) 
               
               
                   
                   
                 (cf. EC 1.1.1.213) 
               
               
                   
                 3(or 17)beta- 
                 Also acts on other 3-beta- or 17-beta- 
               
               
                   
                 hydroxysteroid 
                 hydroxysteroids (cf EC 1.1.1.209) 
               
               
                   
                 dehydrogenase 
               
               
                   
                 Estradiol 17 beta- 
                 Also acts on (S)-20-hydroxypregn-4-en-3-one 
               
               
                   
                 dehydrogenase 
                 and related compounds, oxidizing the (S)-20- 
               
               
                   
                   
                 group B-specific with respect to NAD(P)(+) 
               
               
                   
                 Testosterone 17-beta- 
               
               
                   
                 dehydrogenase 
               
               
                   
                 Testosterone 17-beta- 
                 Also oxidizes 3-hydroxyhexobarbital to 3- 
               
               
                   
                 dehydrogenase 
                 oxohexobarbital 
               
               
                   
                 (NADP+) 
               
               
                   
                 Steroid 11-beta- 
                 Also hydroxylates steroids at the 18-position, 
               
               
                   
                 monooxygenase 
                 and converts 18-hydroxycorticosterone into 
               
               
                   
                   
                 aldosterone 
               
               
                   
                 Estradiol 6-beta- 
               
               
                   
                 monooxygenase 
               
               
                   
                 Androst-4-ene-3,17- 
                 Has a wide specificity A single enzyme from 
               
               
                   
                 dione monooxygenase 
                 Cylindrocarpon radicicola (EC 1.14.13.54) 
               
               
                   
                   
                 catalyses both this reaction and that catalysed 
               
               
                   
                   
                 by EC 1.14.99.4 
               
               
                   
                 3-oxo-5-alpha-steroid 
               
               
                   
                 4-dehydrogenase 
               
               
                   
                 3-oxo-5-beta-steroid 4- 
               
               
                   
                 dehydrogenase 
               
               
                   
                 UDP- 
                 Family of enzymes accepting a wide range of 
               
               
                   
                 glucuronosyltransferase 
                 substrates, including phenols, alcohols, amines 
               
               
                   
                   
                 and fatty acids Some of the activities catalysed 
               
               
                   
                   
                 were previously listed separately as EC 
               
               
                   
                   
                 2.4.1.42, EC 2.4.1.59, EC 2.4.1.61, EC 
               
               
                   
                   
                 2.4.1.76, EC 2.4.1.77, EC 2.4.1.84, EC 
               
               
                   
                   
                 2.4.1.107 and EC 2.4.1.108 A temporary 
               
               
                   
                   
                 nomenclature for the various forms whose 
               
               
                   
                   
                 delineation is in a state of flux 
               
               
                   
                 Steroid sulfotransferase 
                 Broad specificity resembling EC 2.8.2.2, but 
               
               
                   
                   
                 also acts on estrone 
               
               
                   
                 Alcohol 
                 Primary and secondary alcohols, including 
               
               
                   
                 sulfotransferase 
                 aliphatic alcohols, ascorbate, chloramphenicol, 
               
               
                   
                   
                 ephedrine and hydroxysteroids, but not 
               
               
                   
                   
                 phenolic steroids, can act as acceptors (cf. EC 
               
               
                   
                   
                 2.8.2.15) 
               
               
                   
                 Estrone sulfotransferase 
               
               
                   
                 Arylsulfatase 
                 A group of enzymes with rather similar 
               
               
                   
                   
                 specificities 
               
               
                   
                 Steryl-sulfatase 
                 Also acts on some related steryl sulfates 
               
               
                   
                 17-alpha- 
               
               
                   
                 hydroxyprogesterone 
               
               
                   
                 aldolase 
               
               
                   
                 Steroid delta-isomerase 
               
               
                 C21-Steroid 
                 3-beta-hydroxy- 
                 Acts on 3-beta-hydroxyandrost-5-en-17-one to 
               
               
                 hormone 
                 delta(5)-steroid 
                 form androst-4-ene-3,17-dione and on 3-beta- 
               
               
                 metabolism 
                 dehydrogenase 
                 hydroxypregn-5-en-20-one to form 
               
               
                   
                   
                 progesterone 
               
               
                   
                 11-beta-hydroxysteroid 
               
               
                   
                 dehydrogenase 
               
               
                   
                 20-alpha- 
                 A-specific with respect to NAD(P)(+) 
               
               
                   
                 hydroxysteroid 
               
               
                   
                 dehydrogenase 
               
               
                   
                 3-alpha-hydroxysteroid 
                 Acts on other 3-alpha-hydroxysteroids and on 
               
               
                   
                 dehydrogenase (B- 
                 9-, 11- and 15-hydroxyprostaglandin B- 
               
               
                   
                 specific) 
                 specific with respect to NAD(+) or NADP(+) 
               
               
                   
                   
                 (cf. EC 1.1.1.213) 
               
               
                   
                 3-alpha(or 20-beta)- 
                 The 3-alpha-hydroxyl group or 20-beta- 
               
               
                   
                 hydroxysteroid 
                 hydroxyl group of pregnane and androstane 
               
               
                   
                 dehydrogenase 
                 steroids can act as donors 
               
               
                   
                 Steroid 11-beta- 
                 Also hydroxylates steroids at the 18-position, 
               
               
                   
                 monooxygenase 
                 and converts 18-hydroxycorticosterone into 
               
               
                   
                   
                 aldosterone 
               
               
                   
                 Corticosterone 18- 
               
               
                   
                 monooxygenase 
               
               
                   
                 Cholesterol 
                 The reaction proceeds in three stages, with 
               
               
                   
                 monooxygenase (side- 
                 hydroxylation at C-20 and C-22 preceding 
               
               
                   
                 chain cleaving) 
                 scission of the side-chain at C-20 
               
               
                   
                 Steroid 21- 
               
               
                   
                 monooxygenase 
               
               
                   
                 Progesterone 11-alpha- 
               
               
                   
                 monooxygenase 
               
               
                   
                 Steroid 17-alpha- 
               
               
                   
                 monooxygenase 
               
               
                   
                 Cholestenone 5-beta- 
               
               
                   
                 reductase 
               
               
                   
                 Cortisone beta- 
               
               
                   
                 reductase 
               
               
                   
                 Progesterone 5-alpha- 
                 Testosterone and 20-alpha-hydroxy-4-pregnen- 
               
               
                   
                 reductase 
                 3-one can act in place of progesterone 
               
               
                   
                 3-oxo-5-beta-steroid 4- 
               
               
                   
                 dehydrogenase 
               
               
                   
                 Steroid delta-isomerase 
               
               
                 Flavonoids, 
                 Coniferyl-alcohol 
                 Specific for coniferyl alcohol; does not act on 
               
               
                 stilbene and 
                 dehydrogenase 
                 cinnamyl alcohol, 4-coumaryl alcohol or 
               
               
                 lignin 
                   
                 sinapyl alcohol 
               
               
                 biosynthesis 
               
               
                   
                 Cinnamyl-alcohol 
                 Acts on coniferyl alcohol, sinapyl alcohol, 4- 
               
               
                   
                 dehydrogenase 
                 coumaryl alcohol and cinnamyl alcohol (cf. EC 
               
               
                   
                   
                 1.1.1.194) 
               
               
                   
                 Dihydrokaempferol 4- 
                 Also acts, in the reverse direction, on (+)- 
               
               
                   
                 reductase 
                 dihydroquercetin and (+)-dihydromyricetin 
               
               
                   
                   
                 Each dihydroflavonol is reduced to the 
               
               
                   
                   
                 corresponding cis-flavon-3,4-diol NAD(+) can 
               
               
                   
                   
                 act instead of NADP(+), more slowly Involved 
               
               
                   
                   
                 in the biosynthesis of anthocyanidins in plants 
               
               
                   
                 Flavonone 4-reductase 
                 Involved in the biosynthesis of 3- 
               
               
                   
                   
                 deoxyanthocyanidins from flavonones such as 
               
               
                   
                   
                 naringenin or eriodictyol 
               
               
                   
                 Peroxidase 
               
               
                   
                 Caffeate 3,4- 
               
               
                   
                 dioxygenase 
               
               
                   
                 Naringenin 3- 
               
               
                   
                 dioxygenase 
               
               
                   
                 Trans-cinnamate 4- 
                 Also acts on NADH, more slowly 
               
               
                   
                 monooxygenase 
               
               
                   
                 Trans-cinnamate 2- 
               
               
                   
                 monooxygenase 
               
               
                   
                 Flavonoid 3[PRIME]- 
                 Acts on a number of flavonoids, including 
               
               
                   
                 monooxygenase 
                 naringenin and dihydrokaempferol Does not 
               
               
                   
                   
                 act on 4-coumarate or 4-coumaroyl-CoA 
               
               
                   
                 Monophenol 
                 A group of copper proteins that also catalyse 
               
               
                   
                 monooxygenase 
                 the reaction of EC 1.10.3.1, if only 1,2- 
               
               
                   
                   
                 benzenediols are available as substrate 
               
               
                   
                 Cinnamoyl-CoA 
                 Also acts on a number of substituted 
               
               
                   
                 reductase 
                 cinnamoyl esters of coenzyme A 
               
               
                   
                 Caffeoyl-CoA O- 
               
               
                   
                 methyltransferase 
               
               
                   
                 Luteolin O- 
                 Also acts on luteolin-7-O-beta-D-glucoside 
               
               
                   
                 methyltransferase 
               
               
                   
                 Caffeate O- 
                 3,4-dihydroxybenzaldehyde and catechol can 
               
               
                   
                 methyltransferase 
                 act as acceptor, more slowly 
               
               
                   
                 Apigenin 4[PRIME]-O- 
                 Converts apigenin into acacetin Naringenin 
               
               
                   
                 methyltransferase 
                 (5,7,4[PRIME]-trihydroxyflavonone) can also 
               
               
                   
                   
                 act as acceptor, more slowly 
               
               
                   
                 Quercetin 3-O- 
                 Specific for quercetin. Related enzymes bring 
               
               
                   
                 methyltransferase 
                 about the 3-O-methylation of other flavonols, 
               
               
                   
                   
                 such as galangin and kaempferol 
               
               
                   
                 Isoflavone-7-O-beta- 
                 The 6-position of the glucose residue of 
               
               
                   
                 glucoside 
                 formononetin can also act as acceptor Some 
               
               
                   
                 6[PRIME][PRIME]-O- 
                 other 7-O-glucosides of isoflavones, flavones 
               
               
                   
                 malonyltransferase 
                 and flavonols can also act, more slowly 
               
               
                   
                 Pinosylvin synthase 
                 Not identical with EC 2.3.1.74 or EC 2.3.1.95 
               
               
                   
                 Naringenin-chalcone 
                 In the presence of NADH and a reductase, 
               
               
                   
                 synthase 
                 6[PRIME]-deoxychalcone is produced 
               
               
                   
                 Trihydroxystilbene 
                 Not identical with EC 2.3.1.74 or EC 2.3.1.146 
               
               
                   
                 synthase 
               
               
                   
                 Quinate O- 
                 Caffeoyl-CoA and 4-coumaroyl-CoA can also 
               
               
                   
                 hydroxycinnamoyltransferase 
                 act as donors, more slowly Involved in the 
               
               
                   
                   
                 biosynthesis of chlorogenic acid in sweet 
               
               
                   
                   
                 potato and, with EC 2.3.1.98 in the formation 
               
               
                   
                   
                 of caffeoyl-CoA in tomato 
               
               
                   
                 Coniferyl-alcohol 
                 Sinapyl alcohol can also act as acceptor 
               
               
                   
                 glucosyltransferase 
               
               
                   
                 2-coumarate O-beta- 
                 Coumarinate (cis-2-hydroxycinnamate) does 
               
               
                   
                 glucosyltransferase 
                 not act as acceptor 
               
               
                   
                 Scopoletin 
               
               
                   
                 glucosyltransferase 
               
               
                   
                 Flavonol-3-O-glucoside 
                 Converts flavonol 3-O-glucosides to 3-O- 
               
               
                   
                 L-rhamnosyltransferase 
                 rutinosides Also acts, more slowly, on rutin, 
               
               
                   
                   
                 quercetin 3-O-galactoside and flavonol O3- 
               
               
                   
                   
                 rhamnosides 
               
               
                   
                 Flavone 7-O-beta- 
                 A number of flavones, flavonones and 
               
               
                   
                 glucosyltransferase 
                 flavonols can function as acceptors Different 
               
               
                   
                   
                 from EC 2.4.1.91 
               
               
                   
                 Flavonol 3-O- 
                 Acts on a variety of flavonols, including 
               
               
                   
                 glucosyltransferase 
                 quercetin and quercetin 7-O-glucoside 
               
               
                   
                   
                 Different from EC 2.4.1.81 
               
               
                   
                 Flavone 
                 7-O-beta-D-glucosides of a number of 
               
               
                   
                 apiosyltransferase 
                 flavonoids and of 4-substituted phenols can act 
               
               
                   
                   
                 as acceptors 
               
               
                   
                 Coniferin beta- 
                 Also hydrolyzes syringin, 4-cinnamyl alcohol 
               
               
                   
                 glucosidase 
                 beta-glucoside, and, more slowly, some other 
               
               
                   
                   
                 aryl beta-glycosides A plant cell-wall enzyme 
               
               
                   
                   
                 involved in the biosynthesis of lignin 
               
               
                   
                 Beta-glucosidase 
                 Wide specificity for beta-D-glucosides. Some 
               
               
                   
                   
                 examples also hydrolyse one or more of the 
               
               
                   
                   
                 following: beta-D-galactosides, alpha-L- 
               
               
                   
                   
                 arabinosides, beta-D-xylosides, and beta-D- 
               
               
                   
                   
                 fucosides 
               
               
                   
                 Chalcone isomerase 
               
               
                   
                 4-coumarate--CoA 
               
               
                   
                 ligase 
               
               
                   
               
            
           
         
       
     
     
       
         
           
               
               
               
             
               
                   
               
               
                 Pathway Name 
                 Enzyme Description 
                 Enzyme Comments 
               
               
                   
               
             
            
               
                 Ascorbate and aldarate 
                 D-threo-aldose 1- 
                 Acts on L-fucose, D-arabinose and L- 
               
               
                 metabolism 
                 dehydrogenase 
                 xylose The animal enzyme was also 
               
               
                   
                   
                 shown to act on L-arabinose, and the 
               
               
                   
                   
                 enzyme from  Pseudomonas caryophyllion   
               
               
                   
                   
                 L-glucose 
               
               
                   
                 L-threonate 3- 
               
               
                   
                 dehydrogenase 
               
               
                   
                 Glucuronate reductase 
                 Also reduces D-galacturonate May be 
               
               
                   
                   
                 identical with EC 1.1.1.2 
               
               
                   
                 Glucuronolactone 
               
               
                   
                 reductase 
               
               
                   
                 L-arabinose 1- 
               
               
                   
                 dehydrogenase 
               
               
                   
                 L-galactonolactone 
                 Acts on the 1,4-lactones of L-galactonic, 
               
               
                   
                 oxidase 
                 D-altronic, L-fuconic, D-arabinic and D- 
               
               
                   
                   
                 threonic acids Not identical with EC 
               
               
                   
                   
                 1.1.3.8 (cf. EC 1.3.2.3) 
               
               
                   
                 L-gulonolactone 
                 The product spontaneously isomerizes to 
               
               
                   
                 oxidase 
                 L-ascorbate 
               
               
                   
                 L-ascorbate oxidase 
               
               
                   
                 L-ascorbate peroxidase 
               
               
                   
                 Ascorbate 2,3- 
               
               
                   
                 dioxygenase 
               
               
                   
                 2,5-dioxovalerate 
               
               
                   
                 dehydrogenase 
               
               
                   
                 Aldehyde 
                 Wide specificity, including oxidation of 
               
               
                   
                 dehydrogenase (NAD+) 
                 D-glucuronolactone to D-glucarate 
               
               
                   
                 Galactonolactone 
                 Cf. EC 1.1.3.24 
               
               
                   
                 dehydrogenase 
               
               
                   
                 Monodehydroascorbate 
               
               
                   
                 reductase (NADH) 
               
               
                   
                 Glutathione 
               
               
                   
                 dehydrogenase 
               
               
                   
                 (ascorbate) 
               
               
                   
                 L-arabinonolactonase 
               
               
                   
                 Gluconolactonase 
                 Acts on a wide range of hexono-1,5- 
               
               
                   
                   
                 lactones 
               
               
                   
                 Uronolactonase 
               
               
                   
                 1,4-lactonase 
                 Specific for 1,4-lactones with 4-8 carbon 
               
               
                   
                   
                 atoms Does not hydrolyse simple 
               
               
                   
                   
                 aliphatic esters, acetylcholine, sugar 
               
               
                   
                   
                 lactones or substituted aliphatic lactones, 
               
               
                   
                   
                 e.g. 3-hydroxy-4-butyrolactone 
               
               
                   
                 2-dehydro-3- 
               
               
                   
                 deoxyglucarate aldolase 
               
               
                   
                 L-arabinonate 
               
               
                   
                 dehydratase 
               
               
                   
                 Glucarate dehydratase 
               
               
                   
                 5-dehydro-4- 
               
               
                   
                 deoxyglucarate 
               
               
                   
                 dehydratase 
               
               
                   
                 Galactarate dehydratase 
               
               
                   
                 2-dehydro-3-deoxy-L- 
               
               
                   
                 arabinonate 
               
               
                   
                 dehydratase 
               
               
                 Carbon fixation 
                 Malate dehydrogenase 
                 Also oxidizes some other 2- 
               
               
                   
                   
                 hydroxydicarboxylic acids 
               
               
                   
                 Malate dehydrogenase 
                 Does not decarboxylates added 
               
               
                   
                 (decarboxylating) 
                 oxaloacetate 
               
               
                   
                 Malate dehydrogenase 
                 Also decarboxylates added oxaloacetate 
               
               
                   
                 (oxaloacetate 
               
               
                   
                 decarboxylating) 
               
               
                   
                 (NADP+) 
               
               
                   
                 Malate dehydrogenase 
                 Activated by light 
               
               
                   
                 (NADP+) 
               
               
                   
                 Glyceraldehyde-3- 
               
               
                   
                 phosphate 
               
               
                   
                 dehydrogenase 
               
               
                   
                 (NADP+) 
               
               
                   
                 (phosphorylating) 
               
               
                   
                 Transketolase 
                 Wide specificity for both reactants, e.g. 
               
               
                   
                   
                 converts hydroxypyruvate and R—CHO 
               
               
                   
                   
                 into CO(2) and R—CHOH—CO—CH(2)OH 
               
               
                   
                   
                 Transketolase from  Alcaligenes faecalis   
               
               
                   
                   
                 shows high activity with D-erythrose as 
               
               
                   
                   
                 acceptor 
               
               
                   
                 Aspartate 
                 Also acts on L-tyrosine, L-phenylalanine 
               
               
                   
                 aminotransferase 
                 and L-tryptophan. This activity can be 
               
               
                   
                   
                 formed from EC 2.6.1.57 by controlled 
               
               
                   
                   
                 proteolysis 
               
               
                   
                 Alanine 
                 2-aminobutanoate acts slowly instead of 
               
               
                   
                 aminotransferase 
                 alanine 
               
               
                   
                 Sedoheptulokinase 
               
               
                   
                 Phosphoribulokinase 
               
               
                   
                 Pyruvate kinase 
                 UTP, GTP, CTP, ITP and dATP can also 
               
               
                   
                   
                 act as donors Also phosphorylates 
               
               
                   
                   
                 hydroxylamine and fluoride in the 
               
               
                   
                   
                 presence of CO(2) 
               
               
                   
                 Phosphoglycerate 
               
               
                   
                 kinase 
               
               
                   
                 Pyruvate, phosphate 
               
               
                   
                 dikinase 
               
               
                   
                 Fructose- 
                 The animal enzyme also acts on 
               
               
                   
                 bisphosphatase 
                 sedoheptulose 1,7-bisphosphate 
               
               
                   
                 Sedoheptulose- 
               
               
                   
                 bisphosphatase 
               
               
                   
                 Phosphoenolpyruvate 
               
               
                   
                 carboxylase 
               
               
                   
                 Ribulose-bisphosphate 
                 Will utilize O(2) instead of CO(2), 
               
               
                   
                 carboxylase 
                 forming 3-phospho-D-glycerate and 2- 
               
               
                   
                   
                 phosphoglycolate 
               
               
                   
                 Phosphoenolpyruvate 
               
               
                   
                 carboxykinase (ATP) 
               
               
                   
                 Fructose-bisphosphate 
                 Also acts on (3S,4R)-ketose 1-phosphates 
               
               
                   
                 aldolase 
                 The yeast and bacterial enzymes are zinc 
               
               
                   
                   
                 proteins The enzymes increase electron- 
               
               
                   
                   
                 attraction by the carbonyl group, some 
               
               
                   
                   
                 (Class I) forming a protonated imine with 
               
               
                   
                   
                 it, others (Class II), mainly of microbial 
               
               
                   
                   
                 origin, polarizing it with a metal ion, e.g 
               
               
                   
                   
                 zinc 
               
               
                   
                 Phosphoketolase 
               
               
                   
                 Ribulose-phosphate 3- 
                 Also converts D-erythrose 4-phosphate 
               
               
                   
                 epimerase 
                 into D-erythrulose 4-phosphate and D- 
               
               
                   
                   
                 threose 4-phosphate 
               
               
                   
                 Triosephosphate 
               
               
                   
                 isomerase 
               
               
                   
                 Ribose 5-phosphate 
                 Also acts on D-ribose 5-diphosphate and 
               
               
                   
                 epimerase 
                 D-ribose 5-triphosphate 
               
               
                 Phenylalanine 
                 (R)-4- 
                 Also acts, more slowly, on (R)-3- 
               
               
                 metabolism 
                 hydroxyphenyllactate 
                 phenyllactate, (R)-3-(indole-3-yl)lactate 
               
               
                   
                 dehydrogenase 
                 and (R)-lactate 
               
               
                   
                 Hydroxyphenyl- 
                 Also acts on 3-(3,4- 
               
               
                   
                 pyruvate reductase 
                 dihydroxyphenyl)lactate Involved with 
               
               
                   
                   
                 EC 2.3.1.140 in the biosynthesis of 
               
               
                   
                   
                 rosmarinic acid 
               
               
                   
                 Aryl-alcohol 
                 A group of enzymes with broad 
               
               
                   
                 dehydrogenase 
                 specificity towards primary alcohols with 
               
               
                   
                   
                 an aromatic or cyclohex-1-ene ring, but 
               
               
                   
                   
                 with low or no activity towards short- 
               
               
                   
                   
                 chain aliphatic alcohols 
               
               
                   
                 Peroxidase 
               
               
                   
                 Catechol 1,2- 
                 Involved in the metabolism of nitro- 
               
               
                   
                 dioxygenase 
                 aromatic compounds by a strain of 
               
               
                   
                   
                 
                   Pseudomonas putida 
                 
               
               
                   
                 2,3-dihydroxybenzoate 
               
               
                   
                 3,4-dioxygenase 
               
               
                   
                 3-carboxyethylcatechol 
               
               
                   
                 2,3-dioxygenase 
               
               
                   
                 Catechol 2,3- 
                 The enzyme from Alcaligines sp. strain 
               
               
                   
                 dioxygenase 
                 O-1 has also been shown to catalyse the 
               
               
                   
                   
                 reaction: 3-Sulfocatechol + O(2) + H(2)O = 
               
               
                   
                   
                 2-hydroxymuconate + bisulfite. It has 
               
               
                   
                   
                 been referred to as 3-sulfocatechol 2,3- 
               
               
                   
                   
                 dioxygenase. Further work will be 
               
               
                   
                   
                 necessary to show whether or not this is a 
               
               
                   
                   
                 distinct enzyme 
               
               
                   
                 4- 
               
               
                   
                 hydroxyphenylpyruvate 
               
               
                   
                 dioxygenase 
               
               
                   
                 Protocatechuate 3,4- 
               
               
                   
                 dioxygenase 
               
               
                   
                 Hydroxyquinol 1,2- 
                 The product isomerizes to 2- 
               
               
                   
                 dioxygenase 
                 maleylacetate (cis-hex-2-enedioate) 
               
               
                   
                   
                 Highly specific; catechol and pyrogallol 
               
               
                   
                   
                 are acted on at less than 1% of the rate at 
               
               
                   
                   
                 which benzene-1,2,4-triol is oxidized 
               
               
                   
                 Protocatechuate 4,5- 
               
               
                   
                 dioxygenase 
               
               
                   
                 Phenylalanine 2- 
                 Also catalyses a reaction similar to that 
               
               
                   
                 monooxygenase 
                 of EC 1.4.3.2, forming 3-phenylpyruvate, 
               
               
                   
                   
                 NH(3) and H(2)O(2), but more slowly 
               
               
                   
                 Anthranilate 1,2- 
               
               
                   
                 dioxygenase 
               
               
                   
                 (deaminating, 
               
               
                   
                 decarboxylating) 
               
               
                   
                 Benzoate 1,2- 
                 A system, containing a reductase which 
               
               
                   
                 dioxygenase 
                 is an iron-sulfur flavoprotein (FAD), and 
               
               
                   
                   
                 an iron-sulfur oxygenase 
               
               
                   
                 Toluene dioxygenase 
                 A system, containing a reductase which 
               
               
                   
                   
                 is an iron-sulfur flavoprotein (FAD), an 
               
               
                   
                   
                 iron-sulfur oxygenase, and a ferredoxin 
               
               
                   
                   
                 Some other aromatic compounds, 
               
               
                   
                   
                 including ethylbenzene, 4-xylene and 
               
               
                   
                   
                 some halogenated toluenes, are converted 
               
               
                   
                   
                 into the corresponding cis-dihydrodiols 
               
               
                   
                 Naphthalene 1,2- 
                 A system, containing a reductase which 
               
               
                   
                 dioxygenase 
                 is an iron-sulfur flavoprotein (FAD), an 
               
               
                   
                   
                 iron-sulfur oxygenase, and ferredoxin 
               
               
                   
                 Benzene 1,2- 
                 A system, containing a reductase which 
               
               
                   
                 dioxygenase 
                 is an iron-sulfur flavoprotein, an iron- 
               
               
                   
                   
                 sulfur oxygenase and ferredoxin 
               
               
                   
                 Salicylate 1- 
               
               
                   
                 monooxygenase 
               
               
                   
                 Trans-cinnamate 4- 
                 Also acts on NADH, more slowly 
               
               
                   
                 monooxygenase 
               
               
                   
                 Benzoate 4- 
               
               
                   
                 monooxygenase 
               
               
                   
                 4-hydroxybenzoate 3- 
                 Most enzymes from  Pseudomonas  are 
               
               
                   
                 monooxygenase 
                 highly specific for NAD(P)H (cf EC 
               
               
                   
                   
                 1.14.13.33) 
               
               
                   
                 3-hydroxybenzoate 4- 
                 Also acts on a number of analogs of 3- 
               
               
                   
                 monooxygenase 
                 hydroxybenzoate substituted in the 2, 4, 5 
               
               
                   
                   
                 and 6 positions 
               
               
                   
                 3-hydroxybenzoate 6- 
                 Also acts on a number of analogs of 3- 
               
               
                   
                 monooxygenase 
                 hydroxybenzoate substituted in the 2, 4, 5 
               
               
                   
                   
                 and 6 positions NADPH can act instead 
               
               
                   
                   
                 of NADH, more slowly 
               
               
                   
                 4-hydroxybenzoate 3- 
                 The enzyme from  Corynebacterium   
               
               
                   
                 monooxygenase 
                   cyclohexanicum  is highly specific for 4- 
               
               
                   
                 (NAD(P)H) 
                 hydroxybenzoate, but uses NADH and 
               
               
                   
                   
                 NADPH at approximately equal rates (cf. 
               
               
                   
                   
                 EC 1.14.13.2). It is less specific for 
               
               
                   
                   
                 NADPH than EC 1.14.13.2 
               
               
                   
                 Anthranilate 3- 
                 The enzyme from  Aspergillus niger  is an 
               
               
                   
                 monooxygenase 
                 iron protein; that from the yeast 
               
               
                   
                 (deaminating) 
                   Trichosporon cutaneum  is a flavoprotein 
               
               
                   
                   
                 (FAD) 
               
               
                   
                 Melilotate 3- 
               
               
                   
                 monooxygenase 
               
               
                   
                 Phenol 2- 
                 Also active with resorcinol and O-cresol 
               
               
                   
                 monooxygenase 
               
               
                   
                 Mandelate 4- 
               
               
                   
                 monooxygenase 
               
               
                   
                 3-hydroxybenzoate 2- 
               
               
                   
                 monooxygenase 
               
               
                   
                 4-cresol dehydrogenase 
                 Phenazine methosulfate can act as 
               
               
                   
                 (hydroxylating) 
                 acceptor A quinone methide is probably 
               
               
                   
                   
                 formed as intermediate The product is 
               
               
                   
                   
                 oxidized further to 4-hydroxybenzoate 
               
               
                   
                 Benzaldehyde 
               
               
                   
                 dehydrogenase (NAD+) 
               
               
                   
                 Aminomuconate- 
                 Also acts on 2-hydroxymuconate 
               
               
                   
                 semialdehyde 
                 semialdehyde 
               
               
                   
                 dehydrogenase 
               
               
                   
                 Phenylacetaldehyde 
               
               
                   
                 dehydrogenase 
               
               
                   
                 4-carboxy-2- 
                 Does not act on unsubstituted aliphatic or 
               
               
                   
                 hydroxymuconate-6- 
                 aromatic aldehydes or glucose NAD(+) 
               
               
                   
                 semialdehyde 
                 can replace NADP(+), but with lower 
               
               
                   
                 dehydrogenase 
                 affinity 
               
               
                   
                 Aldehyde 
               
               
                   
                 dehydrogenase 
               
               
                   
                 (NAD(P)+) 
               
               
                   
                 Benzaldehyde 
               
               
                   
                 dehydrogenase 
               
               
                   
                 (NADP+) 
               
               
                   
                 Coumarate reductase 
               
               
                   
                 Cis-1,2- 
               
               
                   
                 dihydrobenzene-1,2- 
               
               
                   
                 diol dehydrogenase 
               
               
                   
                 Cis-1,2-dihydro-1,2- 
                 Also acts, at half the rate, on cis- 
               
               
                   
                 dihydroxynaphthalene 
                 anthracene dihydrodiol and cis- 
               
               
                   
                 dehydrogenase 
                 phenanthrene dihydrodiol 
               
               
                   
                 2-enoate reductase 
                 Acts, in the reverse direction, on a wide 
               
               
                   
                   
                 range of alkyl and aryl alpha,beta- 
               
               
                   
                   
                 unsaturated carboxylate ions 2-butenoate 
               
               
                   
                   
                 was the best substrate tested 
               
               
                   
                 Maleylacetate reductase 
               
               
                   
                 Phenylalanine 
                 The enzyme from  Bacillus badius  and 
               
               
                   
                 dehydrogenase 
                 Sporosarcina ureae are highly specific for 
               
               
                   
                   
                 L-phenylalanine, that from  Bacillus   
               
               
                   
                   
                   sphaericus  also acts on L-tyrosine 
               
               
                   
                 L-amino acid oxidase 
               
               
                   
                 Amine oxidase (flavin- 
                 Acts on primary amines, and usually also 
               
               
                   
                 containing) 
                 on secondary and tertiary amines 
               
               
                   
                 Amine oxidase (copper- 
                 A group of enzymes including those 
               
               
                   
                 containing) 
                 oxidizing primary amines, diamines and 
               
               
                   
                   
                 histamine One form of EC 1.3.1.15 from 
               
               
                   
                   
                 rat kidney also catalyses this reaction 
               
               
                   
                 D-amino-acid 
                 Acts to some extent on all D-amino acids 
               
               
                   
                 dehydrogenase 
                 except D-aspartate and D-glutamate 
               
               
                   
                 Aralkylamine 
                 Phenazine methosulfate can act as 
               
               
                   
                 dehydrogenase 
                 acceptor Acts on aromatic amines and, 
               
               
                   
                   
                 more slowly, on some long-chain 
               
               
                   
                   
                 aliphatic amines, but not on methylamine 
               
               
                   
                   
                 or ethylamine (cf EC 1.4.99.3) 
               
               
                   
                 Glutamine N- 
               
               
                   
                 phenylacetyltransferase 
               
               
                   
                 Acetyl-CoA C- 
               
               
                   
                 acyltransferase 
               
               
                   
                 D-amino-acid N- 
               
               
                   
                 acetyltransferase 
               
               
                   
                 Phenylalanine N- 
                 Also acts, more slowly, on L-histidine 
               
               
                   
                 acetyltransferase 
                 and L-alanine 
               
               
                   
                 Glycine N- 
                 Not identical with EC 2.3.1.13 or EC 
               
               
                   
                 benzoyltransferase 
                 2.3.1.68 
               
               
                   
                 Aspartate 
                 Also acts on L-tyrosine, L-phenylalanine 
               
               
                   
                 aminotransferase 
                 and L-tryptophan. This activity can be 
               
               
                   
                   
                 formed from EC 2.6.1.57 by controlled 
               
               
                   
                   
                 proteolysis 
               
               
                   
                 D-alanine 
                 Acts on the D-isomers of leucine, 
               
               
                   
                 aminotransferase 
                 aspartate, glutamate, aminobutyrate, 
               
               
                   
                   
                 norvaline and asparagine 
               
               
                   
                 Tyrosine 
                 L-phenylalanine can act instead of L- 
               
               
                   
                 aminotransferase 
                 tyrosine The mitochondrial enzyme may 
               
               
                   
                   
                 be identical with EC 2.6.1.1 The three 
               
               
                   
                   
                 isoenzymic forms are interconverted by 
               
               
                   
                   
                 EC 3.4.22.4 
               
               
                   
                 Aromatic amino acid 
                 L-methionine can also act as donor, more 
               
               
                   
                 transferase 
                 slowly Oxaloacetate can act as acceptor 
               
               
                   
                   
                 Controlled proteolysis converts the 
               
               
                   
                   
                 enzyme to EC 2.6.1.1 
               
               
                   
                 Histidinol-phosphate 
               
               
                   
                 aminotransferase 
               
               
                   
                 3-oxoadipate CoA- 
               
               
                   
                 transferase 
               
               
                   
                 3-oxoadipate enol- 
                 Acts on the product of EC 4.1.1.44 
               
               
                   
                 lactonase 
               
               
                   
                 Carboxymethylene- 
               
               
                   
                 butenolidase 
               
               
                   
                 2-pyrone-4,6- 
                 The product isomerizes to 4- 
               
               
                   
                 dicarboxylate lactonase 
                 oxalmesaconate 
               
               
                   
                 Hippurate hydrolase 
                 Acts on various N-benzoylamino acids 
               
               
                   
                 Amidase 
               
               
                   
                 Acylphosphatase 
               
               
                   
                 2-hydroxymuconate- 
               
               
                   
                 semialdehyde hydrolase 
               
               
                   
                 Aromatic-L-amino-acid 
                 Also acts on L-tryptophan, 5-hydroxy-L- 
               
               
                   
                 decarboxylase 
                 tryptophan and dihydroxy-L- 
               
               
                   
                   
                 phenylalanine (DOPA) 
               
               
                   
                 Phenylpyruvate 
                 Also acts on indole-3-pyruvate 
               
               
                   
                 decarboxylase 
               
               
                   
                 4-carboxymucono- 
               
               
                   
                 lactone decarboxylase 
               
               
                   
                 O-pyrocatechuate 
               
               
                   
                 decarboxylase 
               
               
                   
                 Phenylalanine 
                 Also acts on tyrosine and other aromatic 
               
               
                   
                 decarboxylase 
                 amino acids 
               
               
                   
                 4-hydroxybenzoate 
               
               
                   
                 decarboxylase 
               
               
                   
                 Protocatechuate 
               
               
                   
                 decarboxylase 
               
               
                   
                 Benzoylformate 
               
               
                   
                 decarboxylase 
               
               
                   
                 4-oxalocrotonate 
                 Involved in the meta-cleavage pathway 
               
               
                   
                 decarboxylase 
                 for the degradation of phenols, cresols 
               
               
                   
                   
                 and catechols 
               
               
                   
                 4-hydroxy-4-methyl-2- 
                 Also acts on 4-hydroxy-4-methyl-2- 
               
               
                   
                 oxoglutarate aldolase 
                 oxoadipate and 4-carboxy-4-hydroxy-2- 
               
               
                   
                   
                 oxohexadioate 
               
               
                   
                 2-oxopent-4-enoate 
                 Also acts, more slowly, on cis-2-oxohex- 
               
               
                   
                 hydratase 
                 4-enoate, but not on the trans-isomer 
               
               
                   
                 Phenylalanine 
                 May also act on L-tyrosine 
               
               
                   
                 ammonia-lyase 
               
               
                   
                 Phenylalanine racemase 
               
               
                   
                 (ATP-hydrolysing) 
               
               
                   
                 Mandelate racemase 
               
               
                   
                 Phenylpyruvate 
                 Also acts on other arylpyruvates 
               
               
                   
                 tautomerase 
               
               
                   
                 5-carboxymethyl-2- 
               
               
                   
                 hydroxymuconate 
               
               
                   
                 delta-isomerase 
               
               
                   
                 Muconolactone delta- 
               
               
                   
                 isomerase 
               
               
                   
                 Muconate 
                 Also acts, in the reverse reaction, on 3- 
               
               
                   
                 cycloisomerase 
                 methyl-cis-cis-hexa-dienedioate and, 
               
               
                   
                   
                 very slowly, on cis-trans-hexadienedioate 
               
               
                   
                   
                 Not identical with EC 5.5.1.7 or EC 
               
               
                   
                   
                 5.5.1.11 
               
               
                   
                 3-carboxy-cis,cis- 
               
               
                   
                 muconate 
               
               
                   
                 cycloisomerase 
               
               
                   
                 Carboxy-cis,cis- 
               
               
                   
                 muconate cyclase 
               
               
                   
                 Chloromuconate 
                 Spontaneous elimination of HCl produces 
               
               
                   
                 cycloisomerase 
                 cis-4-carboxymethylenebut-2-en-4-olide 
               
               
                   
                   
                 Also acts in reverse direction on 2- 
               
               
                   
                   
                 chloro-cis,cis-muconate Not identical 
               
               
                   
                   
                 with EC 5.5.1.1 or EC 5.5.1.11 
               
               
                   
                 Phenylacetate--CoA 
                 Phenoxyacetate can replace phenylacetate 
               
               
                   
                 ligase 
               
               
                   
                 Benzoate--CoA ligase 
                 Also acts on 2-, 3- and 4-fluorobenzoate, 
               
               
                   
                   
                 but only very slowly on the 
               
               
                   
                   
                 corresponding chlorobenzoates 
               
               
                   
                 4-hydroxybenzoate-- 
               
               
                   
                 CoA ligase 
               
               
                   
                 Phenylacetate--CoA 
                 Also acts, more slowly, on acetate, 
               
               
                   
                 ligase 
                 propanoate and butanoate, but not on 
               
               
                   
                   
                 hydroxy derivatives of phenylacetate and 
               
               
                   
                   
                 related compounds 
               
               
                 Phenylalanine, tyrosine 
                 Quinate 5- 
               
               
                 and tryptophan biosynthesis 
                 dehydrogenase 
               
               
                   
                 Shikimate 5- 
               
               
                   
                 dehydrogenase 
               
               
                   
                 Quinate dehydrogenase 
               
               
                   
                 (pyrroloquinoline- 
               
               
                   
                 quinone) 
               
               
                   
                 Phenylalanine 4- 
               
               
                   
                 monooxygenase 
               
               
                   
                 Prephenate 
                 This enzyme in the enteric bacteria also 
               
               
                   
                 dehydrogenase 
                 possesses chorismate mutase activity (EC 
               
               
                   
                   
                 5.4.99.5) and converts chorismate into 
               
               
                   
                   
                 prephenate 
               
               
                   
                 Prephenate 
               
               
                   
                 dehydrogenase 
               
               
                   
                 (NADP+) 
               
               
                   
                 Cyclohexadienyl 
                 Also acts on prephenate and D- 
               
               
                   
                 dehydrogenase 
                 prephenyllactate (cf. EC 1.3.1.12) 
               
               
                   
                 2-methyl-branched- 
                 From  Ascaris suum  The reaction 
               
               
                   
                 chain-enoyl-CoA 
                 proceeds only in the presence of another 
               
               
                   
                 reductase 
                 flavoprotein (ETF = [PRIME]Electron- 
               
               
                   
                   
                 Transferring Flavoprotein[PRIME]) 
               
               
                   
                 Phenylalanine 
                 The enzyme from  Bacillus badius  and 
               
               
                   
                 dehydrogenase 
                   Sporosarcina ureae  are highly specific for 
               
               
                   
                   
                 L-phenylalanine, that from  Bacillus   
               
               
                   
                   
                   sphaericus  also acts on L-tyrosine 
               
               
                   
                 L-amino acid oxidase 
               
               
                   
                 Anthranilate 
                 In some organisms, this enzyme is part of 
               
               
                   
                 phosphoribosyl- 
                 a multifunctional protein together with 
               
               
                   
                 transferase 
                 one or more components of the system 
               
               
                   
                   
                 for biosynthesis of tryptophan (EC 
               
               
                   
                   
                 4.1.1.48, EC 4.1.3.27, EC 4.2.1.20, and 
               
               
                   
                   
                 EC 5.3.1.24) 
               
               
                   
                 3-phosphoshikimate 1- 
               
               
                   
                 carboxyvinyl- 
               
               
                   
                 transferase 
               
               
                   
                 Aspartate 
                 Also acts on L-tyrosine, L-phenylalanine 
               
               
                   
                 aminotransferase 
                 and L-tryptophan. This activity can be 
               
               
                   
                   
                 formed from EC 2.6.1.57 by controlled 
               
               
                   
                   
                 proteolysis 
               
               
                   
                 Tyrosine 
                 L-phenylalanine can act instead of L- 
               
               
                   
                 aminotransferase 
                 tyrosine The mitochondrial enzyme may 
               
               
                   
                   
                 be identical with EC 2.6.1.1 The three 
               
               
                   
                   
                 isoenzymic forms are interconverted by 
               
               
                   
                   
                 EC 3.4.22.4 
               
               
                   
                 Aromatic amino acid 
                 L-methionine can also act as donor, more 
               
               
                   
                 transferase 
                 slowly Oxaloacetate can act as acceptor 
               
               
                   
                   
                 Controlled proteolysis converts the 
               
               
                   
                   
                 enzyme to EC 2.6.1.1 
               
               
                   
                 Histidinol-phosphate 
               
               
                   
                 aminotransferase 
               
               
                   
                 Shikimate kinase 
               
               
                   
                 Indole-3-glycerol- 
                 In some organisms, this enzyme is part of 
               
               
                   
                 phosphate synthase 
                 a multifunctional protein together with 
               
               
                   
                   
                 one or more components of the system 
               
               
                   
                   
                 for biosynthesis of tryptophan (EC 
               
               
                   
                   
                 2.4.2.18, EC 4.1.3.27, EC 4.2.1.20, and 
               
               
                   
                   
                 EC 5.3.1.24) 
               
               
                   
                 2-dehydro-3- 
               
               
                   
                 deoxyphosphoheptonate 
               
               
                   
                 aldolase 
               
               
                   
                 Anthranilate synthase 
                 In some organisms, this enzyme is part of 
               
               
                   
                   
                 a multifunctional protein together with 
               
               
                   
                   
                 one or more components of the system 
               
               
                   
                   
                 for biosynthesis of tryptophan (EC 
               
               
                   
                   
                 2.4.2.18, EC 4.1.1.48, EC 4.2.1.20, and 
               
               
                   
                   
                 EC 5.3.1.24) The native enzyme in the 
               
               
                   
                   
                 complex with uses either glutamine or 
               
               
                   
                   
                 (less efficiently) NH(3). The enzyme 
               
               
                   
                   
                 separated from the complex uses NH(3) 
               
               
                   
                   
                 only 
               
               
                   
                 3-dehydroquinate 
               
               
                   
                 dehydratase 
               
               
                   
                 Phosphopyruvate 
                 Also acts on 3-phospho-D-erythronate 
               
               
                   
                 hydratase 
               
               
                   
                 Tryptophan synthase 
                 Also catalyses the conversion of serine 
               
               
                   
                   
                 and indole into tryptophan and water and 
               
               
                   
                   
                 of indoleglycerol phosphate into indole 
               
               
                   
                   
                 and glyceraldehyde phosphate In some 
               
               
                   
                   
                 organisms, this enzyme is part of a 
               
               
                   
                   
                 multifunctional protein together with one 
               
               
                   
                   
                 or more components of the system for 
               
               
                   
                   
                 biosynthesis of tryptophan (EC 2.4.2.18, 
               
               
                   
                   
                 EC 4.1.1.48, EC 4.1.3.27, and EC 
               
               
                   
                   
                 5.3.1.24) 
               
               
                   
                 Prephenate dehydratase 
                 This enzyme in the enteric bacteria also 
               
               
                   
                   
                 possesses chorismate mutase activity and 
               
               
                   
                   
                 converts chorismate into prephenate 
               
               
                   
                 Carboxycyclohexadienyl 
                 Also acts on prephenate and D- 
               
               
                   
                 dehydratase 
                 prephenyllactate Cf. EC 4.2.1.51 
               
               
                   
                 3-dehydroquinate 
                 The hydrogen atoms on C-7 of the 
               
               
                   
                 synthase 
                 substrate are retained on C-2 of the 
               
               
                   
                   
                 products 
               
               
                   
                 Chorismate synthase 
                 Shikimate is numbered so that the 
               
               
                   
                   
                 double-bond is between C-1 and C-2, but 
               
               
                   
                   
                 some earlier papers numbered in the 
               
               
                   
                   
                 reverse direction 
               
               
                   
                 Phosphoribosylanthranilate 
                 In some organisms, this enzyme is part of 
               
               
                   
                 isomerase 
                 a multifunctional protein together with 
               
               
                   
                   
                 one or more components of the system 
               
               
                   
                   
                 for biosynthesis of tryptophan (EC 
               
               
                   
                   
                 2.4.2.18, EC 4.1.1.48, EC 4.1.3.27, and 
               
               
                   
                   
                 EC 4.2.1.20) 
               
               
                   
                 Chorismate mutase 
               
               
                   
                 Tyrosine--tRNA ligase 
               
               
                   
                 Phenylalanine--tRNA 
               
               
                   
                 ligase 
               
               
                 Starch and sucrose 
                 UDP-glucose 6- 
                 Also acts on UDP-2-deoxyglucose 
               
               
                 metabolism 
                 dehydrogenase 
               
               
                   
                 Glucoside 3- 
                 The enzyme acts on D-glucose, D- 
               
               
                   
                 dehydrogenase 
                 galactose, D-glucosides and D- 
               
               
                   
                   
                 galactosides, but D-glucosides react more 
               
               
                   
                   
                 rapidly than D-galactosides 
               
               
                   
                 CDP-4-dehydro-6- 
                 Two proteins are involved but no partial 
               
               
                   
                 deoxyglucose reductase 
                 reaction has been observed in the 
               
               
                   
                   
                 presence of either alone 
               
               
                   
                 Phosphorylase 
                 The recommended name should be 
               
               
                   
                   
                 qualified in each instance by adding the 
               
               
                   
                   
                 name of the natural substance, e.g. 
               
               
                   
                   
                 maltodextrin phosphorylase, starch 
               
               
                   
                   
                 phosphorylase, glycogen phosphorylase 
               
               
                   
                 Levansucrase 
                 Some other sugars can act as D-fructosyl 
               
               
                   
                   
                 acceptors 
               
               
                   
                 Glycogen (starch) 
                 The recommended name varies according 
               
               
                   
                 synthase 
                 to the source of the enzyme and the 
               
               
                   
                   
                 nature of its synthetic product Glycogen 
               
               
                   
                   
                 synthase from animal tissues is a 
               
               
                   
                   
                 complex of a catalytic subunit and the 
               
               
                   
                   
                 protein glycogenin The enzyme requires 
               
               
                   
                   
                 glucosylated glycogenin as a primer; this 
               
               
                   
                   
                 is the reaction product of EC 2.4.1.186 A 
               
               
                   
                   
                 similar enzyme utilizes ADP-glucose (Cf. 
               
               
                   
                   
                 EC 2.4.1.21) 
               
               
                   
                 Cellulose synthase 
                 Involved in the synthesis of cellulose A 
               
               
                   
                 (UDP-forming) 
                 similar enzyme utilizes GDP-glucose (Cf. 
               
               
                   
                   
                 EC 2.4.1.29) 
               
               
                   
                 Sucrose synthase 
               
               
                   
                 Sucrose-phosphate 
               
               
                   
                 synthase 
               
               
                   
                 Alpha,alpha-trehalose- 
                 See also EC 2.4.1.36 
               
               
                   
                 phosphate synthase 
               
               
                   
                 (UDP-forming) 
               
               
                   
                 UDP- 
                 Family of enzymes accepting a wide 
               
               
                   
                 glucuronosyltransferase 
                 range of substrates, including phenols, 
               
               
                   
                   
                 alcohols, amines and fatty acids Some of 
               
               
                   
                   
                 the activities catalysed were previously 
               
               
                   
                   
                 listed separately as EC 2.4.1.42, EC 
               
               
                   
                   
                 2.4.1.59, EC 2.4.1.61, EC 2.4.1.76, EC 
               
               
                   
                   
                 2.4.1.77, EC 2.4.1.84, EC 2.4.1.107 and 
               
               
                   
                   
                 EC 2.4.1.108 A temporary nomenclature 
               
               
                   
                   
                 for the various forms whose delineation 
               
               
                   
                   
                 is in a state of flux 
               
               
                   
                 1,4-alpha-glucan 
                 Converts amylose into amylopectin The 
               
               
                   
                 branching enzyme 
                 recommended name requires a 
               
               
                   
                   
                 qualification depending on the product, 
               
               
                   
                   
                 glycogen or amylopectin, e.g. glycogen 
               
               
                   
                   
                 branching enzyme, amylopectin 
               
               
                   
                   
                 branching enzyme. The latter has 
               
               
                   
                   
                 frequently been termed Q-enzyme 
               
               
                   
                 Cellobiose 
               
               
                   
                 phosphorylase 
               
               
                   
                 Starch (bacterial 
                 The recommended name various 
               
               
                   
                 glycogen) synthase 
                 according to the source of the enzyme 
               
               
                   
                   
                 and the nature of its synthetic product, 
               
               
                   
                   
                 e.g. starch synthase, bacterial glycogen 
               
               
                   
                   
                 synthase A similar enzyme utilizes UDP- 
               
               
                   
                   
                 glucose (Cf. EC 2.4.1.11) 
               
               
                   
                 4-alpha- 
                 An enzymic activity of this nature forms 
               
               
                   
                 glucanotransferase 
                 part of the mammalian and Yeast 
               
               
                   
                   
                 glycogen branching system (see EC 
               
               
                   
                   
                 3.2.1.33) 
               
               
                   
                 Cellulose synthase 
                 Involved in the synthesis of cellulose A 
               
               
                   
                 (GDP-forming) 
                 similar enzyme utilizes UDP-glucose (Cf. 
               
               
                   
                   
                 EC 2.4.1.12) 
               
               
                   
                 1,3-beta-glucan 
               
               
                   
                 synthase 
               
               
                   
                 Phenol beta- 
                 Acts on a wide range of phenols 
               
               
                   
                 glucosyltransferase 
               
               
                   
                 Amylosucrase 
               
               
                   
                 Polygalacturonate 4- 
               
               
                   
                 alpha- 
               
               
                   
                 galacturonosyltransferase 
               
               
                   
                 Dextransucrase 
               
               
                   
                 Alpha,alpha-trehalose 
               
               
                   
                 phosphorylase 
               
               
                   
                 Sucrose phosphorylase 
                 In the forward reaction, arsenate may 
               
               
                   
                   
                 replace phosphate In the reverse reaction 
               
               
                   
                   
                 various ketoses and L-arabinose may 
               
               
                   
                   
                 replace D-fructose 
               
               
                   
                 Maltose phosphorylase 
               
               
                   
                 1,4-beta-D-xylan 
               
               
                   
                 synthase 
               
               
                   
                 Hexokinase 
                 D-glucose, D-mannose, D-fructose, 
               
               
                   
                   
                 sorbitol and D-glucosamine can act as 
               
               
                   
                   
                 acceptors ITP and dATP can act as 
               
               
                   
                   
                 donors The liver isoenzyme has 
               
               
                   
                   
                 sometimes been called glucokinase 
               
               
                   
                 Phosphoglucokinase 
               
               
                   
                 Glucose-1,6- 
                 D-glucose 6-phosphate can act as 
               
               
                   
                 bisphosphate synthase 
                 acceptor, forming D-glucose 1,6- 
               
               
                   
                   
                 bisphosphate 
               
               
                   
                 Glucokinase 
                 A group of enzymes found in 
               
               
                   
                   
                 invertebrates and microorganisms highly 
               
               
                   
                   
                 specific for glucose 
               
               
                   
                 Fructokinase 
               
               
                   
                 Glucose-1-phosphate 
               
               
                   
                 phosphodismutase 
               
               
                   
                 Protein-N(PI)- 
                 Comprises a group of related enzymes 
               
               
                   
                 phosphohistidine-sugar 
                 The protein substrate is a phosphocarrier 
               
               
                   
                 phosphotransferase 
                 protein of low molecular mass (9.5 Kd) A 
               
               
                   
                   
                 phosphoenzyme intermediate is formed 
               
               
                   
                   
                 The enzyme translocates the sugar it 
               
               
                   
                   
                 phosphorylates into bacteria Aldohexoses 
               
               
                   
                   
                 and their glycosides and alditols are 
               
               
                   
                   
                 phosphorylated on O-6; fructose and 
               
               
                   
                   
                 sorbose on O-1 Glycerol and 
               
               
                   
                   
                 disaccharides are also substrates 
               
               
                   
                 Glucose-1-phosphate 
               
               
                   
                 adenylyltransferase 
               
               
                   
                 Glucose-1-phosphate 
               
               
                   
                 cytidylyltransferase 
               
               
                   
                 Glucose-1-phosphate 
                 Also acts, more slowly, on D-mannose 1- 
               
               
                   
                 guanylyltransferase 
                 phosphate 
               
               
                   
                 UTP--glucose-1- 
               
               
                   
                 phosphate 
               
               
                   
                 uridylyltransferase 
               
               
                   
                 Pectinesterase 
               
               
                   
                 Trehalose-phosphatase 
               
               
                   
                 Sucrose-phosphatase 
               
               
                   
                 Glucose-6-phosphatase 
                 Wide distribution in animal tissues Also 
               
               
                   
                   
                 catalyses potent transphosphorylations 
               
               
                   
                   
                 from carbamoyl phosphate, hexose 
               
               
                   
                   
                 phosphates, pyrophosphate, 
               
               
                   
                   
                 phosphoenolpyruvate and nucleoside di- 
               
               
                   
                   
                 and triphosphates, to D-glucose, D- 
               
               
                   
                   
                 mannose, 3-methyl-D-glucose, or 2- 
               
               
                   
                   
                 deoxy-D-glucose (cf. EC 2.7.1.62, EC 
               
               
                   
                   
                 2.7.1.79, and EC 3.9.1.1) 
               
               
                   
                 Alpha-amylase 
                 Acts on starch, glycogen and related 
               
               
                   
                   
                 polysaccharides and oligosaccharides in a 
               
               
                   
                   
                 random manner; reducing groups are 
               
               
                   
                   
                 liberated in the alpha-configuration 
               
               
                   
                 Oligo-1,6-glucosidase 
                 Also hydrolyses palatinose The enzyme 
               
               
                   
                   
                 from intestinal mucosa is a single 
               
               
                   
                   
                 polypeptide chain also catalysing the 
               
               
                   
                   
                 reaction of EC 3.2.1.48 
               
               
                   
                 Maltose-6[PRIME]- 
                 Hydrolyses a variety of 6-phospho-D- 
               
               
                   
                 phosphate glucosidase 
                 glucosides, including maltose 6- 
               
               
                   
                   
                 phosphate, alpha[PRIME]alpha-trehalose 
               
               
                   
                   
                 6-phosphate, sucrose 6-phosphate and p- 
               
               
                   
                   
                 nitrophenyl-alpha-D-glucopyranoside 6- 
               
               
                   
                   
                 phosphate (as a chromogenic substrate) 
               
               
                   
                   
                 The enzyme is activated by Fe(II), 
               
               
                   
                   
                 Mn(II), Co(II) and Ni(II). It is rapidly 
               
               
                   
                   
                 inactivated in air 
               
               
                   
                 Polygalacturonase 
               
               
                   
                 Beta-amylase 
                 Acts on starch, glycogen and related 
               
               
                   
                   
                 polysaccharides and oligosaccharides 
               
               
                   
                   
                 producing beta-maltose by an inversion 
               
               
                   
                 Alpha-glucosidase 
                 Group of enzymes whose specificity is 
               
               
                   
                   
                 directed mainly towards the 
               
               
                   
                   
                 exohydrolysis of 1,4-alpha-glucosidic 
               
               
                   
                   
                 linkages, and that hydrolyse 
               
               
                   
                   
                 oligosaccharides rapidly, relative to 
               
               
                   
                   
                 polysaccharides, which are hydrolysed 
               
               
                   
                   
                 relatively slowly, or not at all The 
               
               
                   
                   
                 intestinal enzyme also hydrolyses 
               
               
                   
                   
                 polysaccharides, catalysing the reactions 
               
               
                   
                   
                 of EC 3.2.1.3, and, more slowly, 
               
               
                   
                   
                 hydrolyses 1,6-alpha-D-glucose links 
               
               
                   
                 Beta-glucosidase 
                 Wide specificity for beta-D-glucosides. 
               
               
                   
                   
                 Some examples also hydrolyse one or 
               
               
                   
                   
                 more of the following: beta-D- 
               
               
                   
                   
                 galactosides, alpha-L-arabinosides, beta- 
               
               
                   
                   
                 D-xylosides, and beta-D-fucosides 
               
               
                   
                 Beta-fructofuranosidase 
                 Substrates include sucrose Also catalyses 
               
               
                   
                   
                 fructotransferase reactions 
               
               
                   
                 Alpha,alpha-trehalase 
               
               
                   
                 Glucan 1,4-alpha- 
                 Most forms of the enzyme can rapidly 
               
               
                   
                 glucosidase 
                 hydrolyse 1,6-alpha-D-glucosidic bonds 
               
               
                   
                   
                 when the next bond in sequence is 1,4, 
               
               
                   
                   
                 and some preparations of this enzyme 
               
               
                   
                   
                 hydrolyse 1,6- and 1,3-alpha-D- 
               
               
                   
                   
                 glucosidic bonds in other polysaccharides 
               
               
                   
                   
                 This entry covers all such enzymes acting 
               
               
                   
                   
                 on polysaccharides more rapidly than on 
               
               
                   
                   
                 oligosaccharides EC 3.2.1.20 from 
               
               
                   
                   
                 mammalian intestine can catalyse similar 
               
               
                   
                   
                 reactions 
               
               
                   
                 Beta-glucuronidase 
               
               
                   
                 Amylo-1,6-glucosidase 
                 In mammals and yeast this enzyme is 
               
               
                   
                   
                 linked to a glycosyltransferase similar to 
               
               
                   
                   
                 EC 2.4.1.25; together these two activities 
               
               
                   
                   
                 constitute the glycogen debranching 
               
               
                   
                   
                 system 
               
               
                   
                 Xylan 1,4-beta- 
                 Also hydrolyses xylobiose Some other 
               
               
                   
                 xylosidase 
                 exoglycosidase activities have been 
               
               
                   
                   
                 found associated with this enzyme in 
               
               
                   
                   
                 sheep liver 
               
               
                   
                 Glucan endo-1,3-beta- 
                 Very limited action on mixed-link (1,3- 
               
               
                   
                 D-glucosidase 
                 1,4-)-beta-D-glucans Hydrolyses 
               
               
                   
                   
                 laminarin, paramylon and pachyman 
               
               
                   
                   
                 Different from EC 3.2.1.6 
               
               
                   
                 Cellulase 
                 Will also hydrolyse 1,4-linkages in beta- 
               
               
                   
                   
                 D-glucans also containing 1,3-linkages 
               
               
                   
                 Sucrose alpha- 
                 This enzyme is isolated from intestinal 
               
               
                   
                 glucosidase 
                 mucosa as a single polypeptide chain also 
               
               
                   
                   
                 displaying activity towards isomaltose 
               
               
                   
                   
                 (oligo-1,6-glucosidase, cf. EC 3.2.1.10) 
               
               
                   
                 Cyclomaltodextrinase 
                 Also hydrolyses linear maltodextrin 
               
               
                   
                 Glucan 1,3-beta- 
                 Acts on oligosaccharides but very slowly 
               
               
                   
                 glucosidase 
                 on laminaribiose 
               
               
                   
                 Levanase 
               
               
                   
                 Galacturan 1,4-alpha- 
               
               
                   
                 galacturonidase 
               
               
                   
                 Glucan 1,4-beta- 
                 Acts on 1,4-beta-D-glucans and related 
               
               
                   
                 glucosidase 
                 oligosaccharides Cellobiose is 
               
               
                   
                   
                 hydrolysed, very slowly 
               
               
                   
                 Cellulose 1,4-beta- 
               
               
                   
                 cellobiosidase 
               
               
                   
                 Alpha,alpha- 
               
               
                   
                 phosphotrehalase 
               
               
                   
                 ADP-sugar 
                 Has a distinct specificity from the UDP- 
               
               
                   
                 diphosphatase 
                 sugar pyrophosphatase (EC 3.6.1.45) 
               
               
                   
                 Nucleotide 
                 Substrates include NAD(+), NADP(+), 
               
               
                   
                 pyrophosphatase 
                 FAD, CoA and also ATP and ADP 
               
               
                   
                 UDP-glucuronate 
               
               
                   
                 decarboxylase 
               
               
                   
                 CDP-glucose 4,6- 
               
               
                   
                 dehydratase 
               
               
                   
                 CDP-abequose 
               
               
                   
                 epimerase 
               
               
                   
                 UDP-glucuronate 4- 
               
               
                   
                 epimerase 
               
               
                   
                 Glucose-6-phosphate 
                 Also catalyses the anomerization of D- 
               
               
                   
                 isomerase 
                 glucose 6-phosphate 
               
               
                   
                 Phosphoglucomutase 
                 Maximum activity is only obtained in the 
               
               
                   
                   
                 presence of alpha-D-glucose 1,6- 
               
               
                   
                   
                 bisphosphate. This bisphosphate is an 
               
               
                   
                   
                 intermediate in the reaction, being 
               
               
                   
                   
                 formed by transfer of a phosphate residue 
               
               
                   
                   
                 from the enzyme to the substrate, but the 
               
               
                   
                   
                 dissociation of bisphosphate from the 
               
               
                   
                   
                 enzyme complex is much slower than the 
               
               
                   
                   
                 overall isomerization Also, more slowly, 
               
               
                   
                   
                 catalyses the interconversion of 1- 
               
               
                   
                   
                 phosphate and 6-phosphate isomers of 
               
               
                   
                   
                 many other alpha-D-hexoses, and the 
               
               
                   
                   
                 interconversion of alpha-D-ribose 1- 
               
               
                   
                   
                 phosphate and 5-phosphate 
               
               
                   
                 Beta- 
               
               
                   
                 phosphoglucomutase 
               
               
                   
                 Maltose alpha-D- 
               
               
                   
                 glucosyltransferase 
               
               
                 Tryptophan metabolism 
                 Indole-3-lactate 
               
               
                   
                 dehydrogenase 
               
               
                   
                 Indole-3-acetaldehyde 
               
               
                   
                 reductase (NADH) 
               
               
                   
                 Indole-3-acetaldehyde 
               
               
                   
                 reductase (NADPH) 
               
               
                   
                 3-hydroxyacyl-CoA 
                 Also oxidizes S-3-hydroxyacyl-N- 
               
               
                   
                 dehydrogenase 
                 acylthioethanolamine and S-3- 
               
               
                   
                   
                 hydroxyacylhydrolipoate Some enzymes 
               
               
                   
                   
                 act, more slowly, with NADP(+) Broad 
               
               
                   
                   
                 specificity to acyl chain-length (cf. EC 
               
               
                   
                   
                 1.1.1.211) 
               
               
                   
                 O-aminophenol oxidase 
                 Isophenoxazine may be formed by a 
               
               
                   
                   
                 secondary condensation from the initial 
               
               
                   
                   
                 oxidation product 
               
               
                   
                 Catalase 
                 This enzyme can also act as a peroxidase 
               
               
                   
                   
                 (EC 1.11.1.7) for which several organic 
               
               
                   
                   
                 substances, especially ethanol, can act as 
               
               
                   
                   
                 a hydrogen donor A manganese protein 
               
               
                   
                   
                 containing Mn(III) in the resting state, 
               
               
                   
                   
                 which also belongs here, is often called 
               
               
                   
                   
                 pseudocatalase Enzymes from some 
               
               
                   
                   
                 microorganisms, such as  Penicillium   
               
               
                   
                   
                   simplicissimum , which exhibit both 
               
               
                   
                   
                 catalase and peroxidase activity, have 
               
               
                   
                   
                 sometimes been referred to as catalase- 
               
               
                   
                   
                 peroxidase 
               
               
                   
                 7,8- 
               
               
                   
                 dihydroxykynurenate 
               
               
                   
                 8,8A-dioxygenase 
               
               
                   
                 Tryptophan 2,3- 
                 Broad specificity towards tryptamine and 
               
               
                   
                 dioxygenase 
                 derivatives including D- and L- 
               
               
                   
                   
                 tryptophan, 5-hydroxytryptophan and 
               
               
                   
                   
                 serotonin 
               
               
                   
                 Indole 2,3-dioxygenase 
                 The enzyme from jasminum is a 
               
               
                   
                   
                 flavoprotein containing copper, and 
               
               
                   
                   
                 forms anthranilate as the final product 
               
               
                   
                   
                 One enzyme from  Tecoma stans  is also a 
               
               
                   
                   
                 flavoprotein containing copper and uses 
               
               
                   
                   
                 three atoms of oxygen per molecule of 
               
               
                   
                   
                 indole, to form anthranil (3,4- 
               
               
                   
                   
                 benzisoxazole) A second enzyme from 
               
               
                   
                   
                   Tecoma stans , which is not a 
               
               
                   
                   
                 flavoprotein, uses four atoms of oxygen 
               
               
                   
                   
                 and forms anthranilate as the final 
               
               
                   
                   
                 product 
               
               
                   
                 2,3-dihydroxyindole 
               
               
                   
                 2,3-dioxygenase 
               
               
                   
                 Indoleamine-pyrrole 
                 Acts on many substituted and 
               
               
                   
                 2,3-dioxygenase 
                 unsubstituted indoleamines, including 
               
               
                   
                   
                 melatonin Involved in the degradation of 
               
               
                   
                   
                 melatonin 
               
               
                   
                 3-hydroxyanthranilate 
                 The product of the reaction 
               
               
                   
                 3,4-dioxygenase 
                 spontaneously rearrange to quinolinic 
               
               
                   
                   
                 acid (quin) 
               
               
                   
                 Tryptophan 2- 
               
               
                   
                 monooxygenase 
               
               
                   
                 Tryptophan 2[PRIME]- 
                 Acts on a number of indolyl-3-alkane 
               
               
                   
                 dioxygenase 
                 derivatives, oxidizing the 3-side-chain in 
               
               
                   
                   
                 the 2[PRIME]-position. Best substrates 
               
               
                   
                   
                 are L-tryptophan and 5-hydroxy-L- 
               
               
                   
                   
                 tryptophan 
               
               
                   
                 Kynurenine 3- 
               
               
                   
                 monooxygenase 
               
               
                   
                 Unspecific 
                 Acts on a wide range of substrates 
               
               
                   
                 monooxygenase 
                 including many xenobiotics, steroids, 
               
               
                   
                   
                 fatty acids, vitamins and prostaglandins 
               
               
                   
                   
                 Reactions catalysed include 
               
               
                   
                   
                 hydroxylation, epoxidation, N-oxidation, 
               
               
                   
                   
                 sulfooxidation, N-, S- and O- 
               
               
                   
                   
                 dealkylations, desulfation, deamination, 
               
               
                   
                   
                 and reduction of azo, nitro, and N-oxide 
               
               
                   
                   
                 groups 
               
               
                   
                 Anthranilate 3- 
               
               
                   
                 monooxygenase 
               
               
                   
                 Tryptophan 5- 
                 Activated by phosphorylation, catalysed 
               
               
                   
                 monooxygenase 
                 by a CA(2+)-activated protein kinase 
               
               
                   
                 Kynurenine 7,8- 
               
               
                   
                 hydroxylase 
               
               
                   
                 Aldehyde 
                 Wide specificity, including oxidation of 
               
               
                   
                 dehydrogenase (NAD+) 
                 D-glucuronolactone to D-glucarate 
               
               
                   
                 Aminomuconate- 
                 Also acts on 2-hydroxymuconate 
               
               
                   
                 semialdehyde 
                 semialdehyde 
               
               
                   
                 dehydrogenase 
               
               
                   
                 Aldehyde oxidase 
                 Also oxidizes quinoline and pyridine 
               
               
                   
                   
                 derivatives May be identical with EC 
               
               
                   
                   
                 1.1.3.22 
               
               
                   
                 Indole-3-acetaldehyde 
                 Also oxidizes indole-3-aldehyde and 
               
               
                   
                 oxidase 
                 acetaldehyde, more slowly 
               
               
                   
                 Oxoglutarate 
                 Component of the multienzyme 2- 
               
               
                   
                 dehydrogenase 
                 oxoglutarate dehydrogenase complex 
               
               
                   
                 (lipoamide) 
               
               
                   
                 Kynurenate-7,8- 
               
               
                   
                 dihydrodiol 
               
               
                   
                 dehydrogenase 
               
               
                   
                 Glutaryl-CoA 
               
               
                   
                 dehydrogenase 
               
               
                   
                 L-amino acid oxidase 
               
               
                   
                 Amine oxidase (flavin- 
                 Acts on primary amines, and usually also 
               
               
                   
                 containing) 
                 on secondary and tertiary amines 
               
               
                   
                 Amine oxidase (copper- 
                 A group of enzymes including those 
               
               
                   
                 containing) 
                 oxidizing primary amines, diamines and 
               
               
                   
                   
                 histamine One form of EC 1.3.1.15 from 
               
               
                   
                   
                 rat kidney also catalyses this reaction 
               
               
                   
                 Acetylindoxyl oxidase 
               
               
                   
                 Acetylserotonin O- 
                 Some other hydroxyindoles also act as 
               
               
                   
                 methyltransferase 
                 acceptor, more slowly 
               
               
                   
                 Indole-3-pyruvate C- 
               
               
                   
                 methyltransferase 
               
               
                   
                 Amine N- 
                 A wide range of primary, secondary, and 
               
               
                   
                 methyltransferase 
                 tertiary amines can act as acceptors, 
               
               
                   
                   
                 including tryptamine, aniline, nicotine 
               
               
                   
                   
                 and a variety of drugs and other 
               
               
                   
                   
                 xenobiotics 
               
               
                   
                 Aralkylamine N- 
                 Narrow specificity towards 
               
               
                   
                 acetyltransferase 
                 aralkylamines, including serotonin Not 
               
               
                   
                   
                 identical with EC 2.3.1.5 
               
               
                   
                 Acetyl-CoA C- 
               
               
                   
                 acetyltransferase 
               
               
                   
                 Tryptophan 
                 Also acts on 5-hydroxytryptophan and, to 
               
               
                   
                 aminotransferase 
                 a lesser extent on the phenyl amino acids 
               
               
                   
                 Kynurenine-- 
                 Also acts on 3-hydroxykynurenine 
               
               
                   
                 oxoglutarate 
               
               
                   
                 aminotransferase 
               
               
                   
                 Thioglucosidase 
                 Has a wide specificity for thioglycosides 
               
               
                   
                 Amidase 
               
               
                   
                 Formamidase 
                 Also acts, more slowly, on acetamide, 
               
               
                   
                   
                 propanamide and butanamide 
               
               
                   
                 Arylformamidase 
                 Also acts on other aromatic 
               
               
                   
                   
                 formylamines 
               
               
                   
                 Nitrilase 
                 Acts on a wide range of aromatic nitriles 
               
               
                   
                   
                 including (indole-3-yl)-acetonitrile and 
               
               
                   
                   
                 also on some aliphatic nitriles, and on the 
               
               
                   
                   
                 corresponding acid amides (cf. EC 
               
               
                   
                   
                 4.2.1.84) 
               
               
                   
                 Kynureninase 
                 Also acts on 3[PRIME]- 
               
               
                   
                   
                 hydroxykynurenine and some other (3- 
               
               
                   
                   
                 arylcarbonyl)-alanines 
               
               
                   
                 Aromatic-L-amino-acid 
                 Also acts on L-tryptophan, 5-hydroxy-L- 
               
               
                   
                 decarboxylase 
                 tryptophan and dihydroxy-L- 
               
               
                   
                   
                 phenylalanine (DOPA) 
               
               
                   
                 Phenylpyruvate 
                 Also acts on indole-3-pyruvate 
               
               
                   
                 decarboxylase 
               
               
                   
                 Aminocarboxymuconate- 
                 The product rearranges non-enzymically 
               
               
                   
                 semialdehyde 
                 to picolinate 
               
               
                   
                 decarboxylase 
               
               
                   
                 Tryptophanase 
                 Also catalyses the synthesis of 
               
               
                   
                   
                 tryptophan from indole and serine Also 
               
               
                   
                   
                 catalyses 2,3-elimination and beta- 
               
               
                   
                   
                 replacement reactions of some indole- 
               
               
                   
                   
                 substituted tryptophan analogs of L- 
               
               
                   
                   
                 cysteine, L-serine and other 3-substituted 
               
               
                   
                   
                 amino acids 
               
               
                   
                 Enoyl-CoA hydratase 
                 Acts in the reverse direction With cis- 
               
               
                   
                   
                 compounds, yields (3R)-3-hydroxyacyl- 
               
               
                   
                   
                 CoA (cf. EC 4.2.1.74) 
               
               
                   
                 Nitrile hydratase 
                 Acts on short-chain aliphatic nitriles, 
               
               
                   
                   
                 converting them into the corresponding 
               
               
                   
                   
                 acid amides Does not act on these amides 
               
               
                   
                   
                 or on aromatic nitriles (cf EC 3.5.5.1) 
               
               
                   
                 Tryptophan--tRNA 
               
               
                   
                 ligase 
               
               
                 Tyrosine metabolism 
                 Alcohol dehydrogenase 
                 Acts on primary or secondary alcohols or 
               
               
                   
                   
                 hemiacetals The animal, but not the 
               
               
                   
                   
                 yeast, enzyme acts also on cyclic 
               
               
                   
                   
                 secondary alcohols 
               
               
                   
                 (R)-4- 
                 Also acts, more slowly, on (R)-3- 
               
               
                   
                 hydroxyphenyllactate 
                 phenyllactate, (R)-3-(indole-3-yl)lactate 
               
               
                   
                 dehydrogenase 
                 and (R)-lactate 
               
               
                   
                 Hydroxyphenylpyruvate 
                 Also acts on 3-(3,4- 
               
               
                   
                 reductase 
                 dihydroxyphenyl)lactate Involved with 
               
               
                   
                   
                 EC 2.3.1.140 in the biosynthesis of 
               
               
                   
                   
                 rosmarinic acid 
               
               
                   
                 Aryl-alcohol 
                 A group of enzymes with broad 
               
               
                   
                 dehydrogenase 
                 specificity towards primary alcohols with 
               
               
                   
                   
                 an aromatic or cyclohex-1-ene ring, but 
               
               
                   
                   
                 with low or no activity towards short- 
               
               
                   
                   
                 chain aliphatic alcohols 
               
               
                   
                 Catechol oxidase 
                 Also acts on a variety of substituted 
               
               
                   
                   
                 catechols Many of these enzymes also 
               
               
                   
                   
                 catalyse the reaction listed under EC 
               
               
                   
                   
                 1.14.18.1; this is especially true for the 
               
               
                   
                   
                 classical tyrosinase 
               
               
                   
                 Iodide peroxidase 
               
               
                   
                 3,4- 
               
               
                   
                 dihydroxyphenylacetate 
               
               
                   
                 2,3-dioxygenase 
               
               
                   
                 4- 
               
               
                   
                 hydroxyphenylpyruvate 
               
               
                   
                 dioxygenase 
               
               
                   
                 Stizolobate synthase 
                 The intermediate product undergoes ring 
               
               
                   
                   
                 closure and oxidation, with NAD(P)(+) 
               
               
                   
                   
                 as acceptor, to stizolobic acid 
               
               
                   
                 Stizolobinate synthase 
                 The intermediate product undergoes ring 
               
               
                   
                   
                 closure and oxidation, with NAD(P)(+) 
               
               
                   
                   
                 as acceptor, to stizolobinic acid 
               
               
                   
                 Gentisate 1,2- 
               
               
                   
                 dioxygenase 
               
               
                   
                 Homogentisate 1,2- 
               
               
                   
                 dioxygenase 
               
               
                   
                 4-hydroxyphenylacetate 
                 Also acts on 4-hydroxyhydratropate 
               
               
                   
                 1-monooxygenase 
                 forming 2-methylhomogentisate and on 
               
               
                   
                   
                 4-hydroxyphenoxyacetate forming 
               
               
                   
                   
                 hydroquinone and glycolate 
               
               
                   
                 4-hydroxyphenylacetate 
               
               
                   
                 3-monooxygenase 
               
               
                   
                 Tyrosine N- 
               
               
                   
                 monooxygenase 
               
               
                   
                 Hydroxyphenylacetonitrile 
               
               
                   
                 2-monooxygenase 
               
               
                   
                 Tyrosine 3- 
                 Activated by phosphorylation, catalysed 
               
               
                   
                 monooxygenase 
                 by EC 2.7.1.128 
               
               
                   
                 Dopamine-beta- 
                 Stimulated by fumarate 
               
               
                   
                 monooxygenase 
               
               
                   
                 Monophenol 
                 A group of copper proteins that also 
               
               
                   
                 monooxygenase 
                 catalyse the reaction of EC 1.10.3.1, if 
               
               
                   
                   
                 only 1,2-benzenediols are available as 
               
               
                   
                   
                 substrate 
               
               
                   
                 Succinate- 
               
               
                   
                 semialdehyde 
               
               
                   
                 dehydrogenase 
               
               
                   
                 (NAD(P)+) 
               
               
                   
                 Aryl-aldehyde 
                 Oxidizes a number of aromatic 
               
               
                   
                 dehydrogenase 
                 aldehydes, but not aliphatic aldehydes 
               
               
                   
                 Aldehyde 
                 Wide specificity, including oxidation of 
               
               
                   
                 dehydrogenase (NAD+) 
                 D-glucuronolactone to D-glucarate 
               
               
                   
                 4-carboxy-2- 
                 Does not act on unsubstituted aliphatic or 
               
               
                   
                 hydroxymuconate-6- 
                 aromatic aldehydes or glucose NAD(+) 
               
               
                   
                 semialdehyde 
                 can replace NADP(+), but with lower 
               
               
                   
                 dehydrogenase 
                 affinity 
               
               
                   
                 Aldehyde 
               
               
                   
                 dehydrogenase 
               
               
                   
                 (NAD(P)+) 
               
               
                   
                 4- 
                 With EC 4.2.1.87, brings about the 
               
               
                   
                 hydroxyphenylacetaldehyde 
                 metabolism of octopamine in 
               
               
                   
                 dehydrogenase 
                 
                   Pseudomonas 
                 
               
               
                   
                 Aldehyde oxidase 
                 Also oxidizes quinoline and pyridine 
               
               
                   
                   
                 derivatives May be identical with EC 
               
               
                   
                   
                 1.1.3.22 
               
               
                   
                 L-amino acid oxidase 
               
               
                   
                 Amine oxidase (flavin- 
                 Acts on primary amines, and usually also 
               
               
                   
                 containing) 
                 on secondary and tertiary amines 
               
               
                   
                 Amine oxidase (copper- 
                 A group of enzymes including those 
               
               
                   
                 containing) 
                 oxidizing primary amines, diamines and 
               
               
                   
                   
                 histamine One form of EC 1.3.1.15 from 
               
               
                   
                   
                 rat kidney also catalyses this reaction 
               
               
                   
                 Aralkylamine 
                 Phenazine methosulfate can act as 
               
               
                   
                 dehydrogenase 
                 acceptor Acts on aromatic amines and, 
               
               
                   
                   
                 more slowly, on some long-chain 
               
               
                   
                   
                 aliphatic amines, but not on methylamine 
               
               
                   
                   
                 or ethylamine (cf EC 1.4.99.3) 
               
               
                   
                 Phenol O- 
                 Acts on a wide variety of simple alkyl-, 
               
               
                   
                 methyltransferase 
                 methoxy- and halo-phenols 
               
               
                   
                 Tyramine N- 
                 Has some activity on phenylethylamine 
               
               
                   
                 methyltransferase 
                 analogs 
               
               
                   
                 Phenylethanolamine N- 
                 Acts on various phenylethanolamines; 
               
               
                   
                 methyltransferase 
                 converts noradrenalin into adrenalin 
               
               
                   
                 Catechol O- 
                 The mammalian enzymes act more 
               
               
                   
                 methyltransferase 
                 rapidly on catecholamines such as 
               
               
                   
                   
                 adrenaline or noradrenaline than on 
               
               
                   
                   
                 catechols 
               
               
                   
                 Glutamine N- 
               
               
                   
                 phenylacetyltransferase 
               
               
                   
                 Rosmarinate synthase 
                 Involved with EC 1.1.1.237 in the 
               
               
                   
                   
                 biosynthesis of rosmarinic acid 
               
               
                   
                 Hydroxymandelonitrile 
                 3,4-dihydroxymandelonitrile can also act 
               
               
                   
                 glucosyltransferase 
                 as acceptor 
               
               
                   
                 Aspartate 
                 Also acts on L-tyrosine, L-phenylalanine 
               
               
                   
                 aminotransferase 
                 and L-tryptophan. This activity can be 
               
               
                   
                   
                 formed from EC 2.6.1.57 by controlled 
               
               
                   
                   
                 proteolysis 
               
               
                   
                 Dihydroxyphenylalanine 
               
               
                   
                 aminotransferase 
               
               
                   
                 Tyrosine 
                 L-phenylalanine can act instead of L- 
               
               
                   
                 aminotransferase 
                 tyrosine The mitochondrial enzyme may 
               
               
                   
                   
                 be identical with EC 2.6.1.1 The three 
               
               
                   
                   
                 isoenzymic forms are interconverted by 
               
               
                   
                   
                 EC 3.4.22.4 
               
               
                   
                 Aromatic amino acid 
                 L-methionine can also act as donor, more 
               
               
                   
                 transferase 
                 slowly Oxaloacetate can act as acceptor 
               
               
                   
                   
                 Controlled proteolysis converts the 
               
               
                   
                   
                 enzyme to EC 2.6.1.1 
               
               
                   
                 Histidinol-phosphate 
               
               
                   
                 aminotransferase 
               
               
                   
                 Fumarylacetoacetase 
                 Also acts on other 3,5- and 2,4-dioxo 
               
               
                   
                   
                 acids 
               
               
                   
                 Acylpyruvate hydrolase 
                 Acts on formylpyruvate, 2,4- 
               
               
                   
                   
                 dioxopentanoate, 2,4-dioxohexanoate and 
               
               
                   
                   
                 2,4-dioxoheptanoate 
               
               
                   
                 Tyrosine decarboxylase 
                 The bacterial enzyme also acts on 3- 
               
               
                   
                   
                 hydroxytyrosine and, more slowly, on 3- 
               
               
                   
                   
                 hydroxyphenylalanine 
               
               
                   
                 Aromatic-L-amino-acid 
                 Also acts on L-tryptophan, 5-hydroxy-L- 
               
               
                   
                 decarboxylase 
                 tryptophan and dihydroxy-L- 
               
               
                   
                   
                 phenylalanine (DOPA) 
               
               
                   
                 Gentisate 
               
               
                   
                 decarboxylase 
               
               
                   
                 5-oxopent-3-ene-1,2,5- 
               
               
                   
                 tricarboxylate 
               
               
                   
                 decarboxylase 
               
               
                   
                 Tyrosine phenol-lyase 
                 Also slowly catalyses pyruvate formation 
               
               
                   
                   
                 from D-tyrosine, S-methyl-L-cysteine, 
               
               
                   
                   
                 L-cysteine, L-serine and D-serine 
               
               
                   
                 (S)-norcoclaurine 
                 The reaction makes a 6-membered ring 
               
               
                   
                 synthase 
                 by forming a bond between C-6 of the 
               
               
                   
                   
                 3,4-dihydroxyphenyl group of the 
               
               
                   
                   
                 dopamine and C-1 of the aldehyde in the 
               
               
                   
                   
                 imine formed between the substrates The 
               
               
                   
                   
                 product is the precursor of the 
               
               
                   
                   
                 benzylisoquinoline alkaloids in plants 
               
               
                   
                   
                 Will also catalyse the reaction of 4-(2- 
               
               
                   
                   
                 aminoethyl)benzene-1,2-diol + (3,4- 
               
               
                   
                   
                 dihydroxyphenyl)acetaldehyde to form 
               
               
                   
                   
                 (S)-norlaudanosoline, but this alkaloid 
               
               
                   
                   
                 has not been found to occur in plants 
               
               
                   
                 Dihydroxyphenylalanine 
               
               
                   
                 ammonia-lyase 
               
               
                   
                 Phenylalanine 
                 May also act on L-tyrosine 
               
               
                   
                 ammonia-lyase 
               
               
                   
                 Maleylacetoacetate 
                 Also acts on maleylpyruvate 
               
               
                   
                 isomerase 
               
               
                   
                 Maleylpyruvate 
               
               
                   
                 isomerase 
               
               
                   
                 Phenylpyruvate 
                 Also acts on other arylpyruvates 
               
               
                   
                 tautomerase 
               
               
                   
                 5-carboxymethyl-2- 
               
               
                   
                 hydroxymuconate 
               
               
                   
                 delta-isomerase 
               
               
                   
                 Tyrosine 2,3- 
               
               
                   
                 aminomutase 
               
               
                   
                 Phenylacetate--CoA 
                 Also acts, more slowly, on acetate, 
               
               
                   
                 ligase 
                 propanoate and butanoate, but not on 
               
               
                   
                   
                 hydroxy derivatives of phenylacetate and 
               
               
                   
                   
                 related compounds 
               
               
                   
               
            
           
         
       
     
     VII. Promoters as Sentinels 
     Useful promoters include those that are capable of facilitating preferential transcription, i.e. tissue-specific or developmentally regulated gene expression and being a component of  facile  systems to evaluate the metabolic/physiological state of a plant cell, tissue or organ. Many such promoters are included in this application. Operably linking a sequence to these promoters that can act as a reporter and inserting the construct into a plant allows detection of the preferential in plantar transcription. For example, the quantitative state of responses to environmental conditions can be detected by using a plant having a construct that contains a stress-inducible promoter linked to and controlling expression of a sequence encoding GFP. The greater the stress promoter is induced, the greater the levels of fluorescence from GFP will be produced and this provides a measure of the level of stress being expressed by the plant and/or the ability of the plant to respond internally to the stress. 
     More specifically, using this system the activities of any metabolic pathway (catabolic and anabolic), stress-related pathways as on any plant gene repeated activity can be monitored. In addition, assays can be developed using this sentinel system to select for superior genotypes with greater yield characteristics or to select for plants with altered responses to chemical, herbicide, or plant growth regulators or to identify chemical, herbicides or plant growth regulators by their response on such sentinels. 
     Specifically, a promoter that is regulated in plants in the desired way, is operably linked to a reporter such as GFP, RFP, etc., and the constructs are introduced into the plant of interest. The behavior of the reporter is monitored using technologies typically specific for that reporter. With GFP, RFP, etc., it could typically be by microscopy of whole plants, organs, tissues or cells under excitation by an appropriate wavelength of UV light. 
     VIII. How to Make Different Embodiments of the Invention 
     The invention relates to (I) polynucleotides and methods of use thereof, such as
         IA. Probes, Primers and Substrates;   IB. Methods of Detection and Isolation;
           B.1. Hybridization;   B.2. Methods of Mapping;   B.3. Southern Blotting;   B.4. Isolating cDNA from Related Organisms;   B.5. Isolating and/or Identifying Orthologous Genes   
           IC. Methods of Inhibiting Gene Expression
           C.1. Antisense   C.2. Ribozyme Constructs;   C.3. Chimeraplasts;   C.4 Co-Suppression;   C.5. Transcriptional Silencing   C.6. Other Methods to Inhibit Gene Expression   
           ID. Methods of Functional Analysis;   IE. Promoter Sequences and Their Use;   IF. UTRs and/or Intron Sequences and Their Use; and   IG. Coding Sequences and Their Use.       

     The invention also relates to (II) polypeptides and proteins and methods of use thereof, such as
         IIA. Native Polypeptides and Proteins
           A.1 Antibodies   A.2 In Vitro Applications   
           IIB. Polypeptide Variants, Fragments and Fusions
           B.1 Variants   B.2 Fragments   B.3 Fusions   
               

     The invention also includes (III) methods of modulating polypeptide production, such as
         IIIA. Suppression
           A.1 Antisense   A.2 Ribozymes   A.3 Co-suppression   A.4 Insertion of Sequences into the Gene to be Modulated   A.5 Promoter Modulation   A.6 Expression of Genes containing Dominant-Negative Mutations   
           IIIB. Enhanced Expression
           B.1 Insertion of an Exogenous Gene   B.2 Promoter Modulation   
               

     The invention further concerns (IV) gene constructs and vector construction, such as
         IVA. Coding Sequences   IVB. Promoters   IVC. Signal Peptides       

     The invention still further relates to
         V. Transformation Techniques
 
I. Polynucleotides
       

     Exemplified SDFs of the invention represent fragments of the genome of corn, wheat, rice, soybean or  Arabidopsis  and/or represent mRNA expressed from that genome. The isolated nucleic acid of the invention also encompasses corresponding fragments of the genome and/or cDNA complement of other organisms as described in detail below. 
     Polynucleotides of the invention can be isolated from polynucleotide libraries using primers comprising sequences similar to those described, in the attached Reference, Sequences Protein Group, and Protein Group Matrix Tables or complements thereof. See, for example, the methods described in Sambrook et al., supra. 
     Alternatively, the polynucleotides of the invention can be produced by chemical synthesis. Such synthesis methods are described below. 
     It is contemplated that the nucleotide sequences presented herein may contain some small percentage of errors. These errors may arise in the normal course of determination of nucleotide sequences. Sequence errors can be corrected by obtaining seeds deposited under the accession numbers cited above, propagating them, isolating genomic DNA or appropriate mRNA from the resulting plants or seeds thereof, amplifying the relevant fragment of the genomic DNA or mRNA using primers having a sequence that flanks the erroneous sequence, and sequencing the amplification product. 
     I.A. Probes, Primers and Substrates 
     SDFs of the invention can be applied to substrates for use in array applications such as, but not limited to, assays of global gene expression, for example under varying conditions of development, growth conditions. The arrays can also be used in diagnostic or forensic methods (WO95/35505, U.S. Pat. Nos. 5,445,943 and 5,410,270). 
     Probes and primers of the instant invention will hybridize to a polynucleotide comprising a sequence in or encoded by those in the Reference, Sequence, Protein Group, and Protein Group Matrix tables or fragments or complement thereof. Though many different nucleotide sequences can encode an amino acid sequence, the sequences of the reference and Sequence table or sequences that encode polypeptides or fragments thereof described in Protein Group and Protein Group Matrix tables are generally preferred for encoding polypeptides of the invention. However, the sequence of the probes and/or primers of the instant invention need not be identical to those in the Reference and Sequence tables or the complements thereof for example, some variation in probe or primer sequence and/or length can allow additional family members to be detected, as well as orthologous genes and more taxonomically distant related sequences. Similarly, probes and/or primers of the invention can include additional nucleotides that serve as a label for detecting the formed duplex or for subsequent cloning purposes. 
     Probe length will vary depending on the application. For use as primers, probes are 12-40 nucleotides, preferably 18-30 nucleotides long. For use in mapping, probes are preferably 50 to 500 nucleotides, preferably 100-250 nucleotides long. For Southern hybridizations, probes as long as several kilobases can be used as explained below. 
     The probes and/or primers can be produced by synthetic procedures such as the triester method of Matteucci et al.  J. Am. Chem. Soc.  103:3185(1981); or according to Urdea et al.  Proc. Natl. Acad.  80:7461 (1981) or using commercially available automated oligonucleotide synthesizers. 
     I.B. Methods of Detection and Isolation 
     The polynucleotides of the invention can be utilized in a number of methods known to those skilled in the art as probes and/or primers to isolate and detect polynucleotides, including, without limitation: Southerns, Northerns, Branched DNA hybridization assays, polymerase chain reaction, and microarray assays, and variations thereof. Specific methods given by way of examples, and discussed below include:
         Hybridization   Methods of Mapping   Southern Blotting   Isolating cDNA from Related Organisms   Isolating and/or Identifying Orthologous Genes.
 
Also, the nucleic acid molecules of the invention can used in other methods, such as high density oligonucleotide hybridizing assays, described, for example, in U.S. Pat. Nos. 6,004,753; 5,945,306; 5,945,287; 5,945,308; 5,919,686; 5,919,661; 5,919,627; 5,874,248; 5,871,973; 5,871,971; and 5,871,930; and PCT Pub. Nos. WO 9946380; WO 9933981; WO 9933870; WO 9931252; WO 9915658; WO 9906572; WO 9858052; WO 9958672; and WO 9810858.
       

     B.1. Hybridization 
     The isolated SDFs of the Reference and Sequence tables or SDFs encoding polypeptides of the Protein Group and Protein Group Matrix tables or fragments thereof of the present invention can be used as probes and/or primers for detection and/or isolation of related polynucleotide sequences through hybridization. Hybridization of one nucleic acid to another constitutes a physical property that defines the subject SDF of the invention and the identified related sequences. Also, such hybridization imposes structural limitations on the pair. A good general discussion of the factors for determining hybridization conditions is provided by Sambrook et al. (“Molecular Cloning, a Laboratory Manual, 2nd ed., c. 1989 by Cold Spring Harbor Laboratory Press, Cold Spring Harbor, N.Y.; see esp., chapters 11 and 12). Additional considerations and details of the physical chemistry of hybridization are provided by G. H. Keller and M. M. Manak “DNA Probes”, 2 nd  Ed. pp. 1-25, c. 1993 by Stockton Press, New York, N.Y. 
     Depending on the stringency of the conditions under which these probes and/or primers are used, polynucleotides exhibiting a wide range of similarity to those in the Reference and Sequence or encoding polypeptides of the Protein Group and Protein Group Matrix tables or fragments thereof can be detected or isolated. When the practitioner wishes to examine the result of membrane hybridizations under a variety of stringencies, an efficient way to do so is to perform the hybridization under a low stringency condition, then to wash the hybridization membrane under increasingly stringent conditions. 
     When using SDFs to identify orthologous genes in other species, the practitioner will preferably adjust the amount of target DNA of each species so that, as nearly as is practical, the same number of genome equivalents are present for each species examined. This prevents faint signals from species having large genomes, and thus small numbers of genome equivalents per mass of DNA, from erroneously being interpreted as absence of the corresponding gene in the genome. 
     The probes and/or primers of the instant invention can also be used to detect or isolate nucleotides that are “identical” to the probes or primers. Two nucleic acid sequences or polypeptides are said to be “identical” if the sequence of nucleotides or amino acid residues, respectively, in the two sequences is the same when aligned for maximum correspondence as described below. 
     Isolated polynucleotides within the scope of the invention also include allelic variants of the specific sequences presented in the Reference, Sequence, Protein Group, and Protein Group Matrix tables. The probes and/or primers of the invention can also be used to detect and/or isolate polynucleotides exhibiting at least 80% sequence identity with the sequences of the reference, Sequence or encoding polypeptides of the Protein Group and Protein Group Matrix tables or fragments thereof. 
     With respect to nucleotide sequences, degeneracy of the genetic code provides the possibility to substitute at least one base of the base sequence of a gene with a different base without causing the amino acid sequence of the polypeptide produced from the gene to be changed. Hence, the DNA of the present invention may also have any base sequence that has been changed from a sequence in the Reference, Sequence, Protein Group, and Protein Group Matrix tables by substitution in accordance with degeneracy of genetic code. References describing codon usage include: Carels et al.,  J. Mol. Eva  46: 45 (1998) and Fennoy et al.,  Nucl. Acids Res.  21(23): 5294 (1993). 
     B.2. Mapping 
     The isolated SDF DNA of the invention can be used to create various types of genetic and physical maps of the genome of corn,  Arabidopsis , soybean, rice, wheat, or other plants. Some SDFs may be absolutely associated with particular phenotypic traits, allowing construction of gross genetic maps. While not all SDFs will immediately be associated with a phenotype, all SDFs can be used as probes for identifying polymorphisms associated with phenotypes of interest. Briefly, one method of mapping involves total DNA isolation from individuals. It is subsequently cleaved with one or more restriction enzymes, separated according to mass, transferred to a solid support, hybridized with SDF DNA and the pattern of fragments compared. Polymorphisms associated with a particular SDF are visualized as differences in the size of fragments produced between individual DNA samples after digestion with a particular restriction enzyme and hybridization with the SDF. After identification of polymorphic SDF sequences, linkage studies can be conducted. By using the individuals showing polymorphisms as parents in crossing programs, F2 progeny recombinants or recombinant inbreds, for example, are then analyzed. The order of DNA polymorphisms along the chromosomes can be determined based on the frequency with which they are inherited together versus independently. The closer two polymorphisms are together in a chromosome the higher the probability that they are inherited together. Integration of the relative positions of all the polymorphisms and associated marker SDFs can produce a genetic map of the species, where the distances between markers reflect the recombination frequencies in that chromosome segment. 
     The use of recombinant inbred lines for such genetic mapping is described for  Arabidopsis  by Alonso-Blanco et al. ( Methods in Molecular Biology , vol. 82, “ Arabidopsis Protocols ”, pp. 137-146, J. M. Martinez-Zapater and J. Salinas, eds., c. 1998 by Humana Press, Totowa, N.J.) and for corn by Burr (“Mapping Genes with Recombinant Inbreds”, pp. 249-254. In Freeling, M. and V. Walbot (Ed.),  The Maize Handbook , c. 1994 by Springer-Verlag New York, Inc.: New York, N.Y., USA; Berlin Germany; Burr et al.  Genetics  (1998) 118: 519; Gardiner, J. et al., (1993)  Genetics  134: 917). This procedure, however, is not limited to plants and can be used for other organisms (such as yeast) or for individual cells. 
     The SDFs of the present invention can also be used for simple sequence repeat (SSR) mapping. Rice SSR mapping is described by Morgante et al. ( The Plant Journal  (1993) 3: 165), Panaud et al. ( Genome  (1995) 38: 1170); Senior et al. ( Crop Science  (1996) 36: 1676), Taramino et al. ( Genome  (1996) 39: 277) and Alm et al. ( Molecular and General Genetics  (1993) 241: 483-90). SSR mapping can be achieved using various methods. In one instance, polymorphisms are identified when sequence specific probes contained within an SDF flanking an SSR are made and used in polymerase chain reaction (PCR) assays with template DNA from two or more individuals of interest. Here, a change in the number of tandem repeats between the SSR-flanking sequences produces differently sized fragments (U.S. Pat. No. 5,766,847). Alternatively, polymorphisms can be identified by using the PCR fragment produced from the SSR-flanking sequence specific primer reaction as a probe against Southern blots representing different individuals (U. H. Refseth et al., (1997)  Electrophoresis  18: 1519). 
     Genetic and physical maps of crop species have many uses. For example, these maps can be used to devise positional cloning strategies for isolating novel genes from the mapped crop species. In addition, because the genomes of closely related species are largely syntenic (that is, they display the same ordering of genes within the genome), these maps can be used to isolate novel alleles from relatives of crop species by positional cloning strategies. 
     The various types of maps discussed above can be used with the SDFs of the invention to identify Quantitative Trait Loci (QTLs). Many important crop traits, such as the solids content of tomatoes, are quantitative traits and result from the combined interactions of several genes. These genes reside at different loci in the genome, oftentimes on different chromosomes, and generally exhibit multiple alleles at each locus. The SDFs of the invention can be used to identify QTLs and isolate specific alleles as described by de Vicente and Tanksley (Genetics 134:585 (1993)). In addition to isolating QTL alleles in present crop species, the SDFs of the invention can also be used to isolate alleles from the corresponding QTL of wild relatives. Transgenic plants having various combinations of QTL alleles can then be created and the effects of the combinations measured. Once a desired allele combination has been identified, crop improvement can be accomplished either through biotechnological means or by directed conventional breeding programs (for review see Tanksley and McCouch,  Science  277:1063 (1997)). 
     In another embodiment, the SDFs can be used to help create physical maps of the genome of corn,  Arabidopsis  and related species. Where SDFs have been ordered on a genetic map, as described above, they can be used as probes to discover which clones in large libraries of plant DNA fragments in YACs, BACs, etc. contain the same SDF or similar sequences, thereby facilitating the assignment of the large DNA fragments to chromosomal positions. Subsequently, the large BACs, YACs, etc. can be ordered unambiguously by more detailed studies of their sequence composition (e.g. Marra et al. (1997) Genomic Research 7:1072-1084) and by using their end or other sequences to find the identical sequences in other cloned DNA fragments. The overlapping of DNA sequences in this way allows large contigs of plant sequences to be built that, when sufficiently extended, provide a complete physical map of a chromosome. Sometimes the SDFs themselves will provide the means of joining cloned sequences into a contig. 
     The patent publication WO95/35505 and U.S. Pat. Nos. 5,445,943 and 5,410,270 describe scanning multiple alleles of a plurality of loci using hybridization to arrays of oligonucleotides. These techniques are useful for each of the types of mapping discussed above. 
     Following the procedures described above and using a plurality of the SDFs of the present invention, any individual can be genotyped. These individual genotypes can be used for the identification of particular cultivars, varieties, lines, ecotypes and genetically modified plants or can serve as tools for subsequent genetic studies involving multiple phenotypic traits. 
     B.3 Southern Blot Hybridization 
     The sequences from Reference and Sequence and those encoding polypeptides of Protein Group and Protein Group Matrix tables or fragments thereof can be used as probes for various hybridization techniques. These techniques are useful for detecting target polynucleotides in a sample or for determining whether transgenic plants, seeds or host cells harbor a gene or sequence of interest and thus might be expected to exhibit a particular trait or phenotype. 
     In addition, the SDFs from the invention can be used to isolate additional members of gene families from the same or different species and/or orthologous genes from the same or different species. This is accomplished by hybridizing an SDF to, for example, a Southern blot containing the appropriate genomic DNA or cDNA. Given the resulting hybridization data, one of ordinary skill in the art could distinguish and isolate the correct DNA fragments by size, restriction sites, sequence and stated hybridization conditions from a gel or from a library. 
     Identification and isolation of orthologous genes from closely related species and alleles within a species is particularly desirable because of their potential for crop improvement. Many important crop traits, such as the solid content of tomatoes, result from the combined interactions of the products of several genes residing at different loci in the genome. Generally, alleles at each of these loci can make quantitative differences to the trait. By identifying and isolating numerous alleles for each locus from within or different species, transgenic plants with various combinations of alleles can be created and the effects of the combinations measured. Once a more favorable allele combination has been identified, crop improvement can be accomplished either through biotechnological means or by directed conventional breeding programs (Tanksley et al.  Science  277:1063(1997)). 
     The results from hybridizations of the SDFs of the invention to, for example, Southern blots containing DNA from another species can also be used to generate restriction fragment maps for the corresponding genomic regions. These maps provide additional information about the relative positions of restriction sites within fragments, further distinguishing mapped DNA from the remainder of the genome. 
     Physical maps can be made by digesting genomic DNA with different combinations of restriction enzymes. 
     Probes for Southern blotting to distinguish individual restriction fragments can range in size from 15 to 20 nucleotides to several thousand nucleotides. More preferably, the probe is 100 to 1,000 nucleotides long for identifying members of a gene family when it is found that repetitive sequences would complicate the hybridization. For identifying an entire corresponding gene in another species, the probe is more preferably the length of the gene, typically 2,000 to 10,000 nucleotides, but probes 50-1,000 nucleotides long might be used. Some genes, however, might require probes up to 1,500 nucleotides long or overlapping probes constituting the full-length sequence to span their lengths. 
     Also, while it is preferred that the probe be homogeneous with respect to its sequence, it is not necessary. For example, as described below, a probe representing members of a gene family having diverse sequences can be generated using PCR to amplify genomic DNA or RNA templates using primers derived from SDFs that include sequences that define the gene family. 
     For identifying corresponding genes in another species, the next most preferable probe is a cDNA spanning the entire coding sequence, which allows all of the mRNA-coding fragment of the gene to be identified. Probes for Southern blotting can easily be generated from SDFs by making primers having the sequence at the ends of the SDF and using corn or  Arabidopsis  genomic DNA as a template. In instances where the SDF includes sequence conserved among species, primers including the conserved sequence can be used for PCR with genomic DNA from a species of interest to obtain a probe. 
     Similarly, if the SDF includes a domain of interest, that fragment of the SDF can be used to make primers and, with appropriate template DNA, used to make a probe to identify genes containing the domain. Alternatively, the PCR products can be resolved, for example by gel electrophoresis, and cloned and/or sequenced. Using Southern hybridization, the variants of the domain among members of a gene family, both within and across species, can be examined. 
     B.4.1 Isolating DNA from Related Organisms 
     The SDFs of the invention can be used to isolate the corresponding DNA from other organisms. Either cDNA or genomic DNA can be isolated. For isolating genomic DNA, a lambda, cosmid, BAC or YAC, or other large insert genomic library from the plant of interest can be constructed using standard molecular biology techniques as described in detail by Sambrook et al. 1989 (Molecular Cloning: A Laboratory Manual, 2′ d  ed. Cold Spring Harbor Laboratory Press, New York) and by Ausubel et al. 1992 (Current Protocols in Molecular Biology, Greene Publishing, New York). 
     To screen a phage library, for example, recombinant lambda clones are plated out on appropriate bacterial medium using an appropriate  E. coli  host strain. The resulting plaques are lifted from the plates using nylon or nitrocellulose filters. The plaque lifts are processed through denaturation, neutralization, and washing treatments following the standard protocols outlined by Ausubel et al. (1992). The plaque lifts are hybridized to either radioactively labeled or non-radioactively labeled SDF DNA at room temperature for about 16 hours, usually in the presence of 50% formamide and 5×SSC (sodium chloride and sodium citrate) buffer and blocking reagents. The plaque lifts are then washed at 42° C. with 1% Sodium Dodecyl Sulfate (SDS) and at a particular concentration of SSC. The SSC concentration used is dependent upon the stringency at which hybridization occurred in the initial Southern blot analysis performed. For example, if a fragment hybridized under medium stringency (e.g., Tm−20° C.), then this condition is maintained or preferably adjusted to a less stringent condition (e.g., Tm−30° C.) to wash the plaque lifts. Positive clones show detectable hybridization e.g., by exposure to X-ray films or chromogen formation. The positive clones are then subsequently isolated for purification using the same general protocol outlined above. Once the clone is purified, restriction analysis can be conducted to narrow the region corresponding to the gene of interest. The restriction analysis and succeeding subcloning steps can be done using procedures described by, for example Sambrook et al. (1989) cited above. 
     The procedures outlined for the lambda library are essentially similar to those used for YAC library screening, except that the YAC clones are harbored in bacterial colonies. The YAC clones are plated out at reasonable density on nitrocellulose or nylon filters supported by appropriate bacterial medium in petri plates. Following the growth of the bacterial clones, the filters are processed through the denaturation, neutralization, and washing steps following the procedures of Ausubel et al. 1992. The same hybridization procedures for lambda library screening are followed. 
     To isolate cDNA, similar procedures using appropriately modified vectors are employed. For instance, the library can be constructed in a lambda vector appropriate for cloning cDNA such as λgt11. Alternatively, the cDNA library can be made in a plasmid vector. cDNA for cloning can be prepared by any of the methods known in the art, but is preferably prepared as described above. Preferably, a cDNA library will include a high proportion of full-length clones. 
     B. 5. Isolating and/or Identifying Orthologous Genes 
     Probes and primers of the invention can be used to identify and/or isolate polynucleotides related to those in the Reference, Sequence, Protein Group, and Protein Group Matrix tables. Related polynucleotides are those that are native to other plant organisms and exhibit either similar sequence or encode polypeptides with similar biological activity. One specific example is an orthologous gene. Orthologous genes have the same functional activity. As such, orthologous genes may be distinguished from homologous genes. The percentage of identity is a function of evolutionary separation and, in closely related species, the percentage of identity can be 98 to 100%. The amino acid sequence of a protein encoded by an orthologous gene can be less than 75% identical, but tends to be at least 75% or at least 80% identical, more preferably at least 90%, most preferably at least 95% identical to the amino acid sequence of the reference protein. 
     To find orthologous genes, the probes are hybridized to nucleic acids from a species of interest under low stringency conditions, preferably one where sequences containing as much as 40-45% mismatches will be able to hybridize. This condition is established by T m −40° C. to Tm−48° C. (see below). Blots are then washed under conditions of increasing stringency. It is preferable that the wash stringency be such that sequences that are 85 to 100% identical will hybridize. More preferably, sequences 90 to 100% identical will hybridize and most preferably only sequences greater than 95% identical will hybridize. One of ordinary skill in the art will recognize that, due to degeneracy in the genetic code, amino acid sequences that are identical can be encoded by DNA sequences as little as 67% identical or less. Thus, it is preferable, for example, to make an overlapping series of shorter probes, on the order of 24 to 45 nucleotides, and individually hybridize them to the same arrayed library to avoid the problem of degeneracy introducing large numbers of mismatches. 
     As evolutionary divergence increases, genome sequences also tend to diverge. Thus, one of skill will recognize that searches for orthologous genes between more divergent species will require the use of lower stringency conditions compared to searches between closely related species. Also, degeneracy of the genetic code is more of a problem for searches in the genome of a species more distant evolutionarily from the species that is the source of the SDF probe sequences. 
     Therefore the method described in Bouckaert et al., U.S. Ser. No. 60/121,700, filed Feb. 25, 1999, hereby incorporated in its entirety by reference, can be applied to the SDFs of the present invention to isolate related genes from plant species which do not hybridize to the corn  Arabidopsis , soybean, rice, wheat, and other plant sequences of the reference, Sequence, Protein Group, and Protein Group Matrix tables. 
     Identification of the relationship of nucleotide or amino acid sequences among plant species can be done by comparing the nucleotide or amino acid sequences of SDFs of the present application with nucleotide or amino acid sequences of other SDFs such as those present in applications listed in the table below: 
     The SDFs of the invention can also be used as probes to search for genes that are related to the SDF within a species. Such related genes are typically considered to be members of a gene family. In such a case, the sequence similarity will often be concentrated into one or a few fragments of the sequence. The fragments of similar sequence that define the gene family typically encode a fragment of a protein or RNA that has an enzymatic or structural function. The percentage of identity in the amino acid sequence of the domain that defines the gene family is preferably at least 70%, more preferably 80 to 95%, most preferably 85 to 99%. To search for members of a gene family within a species, a low stringency hybridization is usually performed, but this will depend upon the size, distribution and degree of sequence divergence of domains that define the gene family. SDFs encompassing regulatory regions can be used to identify coordinately expressed genes by using the regulatory region sequence of the SDF as a probe. 
     In the instances where the SDFs are identified as being expressed from genes that confer a particular phenotype, then the SDFs can also be used as probes to assay plants of different species for those phenotypes. 
     I.C. Methods to Inhibit Gene Expression 
     The nucleic acid molecules of the present invention can be used to inhibit gene transcription and/or translation. Example of such methods include, without limitation:
         Antisense Constructs;   Ribozyme Constructs;   Chimeraplast Constructs;   Co-Suppression;   Transcriptional Silencing; and   Other Methods of Gene Expression.       

     C.1 Antisense 
     In some instances it is desirable to suppress expression of an endogenous or exogenous gene. A well-known instance is the FLAVOR-SAVOR™ tomato, in which the gene encoding ACC synthase is inactivated by an antisense approach, thus delaying softening of the fruit after ripening. See for example, U.S. Pat. Nos. 5,859,330; 5,723,766; Oeller, et al,  Science,  254:437-439(1991); and Hamilton et al,  Nature,  346:284-287 (1990). Also, timing of flowering can be controlled by suppression of the FLOWERING LOCUS C (FLC); high levels of this transcript are associated with late flowering, while absence of FLC is associated with early flowering (S.D. Michaels et al.,  Plant Cell  11:949 (1999). Also, the transition of apical meristem from production of leaves with associated shoots to flowering is regulated by TERMINAL FLOWER1, APETALA1 and LEAFY. Thus, when it is desired to induce a transition from shoot production to flowering, it is desirable to suppress TFL1 expression (S. J. Liljegren,  Plant Cell  11:1007 (1999)). As another instance, arrested ovule development and female sterility result from suppression of the ethylene forming enzyme but can be reversed by application of ethylene (D. De Martinis et al.,  Plant Cell  11:1061 (1999)). The ability to manipulate female fertility of plants is useful in increasing fruit production and creating hybrids. 
     In the case of polynucleotides used to inhibit expression of an endogenous gene, the introduced sequence need not be perfectly identical to a sequence of the target endogenous gene. The introduced polynucleotide sequence will typically be at least substantially identical to the target endogenous sequence. 
     Some polynucleotide SDFs in the Reference, Sequence, Protein Group, and Protein Group Matrix tables represent sequences that are expressed in corn, wheat, rice, soybean  Arabidopsis  and/or other plants. Thus the invention includes using these sequences to generate antisense constructs to inhibit translation and/or degradation of transcripts of said SDFs, typically in a plant cell. 
     To accomplish this, a polynucleotide segment from the desired gene that can hybridize to the mRNA expressed from the desired gene (the “antisense segment”) is operably linked to a promoter such that the antisense strand of RNA will be transcribed when the construct is present in a host cell. A regulated promoter can be used in the construct to control transcription of the antisense segment so that transcription occurs only under desired circumstances. 
     The antisense segment to be introduced generally will be substantially identical to at least a fragment of the endogenous gene or genes to be repressed. The sequence, however, need not be perfectly identical to inhibit expression. Further, the antisense product may hybridize to the untranslated region instead of or in addition to the coding sequence of the gene. The vectors of the present invention can be designed such that the inhibitory effect applies to other proteins within a family of genes exhibiting homology or substantial homology to the target gene. 
     For antisense suppression, the introduced antisense segment sequence also need not be full length relative to either the primary transcription product or the fully processed mRNA. Generally, a higher percentage of sequence identity can be used to compensate for the use of a shorter sequence. Furthermore, the introduced sequence need not have the same intron or exon pattern, and homology of non-coding segments may be equally effective. Normally, a sequence of between about 30 or 40 nucleotides and the full length of the transcript can be used, though a sequence of at least about 100 nucleotides is preferred, a sequence of at least about 200 nucleotides is more preferred, and a sequence of at least about 500 nucleotides is especially preferred. 
     C.2. Ribozymes 
     It is also contemplated that gene constructs representing ribozymes and based on the SDFs in the Reference and Sequence tables or those encoding polypeptides of the Protein Group and Protein Group Matrix tables and fragment thereof are an object of the invention. Ribozymes can also be used to inhibit expression of genes by suppressing the translation of the mRNA into a polypeptide. It is possible to design ribozymes that specifically pair with virtually any target RNA and cleave the phosphodiester backbone at a specific location, thereby functionally inactivating the target RNA. In carrying out this cleavage, the ribozyme is not itself altered, and is thus capable of recycling and cleaving other molecules, making it a true enzyme. The inclusion of ribozyme sequences within antisense RNAs confers RNA-cleaving activity upon them, thereby increasing the activity of the constructs. 
     A number of classes of ribozymes have been identified. One class of ribozymes is derived from a number of small circular RNAs, which are capable of self-cleavage and replication in plants. The RNAs replicate either alone (viroid RNAs) or with a helper virus (satellite RNAs). Examples include RNAs from avocado sunblotch viroid and the satellite RNAs from tobacco ringspot virus, lucerne transient streak virus, velvet tobacco mottle virus,  solanum nodiflorum  mottle virus and subterranean clover mottle virus. The design and use of target RNA-specific ribozymes is described in Haseloff et al.  Nature,  334:585 (1988). 
     Like the antisense constructs above, the ribozyme sequence fragment necessary for pairing need not be identical to the target nucleotides to be cleaved, nor identical to the sequences in the Reference and Sequence tables or those encoding polypeptide of the Protein Group and Protein Group Matrix tables or fragments thereof. Ribozymes may be constructed by combining the ribozyme sequence and some fragment of the target gene which would allow recognition of the target gene mRNA by the resulting ribozyme molecule. Generally, the sequence in the ribozyme capable of binding to the target sequence exhibits a percentage of sequence identity with at least 80%, preferably with at least 85%, more preferably with at least 90% and most preferably with at least 95%, even more preferably, with at least 96%, 97%, 98% or 99% sequence identity to some fragment of a sequence in the Reference, Sequence, Protein Group, and Protein Group Matrix tables or the complement thereof. The ribozyme can be equally effective in inhibiting mRNA translation by cleaving either in the untranslated or coding regions. Generally, a higher percentage of sequence identity can be used to compensate for the use of a shorter sequence. Furthermore, the introduced sequence need not have the same intron or exon pattern, and homology of non-coding segments may be equally effective. 
     C.3. Chimeraplasts 
     The SDFs of the invention, such as those described by Reference, Sequence, Protein Group, and Protein Group Matrix tables, can also be used to construct chimeraplasts that can be introduced into a cell to produce at least one specific nucleotide change in a sequence corresponding to the SDF of the invention. A chimeraplast is an oligonucleotide comprising DNA and/or RNA that specifically hybridizes to a target region in a manner which creates a mismatched base-pair. This mismatched base-pair signals the cell&#39;s repair enzyme machinery which acts on the mismatched region resulting in the replacement, insertion or deletion of designated nucleotide(s). The altered sequence is then expressed by the cell&#39;s normal cellular mechanisms. Chimeraplasts can be designed to repair mutant genes, modify genes, introduce site-specific mutations, and/or act to interrupt or alter normal gene function (U.S. Pat. Nos. 6,010,907 and 6,004,804; and PCT Pub. No. WO99/58723 and WO99/07865). 
     C.4. Sense Suppression 
     The SDFs of the reference, Sequence, Protein Group, and Protein Group Matrix tables of the present invention are also useful to modulate gene expression by sense suppression. Sense suppression represents another method of gene suppression by introducing at least one exogenous copy or fragment of the endogenous sequence to be suppressed. 
     Introduction of expression cassettes in which a nucleic acid is configured in the sense orientation with respect to the promoter into the chromosome of a plant or by a self-replicating virus has been shown to be an effective means by which to induce degradation of mRNAs of target genes. For an example of the use of this method to modulate expression of endogenous genes see, Napoli et al.,  The Plant Cell  2:279 (1990), and U.S. Pat. Nos. 5,034,323, 5,231,020, and 5,283,184. Inhibition of expression may require some transcription of the introduced sequence. 
     For sense suppression, the introduced sequence generally will be substantially identical to the endogenous sequence intended to be inactivated. The minimal percentage of sequence identity will typically be greater than about 65%, but a higher percentage of sequence identity might exert a more effective reduction in the level of normal gene products. Sequence identity of more than about 80% is preferred, though about 95% to absolute identity would be most preferred. As with antisense regulation, the effect would likely apply to any other proteins within a similar family of genes exhibiting homology or substantial homology to the suppressing sequence. 
     C.5. Transcriptional Silencing 
     The nucleic acid sequences of the invention, including the SDFs of the reference, Sequence, Protein Group, and Protein Group Matrix tables, and fragments thereof, contain sequences that can be inserted into the genome of an organism resulting in transcriptional silencing. Such regulatory sequences need not be operatively linked to coding sequences to modulate transcription of a gene. Specifically, a promoter sequence without any other element of a gene can be introduced into a genome to transcriptionally silence an endogenous gene (see, for example, Vaucheret, H et al. (1998) The Plant Journal 16: 651-659). As another example, triple helices can be formed using oligonucleotides based on sequences from Reference, Sequence, Protein Group, and Protein Group Matrix tables, fragments thereof, and substantially similar sequence thereto. The oligonucleotide can be delivered to the host cell and can bind to the promoter in the genome to form a triple helix and prevent transcription. An oligonucleotide of interest is one that can bind to the promoter and block binding of a transcription factor to the promoter. In such a case, the oligonucleotide can be complementary to the sequences of the promoter that interact with transcription binding factors. 
     C.6. Other Methods to Inhibit Gene Expression 
     Yet another means of suppressing gene expression is to insert a polynucleotide into the gene of interest to disrupt transcription or translation of the gene. 
     Low frequency homologous recombination can be used to target a polynucleotide insert to a gene by flanking the polynucleotide insert with sequences that are substantially similar to the gene to be disrupted. Sequences from Reference, Sequence, Protein Group, and Protein Group Matrix tables, fragments thereof, and substantially similar sequence thereto can be used for homologous recombination. 
     In addition, random insertion of polynucleotides into a host cell genome can also be used to disrupt the gene of interest. Azpiroz-Leehan et al.,  Trends in Genetics  13:152 (1997). In this method, screening for clones from a library containing random insertions is preferred to identifying those that have polynucleotides inserted into the gene of interest. Such screening can be performed using probes and/or primers described above based on sequences from Reference, Sequence, Protein Group, and Protein Group Matrix tables, fragments thereof, and substantially similar sequence thereto. The screening can also be performed by selecting clones or R 1  plants having a desired phenotype. 
     I.D. Methods of Functional Analysis 
     The constructs described in the methods under I.C. above can be used to determine the function of the polypeptide encoded by the gene that is targeted by the constructs. 
     Down-regulating the transcription and translation of the targeted gene in the host cell or organisms, such as a plant, may produce phenotypic changes as compared to a wild-type cell or organism. In addition, in vitro assays can be used to determine if any biological activity, such as calcium flux, DNA transcription, nucleotide incorporation, etc., are being modulated by the down-regulation of the targeted gene. 
     Coordinated regulation of sets of genes, e.g., those contributing to a desired polygenic trait, is sometimes necessary to obtain a desired phenotype. SDFs of the invention representing transcription activation and DNA binding domains can be assembled into hybrid transcriptional activators. These hybrid transcriptional activators can be used with their corresponding DNA elements (i.e., those bound by the DNA-binding SDFs) to effect coordinated expression of desired genes (J.J. Schwarz et al.,  Mol. Cell. Biol.  12:266 (1992), A. Martinez et al.,  Mol. Gen. Genet.  261:546 (1999)). 
     The SDFs of the invention can also be used in the two-hybrid genetic systems to identify networks of protein-protein interactions (L. McAlister-Henn et al.,  Methods  19:330 (1999), J.C. Hu et al.,  Methods  20:80 (2000), M. Golovkin et al.,  J. Biol. Chem.  274:36428 (1999), K. Ichimura et al.,  Biochem. Biophys. Res. Comm.  253:532 (1998)). The SDFs of the invention can also be used in various expression display methods to identify important protein-DNA interactions (e.g. B. Luo et al.,  J. Mol. Biol.  266:479 (1997)). 
     I.E. Promoters 
     The SDFs of the invention are also useful as structural or regulatory sequences in a construct for modulating the expression of the corresponding gene in a plant or other organism, e.g. a symbiotic bacterium. For example, promoter sequences associated to SDFs of the reference, Sequence, Protein Group, and Protein Group Matrix tables of the present invention can be useful in directing expression of coding sequences either as constitutive promoters or to direct expression in particular cell types, tissues, or organs or in response to environmental stimuli. 
     With respect to the SDFs of the present invention a promoter is likely to be a relatively small portion of a genomic DNA (gDNA) sequence located in the first 2000 nucleotides upstream from an initial exon identified in a gDNA sequence or initial “ATG” or methionine codon or translational start site in a corresponding cDNA sequence. Such promoters are more likely to be found in the first 1000 nucleotides upstream of an initial ATG or methionine codon or translational start site of a cDNA sequence corresponding to a gDNA sequence. In particular, the promoter is usually located upstream of the transcription start site. The fragments of a particular gDNA sequence that function as elements of a promoter in a plant cell will preferably be found to hybridize to gDNA sequences presented and described in the Reference table at medium or high stringency, relevant to the length of the probe and its base composition. The promoter control elements of the present invention include those that comprise sequence shown in The Sequence Tables and fragments thereof. The size of the fragments of The Sequence Tables can range from 5 bases to 10 kilobases (kb). Typically, the fragment size is no smaller than 8 bases; more typically, no smaller than 12; more typically, no smaller than 15 bases; more typically, no smaller than 20 bases; more typically, no smaller than 25 bases; even more typically, no more than 30, 35, 40 or 50 bases. Usually, the fragment size is no larger than 5 kb bases; more usually, no larger than 2 kb; more usually, no larger than 1 kb; more usually, no larger than 800 bases; more usually, no larger than 500 bases; even more usually, no more than 250, 200, 150 or 100 bases. 
     Promoters are generally modular in nature. Promoters can consist of a basal promoter that functions as a site for assembly of a transcription complex comprising an RNA polymerase, for example RNA polymerase II. A typical transcription complex will include additional factors such as TF II B, TF II D, and TF II E. Of these, TF II D appears to be the only one to bind DNA directly. The promoter might also contain one or more enhancers and/or suppressors that function as binding sites for additional transcription factors that have the function of modulating the level of transcription with respect to tissue specificity and of transcriptional responses to particular environmental or nutritional factors, and the like. 
     Short DNA sequences representing binding sites for proteins can be separated from each other by intervening sequences of varying length. For example, within a particular functional module, protein binding sites may be constituted by regions of 5 to 60, preferably 10 to 30, more preferably 10 to 20 nucleotides. Within such binding sites, there are typically 2 to 6 nucleotides that specifically contact amino acids of the nucleic acid binding protein. The protein binding sites are usually separated from each other by 10 to several hundred nucleotides, typically by 15 to 150 nucleotides, often by 20 to 50 nucleotides. DNA binding sites in promoter elements often display dyad symmetry in their sequence. Often elements binding several different proteins, and/or a plurality of sites that bind the same protein, will be combined in a region of 50 to 1,000 basepairs. 
     Elements that have transcription regulatory function can be isolated from their corresponding endogenous gene, or the desired sequence can be synthesized, and recombined in constructs to direct expression of a coding region of a gene in a desired tissue-specific, temporal-specific or other desired manner of inducibility or suppression. When hybridizations are performed to identify or isolate elements of a promoter by hybridization to the long sequences presented in the Reference tables, conditions are adjusted to account for the above-described nature of promoters. For example short probes, constituting the element sought, are preferably used under low temperature and/or high salt conditions. When long probes, which might include several promoter elements are used, low to medium stringency conditions are preferred when hybridizing to promoters across species. 
     If a nucleotide sequence of an SDF, or part of the SDF, functions as a promoter or fragment of a promoter, then nucleotide substitutions, insertions or deletions that do not substantially affect the binding of relevant DNA binding proteins would be considered equivalent to the exemplified nucleotide sequence. It is envisioned that there are instances where it is desirable to decrease the binding of relevant DNA binding proteins to silence or down-regulate a promoter, or conversely to increase the binding of relevant DNA binding proteins to enhance or up-regulate a promoter and vice versa. In such instances, polynucleotides representing changes to the nucleotide sequence of the DNA-protein contact region by insertion of additional nucleotides, changes to identity of relevant nucleotides, including use of chemically-modified bases, or deletion of one or more nucleotides are considered encompassed by the present invention. In addition, fragments of the promoter sequences described by Reference tables and variants thereof can be fused with other promoters or fragments to facilitate transcription and/or transcription in specific type of cells or under specific conditions. 
     Promoter function can be assayed by methods known in the art, preferably by measuring activity of a reporter gene operatively linked to the sequence being tested for promoter function. Examples of reporter genes include those encoding luciferase, green fluorescent protein, GUS, neo, cat and bar. 
     I.F. UTRs and Junctions 
     Polynucleotides comprising untranslated (UTR) sequences and intron/exon junctions are also within the scope of the invention. UTR sequences include introns and 5′ or 3′ untranslated regions (5′ UTRs or 3′ UTRs). Fragments of the sequences shown in the Reference and Sequence tables can comprise UTRs and intron/exon junctions. 
     These fragments of SDFs, especially UTRs, can have regulatory functions related to, for example, translation rate and mRNA stability. Thus, these fragments of SDFs can be isolated for use as elements of gene constructs for regulated production of polynucleotides encoding desired polypeptides. 
     Introns of genomic DNA segments might also have regulatory functions. Sometimes regulatory elements, especially transcription enhancer or suppressor elements, are found within introns. Also, elements related to stability of heteronuclear RNA and efficiency of splicing and of transport to the cytoplasm for translation can be found in intron elements. Thus, these segments can also find use as elements of expression vectors intended for use to transform plants. 
     Just as with promoters UTR sequences and intron/exon junctions can vary from those shown in the Reference and Sequence tables. Such changes from those sequences preferably will not affect the regulatory activity of the UTRs or intron/exon junction sequences on expression, transcription, or translation unless selected to do so. However, in some instances, down- or up-regulation of such activity may be desired to modulate traits or phenotypic or in vitro activity. 
     I.G. Coding Sequences 
     Isolated polynucleotides of the invention can include coding sequences that encode polypeptides comprising an amino acid sequence encoded by sequences described in the Reference and Sequence tables or an amino acid sequence presented in the Reference, Sequence, Protein Group, and Protein Group Matrix tables. 
     A nucleotide sequence encodes a polypeptide if a cell (or a cell free in vitro system) expressing that nucleotide sequence produces a polypeptide having the recited amino acid sequence when the nucleotide sequence is transcribed and the primary transcript is subsequently processed and translated by a host cell (or a cell free in vitro system) harboring the nucleic acid. Thus, an isolated nucleic acid that encodes a particular amino acid sequence can be a genomic sequence comprising exons and introns or a cDNA sequence that represents the product of splicing thereof. An isolated nucleic acid encoding an amino acid sequence also encompasses heteronuclear RNA, which contains sequences that are spliced out during expression, and mRNA, which lacks those sequences. 
     Coding sequences can be constructed using chemical synthesis techniques or by isolating coding sequences or by modifying such synthesized or isolated coding sequences as described above. 
     In addition to coding sequences encoding the polypeptide sequences of the reference, Sequence, Protein Group, and Protein Group Matrix tables, which are native to corn,  Arabidopsis , soybean, rice, wheat, and other plants, the isolated polynucleotides can be polynucleotides that encode variants, fragments, and fusions of those native proteins. Such polypeptides are described below in part II. 
     In variant polynucleotides generally, the number of substitutions, deletions or insertions is preferably less than 20%, more preferably less than 15%; even more preferably less than 10%, 5%, 3% or 1% of the number of nucleotides comprising a particularly exemplified sequence. It is generally expected that non-degenerate nucleotide sequence changes that result in 1 to 10, more preferably 1 to 5 and most preferably 1 to 3 amino acid insertions, deletions or substitutions will not greatly affect the function of an encoded polypeptide. The most preferred embodiments are those wherein 1 to 20, preferably 1 to 10, most preferably 1 to 5 nucleotides are added to, or deleted from and/or substituted in the sequences specifically disclosed in the Reference and Sequence tables or polynucleotides that encode polypeptides of the Protein Group, and Protein Group Matrix tables or fragments thereof. 
     Insertions or deletions in polynucleotides intended to be used for encoding a polypeptide preferably preserve the reading frame. This consideration is not so important in instances when the polynucleotide is intended to be used as a hybridization probe. 
     II. Polypeptides and Proteins 
     IIA. Native Polypeptides and Proteins 
     Polypeptides within the scope of the invention include both native proteins as well as variants, fragments, and fusions thereof. Polypeptides of the invention are those encoded by any of the six reading frames of sequences shown in the Reference and Sequence tables, preferably encoded by the three frames reading in the 5′ to 3′ direction of the sequences as shown. 
     Native polypeptides include the proteins encoded by the sequences shown in the Reference and Sequence tables. Such native polypeptides include those encoded by allelic variants. 
     Polypeptide and protein variants will exhibit at least 75% sequence identity to those native polypeptides of the Reference and Sequence tables. More preferably, the polypeptide variants will exhibit at least 85% sequence identity; even more preferably, at least 90% sequence identity; more preferably at least 95%, 96%, 97%, 98%, or 99% sequence identity. Fragments of polypeptide or fragments of polypeptides will exhibit similar percentages of sequence identity to the relevant fragments of the native polypeptide. Fusions will exhibit a similar percentage of sequence identity in that fragment of the fusion represented by the variant of the native peptide. 
     Polypeptide and protein variants of the invention will exhibit at least 75% sequence identity to those motifs or consensus sequences of the Protein Group and Protein Group Matrix tables. More preferably, the polypeptide variants will exhibit at least 85% sequence identity; even more preferably, at least 90% sequence identity; more preferably at least 95%, 96%, 97%, 98%, or 99% sequence identity. Fragments of polypeptide or fragments of polypeptides will exhibit similar percentages of sequence identity to the relevant fragments of the native polypeptide that are indicated in the Protein Group table. Fusions will exhibit a similar percentage of sequence identity in that fragment of the fusion represented by the variant of the native peptide. 
     Furthermore, polypeptide variants will exhibit at least one of the functional properties of the native protein. Such properties include, without limitation, protein interaction, DNA interaction, biological activity, immunological activity, receptor binding, signal transduction, transcription activity, growth factor activity, secondary structure, three-dimensional structure, etc. As to properties related to in vitro or in vivo activities, the variants preferably exhibit at least 60% of the activity of the native protein; more preferably at least 70%, even more preferably at least 80%, 85%, 90% or 95% of at least one activity of the native protein. 
     One type of variant of native polypeptides comprises amino acid substitutions, deletions and/or insertions. Conservative substitutions are preferred to maintain the function or activity of the polypeptide. 
     Within the scope of percentage of sequence identity described above, a polypeptide of the invention may have additional individual amino acids or amino acid sequences inserted into the polypeptide in the middle thereof and/or at the N-terminal and/or C-terminal ends thereof. Likewise, some of the amino acids or amino acid sequences may be deleted from the polypeptide. 
     A.1 Antibodies 
     Isolated polypeptides can be utilized to produce antibodies. Polypeptides of the invention can generally be used, for example, as antigens for raising antibodies by known techniques. The resulting antibodies are useful as reagents for determining the distribution of the antigen protein within the tissues of a plant or within a cell of a plant. The antibodies are also useful for examining the production level of proteins in various tissues, for example in a wild-type plant or following genetic manipulation of a plant, by methods such as Western blotting. 
     Antibodies of the present invention, both polyclonal and monoclonal, may be prepared by conventional methods. In general, the polypeptides of the invention are first used to immunize a suitable animal, such as a mouse, rat, rabbit, or goat. Rabbits and goats are preferred for the preparation of polyclonal sera due to the volume of serum obtainable, and the availability of labeled anti-rabbit and anti-goat antibodies as detection reagents. Immunization is generally performed by mixing or emulsifying the protein in saline, preferably in an adjuvant such as Freund&#39;s complete adjuvant, and injecting the mixture or emulsion parenterally (generally subcutaneously or intramuscularly). A dose of 50-200 μg/injection is typically sufficient. Immunization is generally boosted 2-6 weeks later with one or more injections of the protein in saline, preferably using Freund&#39;s incomplete adjuvant. One may alternatively generate antibodies by in vitro immunization using methods known in the art, which for the purposes of this invention is considered equivalent to in vivo immunization. 
     Polyclonal antisera is obtained by bleeding the immunized animal into a glass or plastic container, incubating the blood at 25° C. for one hour, followed by incubating the blood at 4° C. for 2-18 hours. The serum is recovered by centrifugation (e.g., 1,000×g for 10 minutes). About 20-50 ml per bleed may be obtained from rabbits. 
     Monoclonal antibodies are prepared using the method of Kohler and Milstein,  Nature  256: 495 (1975), or modification thereof. Typically, a mouse or rat is immunized as described above. However, rather than bleeding the animal to extract serum, the spleen (and optionally several large lymph nodes) is removed and dissociated into single cells. If desired, the spleen cells can be screened (after removal of nonspecifically adherent cells) by applying a cell suspension to a plate, or well, coated with the protein antigen. B-cells producing membrane-bound immunoglobulin specific for the antigen bind to the plate, and are not rinsed away with the rest of the suspension. Resulting B-cells, or all dissociated spleen cells, are then induced to fuse with myeloma cells to form hybridomas, and are cultured in a selective medium (e.g., hypoxanthine, aminopterin, thymidine medium, “HAT”). The resulting hybridomas are plated by limiting dilution, and are assayed for the production of antibodies which bind specifically to the immunizing antigen (and which do not bind to unrelated antigens). The selected Mab-secreting hybridomas are then cultured either in vitro (e.g., in tissue culture bottles or hollow fiber reactors), or in vivo (as ascites in mice). 
     Other methods for sustaining antibody-producing B-cell clones, such as by EBV transformation, are known. 
     If desired, the antibodies (whether polyclonal or monoclonal) may be labeled using conventional techniques. Suitable labels include fluorophores, chromophores, radioactive atoms (particularly  32 P and  125 1), electron-dense reagents, enzymes, and ligands having specific binding partners. Enzymes are typically detected by their activity. For example, horseradish peroxidase is usually detected by its ability to convert 3,3′,5,5′-tetramethylbenzidine (TNB) to a blue pigment, quantifiable with a spectrophotometer. 
     A.2 In Vitro Applications of Polypeptides 
     Some polypeptides of the invention will have enzymatic activities that are useful in vitro. For example, the soybean trypsin inhibitor (Kunitz) family is one of the numerous families of proteinase inhibitors. It comprises plant proteins which have inhibitory activity against serine proteinases from the trypsin and subtilisin families, thiol proteinases and aspartic proteinases. Thus, these peptides find in vitro use in protein purification protocols and perhaps in therapeutic settings requiring topical application of protease inhibitors. 
     Delta-aminolevulinic acid dehydratase (EC 4.2.1.24) (ALAD) catalyzes the second step in the biosynthesis of heme, the condensation of two molecules of 5-aminolevulinate to form porphobilinogen and is also involved in chlorophyll biosynthesis (Kaczor et al. (1994) Plant Physiol. 1-4: 1411-7; Smith (1988) Biochem. J. 249: 423-8; Schneider (1976) Z. naturforsch. [C] 31: 55-63). Thus, ALAD proteins can be used as catalysts in synthesis of heme derivatives. Enzymes of biosynthetic pathways generally can be used as catalysts for in vitro synthesis of the compounds representing products of the pathway. 
     Polypeptides encoded by SDFs of the invention can be engineered to provide purification reagents to identify and purify additional polypeptides that bind to them. This allows one to identify proteins that function as multimers or elucidate signal transduction or metabolic pathways. In the case of DNA binding proteins, the polypeptide can be used in a similar manner to identify the DNA determinants of specific binding (S. Pierrou et al.,  Anal. Biochem.  229:99 (1995), S. Chusacultanachai et al.,  J. Biol. Chem.  274:23591 (1999), Q. Lin et al.,  J Biol. Chem.  272:27274 (1997)). 
     II.B. Polypeptide Variants, Fragments, and Fusions 
     Generally, variants, fragments, or fusions of the polypeptides encoded by the maximum length sequence (MLS) can exhibit at least one of the activities of the identified domains and/or related polypeptides described in Sections (C) and (D) of The Reference tables corresponding to the MLS of interest. 
     II.B.(1) Variants 
     A type of variant of the native polypeptides comprises amino acid substitutions. Conservative substitutions, described above (see II.), are preferred to maintain the function or activity of the polypeptide. Such substitutions include conservation of charge, polarity, hydrophobicity, size, etc. For example, one or more amino acid residues within the sequence can be substituted with another amino acid of similar polarity that acts as a functional equivalent, for example providing a hydrogen bond in an enzymatic catalysis. Substitutes for an amino acid within an exemplified sequence are preferably made among the members of the class to which the amino acid belongs. For example, the nonpolar (hydrophobic) amino acids include alanine, leucine, isoleucine, valine, proline, phenylalanine, tryptophan and methionine. The polar neutral amino acids include glycine, serine, threonine, cysteine, tyrosine, asparagine, and glutamine. The positively charged (basic) amino acids include arginine, lysine and histidine. The negatively charged (acidic) amino acids include aspartic acid and glutamic acid. 
     Within the scope of percentage of sequence identity described above, a polypeptide of the invention may have additional individual amino acids or amino acid sequences inserted into the polypeptide in the middle thereof and/or at the N-terminal and/or C-terminal ends thereof. Likewise, some of the amino acids or amino acid sequences may be deleted from the polypeptide. Amino acid substitutions may also be made in the sequences; conservative substitutions being preferred. 
     One preferred class of variants are those that comprise (1) the domain of an encoded polypeptide and/or (2) residues conserved between the encoded polypeptide and related polypeptides. For this class of variants, the encoded polypeptide sequence is changed by insertion, deletion, or substitution at positions flanking the domain and/or conserved residues. 
     Another class of variants includes those that comprise an encoded polypeptide sequence that is changed in the domain or conserved residues by a conservative substitution. 
     Yet another class of variants includes those that lack one of the in vitro activities, or structural features of the encoded polypeptides. One example is polypeptides or proteins produced from genes comprising dominant negative mutations. Such a variant may comprise an encoded polypeptide sequence with non-conservative changes in a particular domain or group of conserved residues. 
     II. A.(2) Fragments 
     Fragments of particular interest are those that comprise a domain identified for a polypeptide encoded by an MLS of the instant invention and variants thereof. Also, fragments that comprise at least one region of residues conserved between an MLS encoded polypeptide and its related polypeptides are of great interest. Fragments are sometimes useful as polypeptides corresponding to genes comprising dominant negative mutations are. 
     II.A.(3) Fusions 
     Of interest are chimeras comprising (1) a fragment of the MLS encoded polypeptide or variants thereof of interest and (2) a fragment of a polypeptide comprising the same domain. For example, an AP2 helix encoded by a MLS of the invention fused to second AP2 helix from ANT protein, which comprises two AP2 helices. The present invention also encompasses fusions of MLS encoded polypeptides, variants, or fragments thereof fused with related proteins or fragments thereof. 
     Definition of Domains 
     The polypeptides of the invention may possess identifying domains as shown in The Reference tables. Specific domains within the MLS encoded polypeptides are indicated in The Reference tables. In addition, the domains within the MLS encoded polypeptide can be defined by the region that exhibits at least 70% sequence identity with the consensus sequences listed in the detailed description below of each of the domains. 
     The majority of the protein domain descriptions given in the protein domain table are obtained from Prosite (available on the internet) and Pfam (also available on the internet). Examples of domain descriptions are listed in the Protein Domain table. 
     A. Activities of Polypeptides Comprising Signal Peptides 
     Polypeptides comprising signal peptides are a family of proteins that are typically targeted to (1) a particular organelle or intracellular compartment, (2) interact with a particular molecule or (3) for secretion outside of a host cell. Example of polypeptides comprising signal peptides include, without limitation, secreted proteins, soluble proteins, receptors, proteins retained in the ER, etc. 
     These proteins comprising signal peptides are useful to modulate ligand-receptor interactions, cell-to-cell communication, signal transduction, intracellular communication, and activities and/or chemical cascades that take part in an organism outside or within of any particular cell. 
     One class of such proteins are soluble proteins which are transported out of the cell. These proteins can act as ligands that bind to receptor to trigger signal transduction or to permit communication between cells. 
     Another class is receptor proteins which also comprise a retention domain that lodges the receptor protein in the membrane when the cell transports the receptor to the surface of the cell. Like the soluble ligands, receptors can also modulate signal transduction and communication between cells. 
     In addition the signal peptide itself can serve as a ligand for some receptors. An example is the interaction of the ER targeting signal peptide with the signal recognition particle (SRP). Here, the SRP binds to the signal peptide, halting translation, and the resulting SRP complex then binds to docking proteins located on the surface of the ER, prompting transfer of the protein into the ER. 
     A description of signal peptide residue composition is described below in Subsection IV.C.1. 
     III. Methods of Modulating Polypeptide Production 
     It is contemplated that polynucleotides of the invention can be incorporated into a host cell or in-vitro system to modulate polypeptide production. For instance, the SDFs prepared as described herein can be used to prepare expression cassettes useful in a number of techniques for suppressing or enhancing expression. 
     An example are polynucleotides comprising sequences to be transcribed, such as coding sequences, of the present invention can be inserted into nucleic acid constructs to modulate polypeptide production. Typically, such sequences to be transcribed are heterologous to at least one element of the nucleic acid construct to generate a chimeric gene or construct. 
     Another example of useful polynucleotides are nucleic acid molecules comprising regulatory sequences of the present invention. Chimeric genes or constructs can be generated when the regulatory sequences of the invention linked to heterologous sequences in a vector construct. Within the scope of invention are such chimeric gene and/or constructs. 
     Also within the scope of the invention are nucleic acid molecules, whereof at least a part or fragment of these DNA molecules are presented in the Reference and Sequence tables or polynucleotide encoding polypeptides of the Protein Group or Protein Group Matrix tables of the present application, and wherein the coding sequence is under the control of its own promoter and/or its own regulatory elements. Such molecules are useful for transforming the genome of a host cell or an organism regenerated from said host cell for modulating polypeptide production. 
     Additionally, a vector capable of producing the oligonucleotide can be inserted into the host cell to deliver the oligonucleotide. 
     More detailed description of components to be included in vector constructs are described both above and below. 
     Whether the chimeric vectors or native nucleic acids are utilized, such polynucleotides can be incorporated into a host cell to modulate polypeptide production. Native genes and/or nucleic acid molecules can be effective when exogenous to the host cell. 
     Methods of modulating polypeptide expression includes, without limitation:
         Suppression methods, such as
           Antisense   Ribozymes   Co-suppression   Insertion of Sequences into the Gene to be Modulated   Regulatory Sequence Modulation.   
           as well as Methods for Enhancing Production, such as
           Insertion of Exogenous Sequences; and   Regulatory Sequence Modulation.   
               

     III.A. Suppression 
     Expression cassettes of the invention can be used to suppress expression of endogenous genes which comprise the SDF sequence. Inhibiting expression can be useful, for instance, to tailor the ripening characteristics of a fruit (Geller et al.,  Science  254:437 (1991)) or to influence seed size_(WO98/07842) or to provoke cell ablation (Mariani et al., Nature 357: 384-387 (1992). 
     As described above, a number of methods can be used to inhibit gene expression in plants, such as antisense, ribozyme, introduction of exogenous genes into a host cell, insertion of a polynucleotide sequence into the coding sequence and/or the promoter of the endogenous gene of interest, and the like. 
     III.A.1. Antisense 
     An expression cassette as described above can be transformed into host cell or plant to produce an antisense strand of RNA. For plant cells, antisense RNA inhibits gene expression by preventing the accumulation of mRNA which encodes the enzyme of interest, see, e.g., Sheehy et al.,  Proc. Nat. Acad. Sci. USA,  85:8805 (1988), and Hiatt et al., U.S. Pat. No. 4,801,340. 
     III.A.2. Ribozymes 
     Similarly, ribozyme constructs can be transformed into a plant to cleave mRNA and down-regulate translation. 
     III.A.3. Co-Suppression 
     Another method of suppression is by introducing an exogenous copy of the gene to be suppressed. Introduction of expression cassettes in which a nucleic acid is configured in the sense orientation with respect to the promoter has been shown to prevent the accumulation of mRNA. A detailed description of this method is described above. 
     III.A.4. Insertion of Sequences into the Gene to be Modulated 
     Yet another means of suppressing gene expression is to insert a polynucleotide into the gene of interest to disrupt transcription or translation of the gene. 
     Homologous recombination could be used to target a polynucleotide insert to a gene using the Cre-Lox system (A. C. Vergunst et al.,  Nucleic Acids Res.  26:2729 (1998), A. C. Vergunst et al.,  Plant Mol. Biol.  38:393 (1998), H. Albert et al.,  Plant J.  7:649 (1995)). 
     In addition, random insertion of polynucleotides into a host cell genome can also be used to disrupt the gene of interest. Azpiroz-Leehan et al.,  Trends in Genetics  13:152 (1997). In this method, screening for clones from a library containing random insertions is preferred for identifying those that have polynucleotides inserted into the gene of interest. Such screening can be performed using probes and/or primers described above based on sequences from the Reference and Sequence tables or polynucleotides encoding polypeptides of the Protein Group or Protein Group Matrix tables, fragments thereof, and substantially similar sequence thereto. The screening can also be performed by selecting clones or any transgenic plants having a desired phenotype. 
     III.A.5. Regulatory Sequence Modulation 
     The SDFs described in the Reference and Sequence tables or polynucleotides encoding polypeptides of the Protein Group or Protein Group Matrix tables, and fragments thereof are examples of nucleotides of the invention that contain regulatory sequences that can be used to suppress or inactivate transcription and/or translation from a gene of interest as discussed in I.C.5. 
     III.A.6. Genes Comprising Dominant-Negative Mutations 
     When suppression of production of the endogenous, native protein is desired it is often helpful to express a gene comprising a dominant negative mutation. Production of protein variants produced from genes comprising dominant negative mutations is a useful tool for research Genes comprising dominant negative mutations can produce a variant polypeptide which is capable of competing with the native polypeptide, but which does not produce the native result. Consequently, over expression of genes comprising these mutations can titrate out an undesired activity of the native protein. For example, the product from a gene comprising a dominant negative mutation of a receptor can be used to constitutively activate or suppress a signal transduction cascade, allowing examination of the phenotype and thus the trait(s) controlled by that receptor and pathway. Alternatively, the protein arising from the gene comprising a dominant-negative mutation can be an inactive enzyme still capable of binding to the same substrate as the native protein and therefore competes with such native protein. 
     Products from genes comprising dominant-negative mutations can also act upon the native protein itself to prevent activity. For example, the native protein may be active only as a homo-multimer or as one subunit of a hetero-multimer. Incorporation of an inactive subunit into the multimer with native subunit(s) can inhibit activity. 
     Thus, gene function can be modulated in host cells of interest by insertion into these cells vector constructs comprising a gene comprising a dominant-negative mutation. 
     III.B. Enhanced Expression 
     Enhanced expression of a gene of interest in a host cell can be accomplished by either (1) insertion of an exogenous gene; or (2) promoter modulation. 
     III.B.1. Insertion of an Exogenous Gene 
     Insertion of an expression construct encoding an exogenous gene can boost the number of gene copies expressed in a host cell. 
     Such expression constructs can comprise genes that either encode the native protein that is of interest or that encode a variant that exhibits enhanced activity as compared to the native protein. Such genes encoding proteins of interest can be constructed from the sequences from the Reference and Sequence tables or polynucleotides encoding polypeptides of the Protein Group or Protein Group Matrix tables, fragments thereof, and substantially similar sequence thereto. 
     Such an exogenous gene can include either a constitutive promoter permitting expression in any cell in a host organism or a promoter that directs transcription only in particular cells or times during a host cell life cycle or in response to environmental stimuli. 
     III.B.2. Regulatory Sequence Modulation 
     The SDFs of the Reference and Sequence tables, and fragments thereof, contain regulatory sequences that can be used to enhance expression of a gene of interest. For example, some of these sequences contain useful enhancer elements. In some cases, duplication of enhancer elements or insertion of exogenous enhancer elements will increase expression of a desired gene from a particular promoter. As other examples, all 11 promoters require binding of a regulatory protein to be activated, while some promoters may need a protein that signals a promoter binding protein to expose a polymerase binding site. In either case, over-production of such proteins can be used to enhance expression of a gene of interest by increasing the activation time of the promoter. 
     Such regulatory proteins are encoded by some of the sequences in the Reference and Sequence tables or polynucleotides encoding polypeptides of the Protein Group or Protein Group Matrix tables, fragments thereof, and substantially similar sequences thereto. 
     Coding sequences for these proteins can be constructed as described above. 
     IV. Gene Constructs and Vector Construction 
     To use isolated SDFs of the present invention or a combination of them or parts and/or mutants and/or fusions of said SDFs in the above techniques, recombinant DNA vectors which comprise said SDFs and are suitable for transformation of cells, such as plant cells, are usually prepared. The SDF construct can be made using standard recombinant DNA techniques (Sambrook et al. 1989) and can be introduced to the species of interest by  Agrobacterium -mediated transformation or by other means of transformation (e.g., particle gun bombardment) as referenced below. 
     The vector backbone can be any of those typical in the art such as plasmids, viruses, artificial chromosomes, BACs, YACs and PACs and vectors of the sort described by
         (a) BAC: Shizuya et al., Proc. Natl. Acad. Sci. USA 89: 8794-8797 (1992); Hamilton et al., Proc. Natl. Acad. Sci. USA 93: 9975-9979 (1996);   (b) YAC: Burke et al., Science 236:806-812 (1987);   (c) PAC: Sternberg N. et al., Proc Natl Acad Sci USA. January; 87(1):103-7 (1990);   (d) Bacteria-Yeast Shuttle Vectors: Bradshaw et al., Nucl Acids Res 23: 4850-4856 (1995);   (e) Lambda Phage Vectors: Replacement Vector, e.g., Frischauf et al., J. Mol Biol 170: 827-842 (1983); or Insertion vector, e.g., Huynh et al., In: Glover NM (ed) DNA Cloning: A practical Approach, Vol. 1 Oxford: IRL Press (1985);   (f) T-DNA gene fusion vectors: Walden et al., Mol Cell Biol 1: 175-194 (1990); and   (g) Plasmid vectors: Sambrook et al., infra.       

     Typically, a vector will comprise the exogenous gene, which in its turn comprises an SDF of the present invention to be introduced into the genome of a host cell, and which gene may be an antisense construct, a ribozyme construct chimeraplast, or a coding sequence with any desired transcriptional and/or translational regulatory sequences, such as promoters, UTRs, and 3′ end termination sequences. Vectors of the invention can also include origins of replication, scaffold attachment regions (SARs), markers, homologous sequences, introns, etc. 
     A DNA sequence coding for the desired polypeptide, for example a cDNA sequence encoding a full length protein, will preferably be combined with transcriptional and translational initiation regulatory sequences which will direct the transcription of the sequence from the gene in the intended tissues of the transformed plant. 
     For example, for over-expression, a plant promoter fragment may be employed that will direct transcription of the gene in all tissues of a regenerated plant. Alternatively, the plant promoter may direct transcription of an SDF of the invention in a specific tissue (tissue-specific promoters) or may be otherwise under more precise environmental control (inducible promoters). 
     If proper polypeptide productionis desired, a polyadenylation region at the 3′-end of the coding region is typically included. The polyadenylation region can be derived from the natural gene, from a variety of other plant genes, or from T-DNA. 
     The vector comprising the sequences from genes or SDF or the invention may comprise a marker gene that confers a selectable phenotype on plant cells. The vector can include promoter and coding sequence, for instance. For example, the marker may encode biocide resistance, particularly antibiotic resistance, such as resistance to kanamycin, G418, bleomycin, hygromycin, or herbicide resistance, such as resistance to chlorosulfuron or phosphinotricin. 
     IV.A. Coding Sequences 
     Generally, the sequence in the transformation vector and to be introduced into the genome of the host cell does not need to be absolutely identical to an SDF of the present invention. Also, it is not necessary for it to be full length, relative to either the primary transcription product or fully processed mRNA. Furthermore, the introduced sequence need not have the same intron or exon pattern as a native gene. Also, heterologous non-coding segments can be incorporated into the coding sequence without changing the desired amino acid sequence of the polypeptide to be produced. 
     IV.B. Promoters 
     As explained above, introducing an exogenous SDF from the same species or an orthologous SDF from another species are useful to modulate the expression of a native gene corresponding to that SDF of interest. Such an SDF construct can be under the control of either a constitutive promoter or a highly regulated inducible promoter (e.g., a copper inducible promoter). The promoter of interest can initially be either endogenous or heterologous to the species in question. When re-introduced into the genome of said species, such promoter becomes exogenous to said species. Over-expression of an SDF transgene can lead to co-suppression of the homologous endogeneous sequence thereby creating some alterations in the phenotypes of the transformed species as demonstrated by similar analysis of the chalcone synthase gene (Napoli et al.,  Plant Cell  2:279 (1990) and van der Krol et al.,  Plant Cell  2:291 (1990)). If an SDF is found to encode a protein with desirable characteristics, its over-production can be controlled so that its accumulation can be manipulated in an organ- or tissue-specific manner utilizing a promoter having such specificity. 
     Likewise, if the promoter of an SDF (or an SDF that includes a promoter) is found to be tissue-specific or developmentally regulated, such a promoter can be utilized to drive or facilitate the transcription of a specific gene of interest (e.g., seed storage protein or root-specific protein). Thus, the level of accumulation of a particular protein can be manipulated or its spatial localization in an organ- or tissue-specific manner can be altered. 
     IV. C Signal Peptides 
     SDFs of the present invention containing signal peptides are indicated in the Reference, Sequence, the Protein Group and Protein Group Matrix tables. In some cases it may be desirable for the protein encoded by an introduced exogenous or orthologous SDF to be targeted (1) to a particular organelle intracellular compartment, (2) to interact with a particular molecule such as a membrane molecule or (3) for secretion outside of the cell harboring the introduced SDF. This will be accomplished using a signal peptide. 
     Signal peptides direct protein targeting, are involved in ligand-receptor interactions and act in cell to cell communication. Many proteins, especially soluble proteins, contain a signal peptide that targets the protein to one of several different intracellular compartments. In plants, these compartments include, but are not limited to, the endoplasmic reticulum (ER), mitochondria, plastids (such as chloroplasts), the vacuole, the Golgi apparatus, protein storage vessicles (PSV) and, in general, membranes. Some signal peptide sequences are conserved, such as the Asn-Pro-Ile-Arg amino acid motif found in the N-terminal propeptide signal that targets proteins to the vacuole (Marty (1999)  The Plant Cell  11: 587-599). Other signal peptides do not have a consensus sequence per se, but are largely composed of hydrophobic amino acids, such as those signal peptides targeting proteins to the ER (Vitale and Denecke (1999)  The Plant Cell  11: 615-628). Still others do not appear to contain either a consensus sequence or an identified common secondary sequence, for instance the chloroplast stromal targeting signal peptides (Keegstra and Cline (1999)  The Plant Cell  11: 557-570). Furthermore, some targeting peptides are bipartite, directing proteins first to an organelle and then to a membrane within the organelle (e.g. within the thylakoid lumen of the chloroplast; see Keegstra and Cline (1999)  The Plant Cell  11: 557-570). In addition to the diversity in sequence and secondary structure, placement of the signal peptide is also varied. Proteins destined for the vacuole, for example, have targeting signal peptides found at the N-terminus, at the C-terminus and at a surface location in mature, folded proteins. Signal peptides also serve as ligands for some receptors. 
     These characteristics of signal proteins can be used to more tightly control the phenotypic expression of introduced SDFs. In particular, associating the appropriate signal sequence with a specific SDF can allow sequestering of the protein in specific organelles (plastids, as an example), secretion outside of the cell, targeting interaction with particular receptors, etc. Hence, the inclusion of signal proteins in constructs involving the SDFs of the invention increases the range of manipulation of SDF phenotypic expression. The nucleotide sequence of the signal peptide can be isolated from characterized genes using common molecular biological techniques or can be synthesized in vitro. 
     In addition, the native signal peptide sequences, both amino acid and nucleotide, described in the Reference, Sequence, Protein Group or Protein Group Matrix tables can be used to modulate polypeptide transport. Further variants of the native signal peptides described in the Reference, Sequence, Protein Group or Protein Group Matrix tables are contemplated. Insertions, deletions, or substitutions can be made. Such variants will retain at least one of the functions of the native signal peptide as well as exhibiting some degree of sequence identity to the native sequence. 
     Also, fragments of the signal peptides of the invention are useful and can be fused with other signal peptides of interest to modulate transport of a polypeptide. 
     V. Transformation Techniques 
     A wide range of techniques for inserting exogenous polynucleotides are known for a number of host cells, including, without limitation, bacterial, yeast, mammalian, insect and plant cells. 
     Techniques for transforming a wide variety of higher plant species are well known and described in the technical and scientific literature. See, e.g. Weising et al.,  Ann. Rev. Genet.  22:421 (1988); and Christou, Euphytica, v. 85, n. 1-3:13-27, (1995). 
     DNA constructs of the invention may be introduced into the genome of the desired plant host by a variety of conventional techniques. For example, the DNA construct may be introduced directly into the genomic DNA of the plant cell using techniques such as electroporation and microinjection of plant cell protoplasts, or the DNA constructs can be introduced directly to plant tissue using ballistic methods, such as DNA particle bombardment. Alternatively, the DNA constructs may be combined with suitable T-DNA flanking regions and introduced into a conventional  Agrobacterium tumefaciens  host vector. The virulence functions of the  Agrobacterium tumefaciens  host will direct the insertion of the construct and adjacent marker into the plant cell DNA when the cell is infected by the bacteria (McCormac et al.,  Mol. Biotechnol.  8:199 (1997); Hamilton,  Gene  200:107 (1997)); Salomon et al.  EMBO J  3:141 (1984); Herrera-Estrella et al.  EMBO  2:987 (1983). 
     Microinjection techniques are known in the art and well described in the scientific and patent literature. The introduction of DNA constructs using polyethylene glycol precipitation is described in Paszkowski et al.  EMBO J.  3:2717 (1984). Electroporation techniques are described in Fromm et al.  Proc. Natl Acad. Sci. USA  82:5824 (1985). Ballistic transformation techniques are described in Klein et al.  Nature  327:773 (1987).  Agrobacterium tumefaciens -mediated transformation techniques, including disarming and use of binary or co-integrate vectors, are well described in the scientific literature. See, for example Hamilton, C M,  Gene  200:107 (1997); Müller et al.  Mol. Gen. Genet.  207:171 (1987); Komari et al.  Plant J.  10:165 (1996); Venkateswarlu et al.  Biotechnology  9:1103 (1991) and Gleave, A P.,  Plant Mol. Biol.  20:1203 (1992); Graves and Goldman,  Plant Mol. Biol.  7:34 (1986) and Gould et al.,  Plant Physiology  95:426 (1991). 
     Transformed plant cells which are derived by any of the above transformation techniques can be cultured to regenerate a whole plant that possesses the transformed genotype and thus the desired phenotype such as seedlessness. Such regeneration techniques rely on manipulation of certain phytohormones in a tissue culture growth medium, typically relying on a biocide and/or herbicide marker which has been introduced together with the desired nucleotide sequences. Plant regeneration from cultured protoplasts is described in Evans et al.,  Protoplasts Isolation and Culture  in “Handbook of Plant Cell Culture,” pp. 124-176, MacMillan Publishing Company, New York, 1983; and Binding,  Regeneration of Plants, Plant Protoplasts , pp. 21-73, CRC Press, Boca Raton, 1988. Regeneration can also be obtained from plant callus, explants, organs, or parts thereof. Such regeneration techniques are described generally in Klee et al.  Ann. Rev. of Plant Phys.  38:467 (1987). Regeneration of monocots (rice) is described by Hosoyama et al. ( Biosci. Biotechnol. Biochem.  58:1500 (1994)) and by Ghosh et al. ( J. Biotechnol.  32:1 (1994)). The nucleic acids of the invention can be used to confer desired traits on essentially any plant. 
     Thus, the invention has use over a broad range of plants, including species from the genera  Anacardium, Arachis, Asparagus, Atropa, Avena, Brassica, Citrus, Citrullus, Capsicum, Carthamus, Cocos, Coffea, Cucumis, Cucurbita, Daucus, Elaeis, Fragaria, Glycine, Gossypium, Helianthus, Heterocallis, Hordeum, Hyoscyamus, Lactuca, Linum, Lolium, Lupinus, Lycopersicon, Malus, Manihot, Majorana, Medicago, Nicotiana, Olea, Oryza, Panieum, Pannesetum, Persea, Phaseolus, Pistachia, Pisum, Pyrus, Prunus, Raphanus, Ricinus, Secale, Senecio, Sinapis, Solanum, Sorghum, Theobromus, Trigonella, Triticum, Vicia, Vitis, Vigna , and,  Zea.    
     One of skill will recognize that after the expression cassette is stably incorporated in transgenic plants and confirmed to be operable, it can be introduced into other plants by sexual crossing. Any of a number of standard breeding techniques can be used, depending upon the species to be crossed. 
     The particular sequences of SDFs identified are provided in the attached Reference and Sequence tables. 
     IX. Definitions 
     The following terms are utilized throughout this application: 
     Allelic variant: An “allelic variant” is an alternative form of the same SDF, which resides at the same chromosomal locus in the organism. Allelic variations can occur in any portion of the gene sequence, including regulatory regions. Allelic variants can arise by normal genetic variation in a population. Allelic variants can also be produced by genetic engineering methods. An allelic variant can be one that is found in a naturally occurring plant, including a cultivar or ecotype. An allelic variant may or may not give rise to a phenotypic change, and may or may not be expressed. An allele can result in a detectable change in the phenotype of the trait represented by the locus. A phenotypically silent allele can give rise to a product. 
     Alternatively spliced messages: Within the context of the current invention, “alternatively spliced messages” refers to mature mRNAs originating from a single gene with variations in the number and/or identity of exons, introns and/or intron-exon junctions. 
     Chimeric: The term “chimeric” is used to describe genes, as defined supra, or contructs wherein at least two of the elements of the gene or construct, such as the promoter and the coding sequence and/or other regulatory sequences and/or filler sequences and/or complements thereof, are heterologous to each other. 
     Constitutive Promoter: Promoters referred to herein as “constitutive promoters” actively promote transcription under most, but not necessarily all, environmental conditions and states of development or cell differentiation. Examples of constitutive promoters include the cauliflower mosaic virus (CaMV) 35S transcript initiation region and the 1′ or 2′ promoter derived from T-DNA of  Agrobacterium tumefaciens , and other transcription initiation regions from various plant genes, such as the maize ubiquitin-1 promoter, known to those of skill. 
     Coordinately Expressed: The term “coordinately expressed,” as used in the current invention, refers to genes that are expressed at the same or a similar time and/or stage and/or under the same or similar environmental conditions. 
     Domain: Domains are fingerprints or signatures that can be used to characterize protein families and/or parts of proteins. Such fingerprints or signatures can comprise conserved (1) primary sequence, (2) secondary structure, and/or (3) three-dimensional conformation. Generally, each domain has been associated with either a family of proteins or motifs. Typically, these families and/or motifs have been correlated with specific in-vitro and/or in-vivo activities. A domain can be any length, including the entirety of the sequence of a protein. Detailed descriptions of the domains, associated families and motifs, and correlated activities of the polypeptides of the instant invention are described below. Usually, the polypeptides with designated domain(s) can exhibit at least one activity that is exhibited by any polypeptide that comprises the same domain(s). 
     Endogenous: The term “endogenous,” within the context of the current invention refers to any polynucleotide, polypeptide or protein sequence which is a natural part of a cell or organisms regenerated from said cell. 
     Exogenous: “Exogenous,” as referred to within, is any polynucleotide, polypeptide or protein sequence, whether chimeric or not, that is initially or subsequently introduced into the genome of an individual host cell or the organism regenerated from said host cell by any means other than by a sexual cross. Examples of means by which this can be accomplished are described below, and include  Agrobacterium -mediated transformation (of dicots—e.g. Salomon et al.  EMBO  J. 3:141 (1984); Herrera-Estrella et al.  EMBO J.  2:987 (1983); of monocots, representative papers are those by Escudero et al.,  Plant J.  10:355 (1996), Ishida et al.,  Nature  Biotechnology 14:745 (1996), May et al.,  Bio/Technology  13:486 (1995)), biolistic methods (Armaleo et al.,  Current Genetics  17:97 1990)), electroporation, in planta techniques, and the like. Such a plant containing the exogenous nucleic acid is referred to here as a T 0  for the primary transgenic plant and T 1  for the first generation. The term “exogenous” as used herein is also intended to encompass inserting a naturally found element into a non-naturally found location. 
     Filler sequence: As used herein, “filler sequence” refers to any nucleotide sequence that is inserted into DNA construct to evoke a particular spacing between particular components such as a promoter and a coding region and may provide an additional attribute such as a restriction enzyme site. 
     Gene: The term “gene,” as used in the context of the current invention, encompasses all regulatory and coding sequence contiguously associated with a single hereditary unit with a genetic function (see SCHEMATIC 1). Genes can include non-coding sequences that modulate the genetic function that include, but are not limited to, those that specify polyadenylation, transcriptional regulation, DNA conformation, chromatin conformation, extent and position of base methylation and binding sites of proteins that control all of these. Genes comprised of “exons” (coding sequences), which may be interrupted by “introns” (non-coding sequences), encode proteins. A gene&#39;s genetic function may require only RNA expression or protein production, or may only require binding of proteins and/or nucleic acids without associated expression. In certain cases, genes adjacent to one another may share sequence in such a way that one gene will overlap the other. A gene can be found within the genome of an organism, artificial chromosome, plasmid, vector, etc., or as a separate isolated entity. 
     Gene Family: “Gene family” is used in the current invention to describe a group of functionally related genes, each of which encodes a separate protein. 
     Heterologous sequences: “Heterologous sequences” are those that are not operatively linked or are not contiguous to each other in nature. For example, a promoter from corn is considered heterologous to an  Arabidopsis  coding region sequence. Also, a promoter from a gene encoding a growth factor from corn is considered heterologous to a sequence encoding the corn receptor for the growth factor. Regulatory element sequences, such as UTRs or 3′ end termination sequences that do not originate in nature from the same gene as the coding sequence originates from, are considered heterologous to said coding sequence. Elements operatively linked in nature and contiguous to each other are not heterologous to each other. On the other hand, these same elements remain operatively linked but become heterologous if other filler sequence is placed between them. Thus, the promoter and coding sequences of a corn gene expressing an amino acid transporter are not heterologous to each other, but the promoter and coding sequence of a corn gene operatively linked in a novel manner are heterologous. 
     Homologous gene: In the current invention, “homologous gene” refers to a gene that shares sequence similarity with the gene of interest. This similarity may be in only a fragment of the sequence and often represents a functional domain such as, examples including without limitation a DNA binding domain, a domain with tyrosine kinase activity, or the like. The functional activities of homologous genes are not necessarily the same. 
     Inducible Promoter: An “inducible promoter” in the context of the current invention refers to a promoter which is regulated under certain conditions, such as light, chemical concentration, protein concentration, conditions in an organism, cell, or organelle, etc. A typical example of an inducible promoter, which can be utilized with the polynucleotides of the present invention, is PARSK1, the promoter from the  Arabidopsis  gene encoding a serine-threonine kinase enzyme, and which promoter is induced by dehydration, abscissic acid and sodium chloride (Wang and Goodman,  Plant J.  8:37 (1995)) Examples of environmental conditions that may affect transcription by inducible promoters include anaerobic conditions, elevated temperature, or the presence of light. 
     Intergenic region: “Intergenic region,” as used in the current invention, refers to nucleotide sequence occurring in the genome that separates adjacent genes. 
     Mutant gene: In the current invention, “mutant” refers to a heritable change in DNA sequence at a specific location. Mutants of the current invention may or may not have an associated identifiable function when the mutant gene is transcribed. 
     Orthologous Gene: In the current invention “orthologous gene” refers to a second gene that encodes a gene product that performs a similar function as the product of a first gene. The orthologous gene may also have a degree of sequence similarity to the first gene. The orthologous gene may encode a polypeptide that exhibits a degree of sequence similarity to a polypeptide corresponding to a first gene. The sequence similarity can be found within a functional domain or along the entire length of the coding sequence of the genes and/or their corresponding polypeptides. 
     Percentage of sequence identity: “Percentage of sequence identity,” as used herein, is determined by comparing two optimally aligned sequences over a comparison window, where the fragment of the polynucleotide or amino acid sequence in the comparison window may comprise additions or deletions (e.g., gaps or overhangs) as compared to the reference sequence (which does not comprise additions or deletions) for optimal alignment of the two sequences. The percentage is calculated by determining the number of positions at which the identical nucleic acid base or amino acid residue occurs in both sequences to yield the number of matched positions, dividing the number of matched positions by the total number of positions in the window of comparison and multiplying the result by 100 to yield the percentage of sequence identity. Optimal alignment of sequences for comparison may be conducted by the local homology algorithm of Smith and Waterman  Add. APL. Math.  2:482 (1981), by the homology alignment algorithm of Needleman and Wunsch  J. Mol. Biol.  48:443 (1970), by the search for similarity method of Pearson and Lipman  Proc. Natl. Acad Sci . ( USA ) 85: 2444 (1988), by computerized implementations of these algorithms (GAP, BESTFIT, BLAST, PASTA, and TFASTA in the Wisconsin Genetics Software Package, Genetics Computer Group (GCG), 575 Science Dr., Madison, Wis.), or by inspection. Given that two sequences have been identified for comparison, GAP and BESTFIT are preferably employed to determine their optimal alignment. Typically, the default values of 5.00 for gap weight and 0.30 for gap weight length are used. The term “substantial sequence identity” between polynucleotide or polypeptide sequences refers to polynucleotide or polypeptide comprising a sequence that has at least 80% sequence identity, preferably at least 85%, more preferably at least 90% and most preferably at least 95%, even more preferably, at least 96%, 97%, 98% or 99% sequence identity compared to a reference sequence using the programs. 
     Plant Promoter: A “plant promoter” is a promoter capable of initiating transcription in plant cells and can drive or facilitate transcription of a fragment of the SDF of the instant invention or a coding sequence of the SDF of the instant invention. Such promoters need not be of plant origin. For example, promoters derived from plant viruses, such as the CaMV35S promoter or from  Agrobacterium tumefaciens  such as the T-DNA promoters, can be plant promoters. A typical example of a plant promoter of plant origin is the maize ubiquitin-1 (ubi-1)promoter known to those of skill. 
     Promoter: The term “promoter,” as used herein, refers to a region of sequence determinants located upstream from the start of transcription of a gene and which are involved in recognition and binding of RNA polymerase and other proteins to initiate and modulate transcription. A basal promoter is the minimal sequence necessary for assembly of a transcription complex required for transcription initiation. Basal promoters frequently include a “TATA box” element usually located between 15 and 35 nucleotides upstream from the site of initiation of transcription. Basal promoters also sometimes include a “CCAAT box” element (typically a sequence CCAAT) (SEQ ID NO:200515) and/or a GGGCG sequence (SEQ ID NO:200516), usually located between 40 and 200 nucleotides, preferably 60 to 120 nucleotides, upstream from the start site of transcription. 
     Public sequence: The term “public sequence,” as used in the context of the instant application, refers to any sequence that has been deposited in a publicly accessible database. This term encompasses both amino acid and nucleotide sequences. Such sequences are publicly accessible, for example, on the BLAST databases on the NCBI FTP web site (accessible at ncbi.nlm.gov/blast). The database at the NCBI GTP site utilizes “gi” numbers assigned by NCBI as a unique identifier for each sequence in the databases, thereby providing a non-redundant database for sequence from various databases, including GenBank, EMBL, DBBJ, (DNA Database of Japan) and PDB (Brookhaven Protein Data Bank). 
     Regulatory Sequence: The term “regulatory sequence,” as used in the current invention, refers to any nucleotide sequence that influences transcription or translation initiation and rate, and stability and/or mobility of the transcript or polypeptide product. Regulatory sequences include, but are not limited to, promoters, promoter control elements, protein binding sequences, 5′ and 3′ UTRs, transcriptional start site, termination sequence, polyadenylation sequence, introns, certain sequences within a coding sequence, etc. 
     Related Sequences: “Related sequences” refer to either a polypeptide or a nucleotide sequence that exhibits some degree of sequence similarity with a sequence described by The Reference tables and The Sequence tables. 
     Scaffold Attachment Region (SAR): As used herein, “scaffold attachment region” is a DNA sequence that anchors chromatin to the nuclear matrix or scaffold to generate loop domains that can have either a transcriptionally active or inactive structure (Spiker and Thompson (1996) Plant Physiol. 110: 15-21). 
     Sequence-determined DNA fragments (SDFs): “Sequence-determined DNA fragments” as used in the current invention are isolated sequences of genes, fragments of genes, intergenic regions or contiguous DNA from plant genomic DNA or cDNA or RNA the sequence of which has been determined. 
     Signal Peptide: A “signal peptide” as used in the current invention is an amino acid sequence that targets the protein for secretion, for transport to an intracellular compartment or organelle or for incorporation into a membrane. Signal peptides are indicated in the tables and a more detailed description located below. 
     Specific Promoter: In the context of the current invention, “specific promoters” refers to a subset of inducible promoters that have a high preference for being induced in a specific tissue or cell and/or at a specific time during development of an organism. By “high preference” is meant at least 3-fold, preferably 5-fold, more preferably at least 10-fold still more preferably at least 20-fold, 50-fold or 100-fold increase in transcription in the desired tissue over the transcription in any other tissue. Typical examples of temporal and/or tissue specific promoters of plant origin that can be used with the polynucleotides of the present invention, are: PTA29, a promoter which is capable of driving gene transcription specifically in tapetum and only during anther development (Koltonow et al.,  Plant Cell  2:1201 (1990); RCc2 and RCc3, promoters that direct root-specific gene transcription in rice (Xu et al.,  Plant Mol. Biol.  27:237 (1995); TobRB27, a root-specific promoter from tobacco (Yamamoto et al.,  Plant Cell  3:371 (1991)). Examples of tissue-specific promoters under developmental control include promoters that initiate transcription only in certain tissues or organs, such as root, ovule, fruit, seeds, or flowers. Other suitable promoters include those from genes encoding storage proteins or the lipid body membrane protein, oleosin. A few root-specific promoters are noted above. 
     Stringency: “Stringency” as used herein is a function of probe length, probe composition (G+C content), and salt concentration, organic solvent concentration, and temperature of hybridization or wash conditions. Stringency is typically compared by the parameter T m , which is the temperature at which 50% of the complementary molecules in the hybridization are hybridized, in terms of a temperature differential from T m . High stringency conditions are those providing a condition of T m −5° C. to T m −10° C. Medium or moderate stringency conditions are those providing T m −20° C. to T m −29° C. Low stringency conditions are those providing a condition of T m −40° C. to T m −48° C. The relationship of hybridization conditions to T m  (in ° C.) is expressed in the mathematical equation
 
 T   m =81.5−16.6(log 10 [Na + ])+0.41(%  G+C )−(600/ N )  (1)
 
where N is the length of the probe. This equation works well for probes 14 to 70 nucleotides in length that are identical to the target sequence. The equation below for T m  of DNA-DNA hybrids is useful for probes in the range of 50 to greater than 500 nucleotides, and for conditions that include an organic solvent (formamide).
 
 T   m =81.5+16.6 log {[Na + ]/(1+0.7[Na + ])}+0.41(%  G+C )−500/ L  0.63(% formamide)  (2)
 
where L is the length of the probe in the hybrid. (P. Tijessen, “Hybridization with Nucleic Acid Probes” in Laboratory Techniques in Biochemistry and Molecular Biology, P. C. vand der Vliet, ed., c. 1993 by Elsevier, Amsterdam.) The T m  of equation (2) is affected by the nature of the hybrid; for DNA-RNA hybrids T m  is 10-15° C. higher than calculated, for RNA-RNA hybrids T m  is 20-25° C. higher. Because the T m  decreases about 1° C. for each 1% decrease in homology when a long probe is used (Bonner et al.,  J. Mol. Biol.  81:123 (1973)), stringency conditions can be adjusted to favor detection of identical genes or related family members.
 
     Equation (2) is derived assuming equilibrium and therefore, hybridizations according to the present invention are most preferably performed under conditions of probe excess and for sufficient time to achieve equilibrium. The time required to reach equilibrium can be shortened by inclusion of a hybridization accelerator such as dextran sulfate or another high volume polymer in the hybridization buffer. 
     Stringency can be controlled during the hybridization reaction or after hybridization has occurred by altering the salt and temperature conditions of the wash solutions used. The formulas shown above are equally valid when used to compute the stringency of a wash solution. Preferred wash solution stringencies lie within the ranges stated above; high stringency is 5-8° C. below T m , medium or moderate stringency is 26-29° C. below T m  and low stringency is 45-48° C. below T m . 
     Substantially free of: A composition containing A is “substantially free of” B when at least 85% by weight of the total A+B in the composition is A. Preferably, A comprises at least about 90% by weight of the total of A+B in the composition, more preferably at least about 95% or even 99% by weight. For example, a plant gene or DNA sequence can be considered substantially free of other plant genes or DNA sequences. 
     Translational start site: In the context of the current invention, a “translational start site” is usually an ATG in the cDNA transcript, more usually the first ATG. A single cDNA, however, may have multiple translational start sites. 
     Transcription start site: “Transcription start site” is used in the current invention to describe the point at which transcription is initiated. This point is typically located about 25 nucleotides downstream from a TFIID binding site, such as a TATA box. Transcription can initiate at one or more sites within the gene, and a single gene may have multiple transcriptional start sites, some of which may be specific for transcription in a particular cell-type or tissue. 
     Untranslated region (UTR): A “UTR” is any contiguous series of nucleotide bases that is transcribed, but is not translated. These untranslated regions may be associated with particular functions such as increasing mRNA message stability. Examples of UTRs include, but are not limited to polyadenylation signals, terminations sequences, sequences located between the transcriptional start site and the first exon (5′ UTR) and sequences located between the last exon and the end of the mRNA (3′ UTR). 
     Variant: The term “variant” is used herein to denote a polypeptide or protein or polynucleotide molecule that differs from others of its kind in some way. For example, polypeptide and protein variants can consist of changes in amino acid sequence and/or charge and/or post-translational modifications (such as glycosylation, etc). 
     X. Examples 
     The invention is illustrated by way of the following examples. The invention is not limited by these examples as the scope of the invention is defined solely by the claims following. 
     Example 1: cDNA Preparation 
     A number of the nucleotide sequences disclosed in the Reference and Sequence tables or polynucleotides encoding polypeptides of the Protein Group or Protein Group Matrix tables, herein as representative of the SDFs of the invention can be obtained by sequencing genomic DNA (gDNA) and/or cDNA from corn plants grown from HYBRID SEED #35A19, purchased from Pioneer Hi-Bred International, Inc., Supply Management, P.O. Box 256, Johnston, Iowa 50131-0256. 
     A number of the nucleotide sequences disclosed in the Reference and Sequence tables or polynucleotides encoding polypeptides of the Protein Group or Protein Group Matrix tables, herein as representative of the SDFs of the invention can also be obtained by sequencing genomic DNA from  Arabidopsis thaliana , Wassilewskija ecotype or by sequencing cDNA obtained from mRNA from such plants as described below. This is a true breeding strain. Seeds of the plant are available from the  Arabidopsis  Biological Resource Center at the Ohio State University, under the accession number CS2360. Seeds of this plant were deposited under the terms and conditions of the Budapest Treaty at the American Type Culture Collection, Manassas, Va. on Aug. 31, 1999, and were assigned ATCC No. PTA-595. 
     Other methods for cloning full-length cDNA are described, for example, by Seki et al.,  Plant Journal  15:707-720 (1998) “High-efficiency cloning of  Arabidopsis  full-length cDNA by biotinylated Cap trapper”; Maruyama et al.,  Gene  138:171 (1994) “Oligo-capping a simple method to replace the cap structure of eukaryotic mRNAs with oligoribonucleotides”; and WO 96/34981. 
     Tissues were, or each organ was, individually pulverized and frozen in liquid nitrogen. Next, the samples were homogenized in the presence of detergents and then centrifuged. The debris and nuclei were removed from the sample and more detergents were added to the sample. The sample was centrifuged and the debris was removed. Then the sample was applied to a 2M sucrose cushion to isolate polysomes. The RNA was isolated by treatment with detergents and proteinase K followed by ethanol precipitation and centrifugation. The polysomal RNA from the different tissues was pooled according to the following mass ratios: 15/15/1 for male inflorescences, female inflorescences and root, respectively. The pooled material was then used for cDNA synthesis by the methods described below. 
     Starting material for cDNA synthesis for the exemplary corn cDNA clones with sequences presented in the Reference and Sequence tables or polynucleotides encoding polypeptides of the Protein Group or Protein Group Matrix tables was poly(A)-containing polysomal mRNAs from inflorescences and root tissues of corn plants grown from HYBRID SEED #35A19. Male inflorescences and female (pre- and post-fertilization) inflorescences were isolated at various stages of development. Selection for poly(A) containing polysomal RNA was done using oligo d(T) cellulose columns, as described by Cox and Goldberg, “Plant Molecular Biology: A Practical Approach”, pp. 1-35, Shaw ed., c. 1988 by IRL, Oxford. The quality and the integrity of the polyA+ RNAs were evaluated. 
     Starting material for cDNA synthesis for the exemplary  Arabidopsis  cDNA clones with sequences presented in the Reference and Sequence tables or polynucleotides encoding polypeptides of the Protein Group or Protein Group Matrix tables was polysomal RNA isolated from the top-most inflorescence tissues of  Arabidopsis thaliana  Wassilewskija (Ws.) and from roots of  Arabidopsis thaliana  Landsberg  erecta  (L. er.), also obtained from the  Arabidopsis  Biological Resource Center. Nine parts inflorescence to every part root was used, as measured by wet mass. Tissue was pulverized and exposed to liquid nitrogen. Next, the sample was homogenized in the presence of detergents and then centrifuged. The debris and nuclei were removed from the sample and more detergents were added to the sample. The sample was centrifuged and the debris was removed and the sample was applied to a 2M sucrose cushion to isolate polysomal RNA. Cox et al., “Plant Molecular Biology: A Practical Approach”, pp. 1-35, Shaw ed., c. 1988 by IRL, Oxford. The polysomal RNA was used for cDNA synthesis by the methods described below. Polysomal mRNA was then isolated as described above for corn cDNA. The quality of the RNA was assessed electrophoretically. 
     Following preparation of the mRNAs from various tissues as described above, selection of mRNA with intact 5′ ends and specific attachment of an oligonucleotide tag to the 5′ end of such mRNA was performed using either a chemical or enzymatic approach. Both techniques take advantage of the presence of the “cap” structure, which characterizes the 5′ end of most intact mRNAs and which comprises a guanosine generally methylated once, at the 7 position. 
     The chemical modification approach involves the optional elimination of the 2′,3′-cis diol of the 3′ terminal ribose, the oxidation of the 2′,3′-cis diol of the ribose linked to the cap of the 5′ ends of the mRNAs into a dialdehyde, and the coupling of the such obtained dialdehyde to a derivatized oligonucleotide tag. Further detail regarding the chemical approaches for obtaining mRNAs having intact 5′ ends are disclosed in International Application No. WO96/34981 published Nov. 7, 1996. 
     The enzymatic approach for ligating the oligonucleotide tag to the intact 5′ ends of mRNAs involves the removal of the phosphate groups present on the 5′ ends of uncapped incomplete mRNAs, the subsequent decapping of mRNAs having intact 5′ ends and the ligation of the phosphate present at the 5′ end of the decapped mRNA to an oligonucleotide tag. Further detail regarding the enzymatic approaches for obtaining mRNAs having intact 5′ ends are disclosed in Dumas Milne Edwards J. B. (Doctoral Thesis of Paris VI University, Le clonage des ADNc complets: difficultés et perspectives nouvelles. Apports pour l&#39;etude de la regulation de l&#39;expression de la tryptophane hydroxylase de rat, 20 Dec. 1993), EPO 625572 and Kato et al.,  Gene  150:243-250 (1994). 
     In both the chemical and the enzymatic approach, the oligonucleotide tag has a restriction enzyme site (e.g. an EcoRI site) therein to facilitate later cloning procedures. Following attachment of the oligonucleotide tag to the mRNA, the integrity of the mRNA is examined by performing a Northern blot using a probe complementary to the oligonucleotide tag. 
     For the mRNAs joined to oligonucleotide tags using either the chemical or the enzymatic method, first strand cDNA synthesis is performed using an oligo-dT primer with reverse transcriptase. This oligo-dT primer can contain an internal tag of at least 4 nucleotides, which can be different from one mRNA preparation to another. Methylated dCTP is used for cDNA first strand synthesis to protect the internal EcoRI sites from digestion during subsequent steps. The first strand cDNA is precipitated using isopropanol after removal of RNA by alkaline hydrolysis to eliminate residual primers. 
     Second strand cDNA synthesis is conducted using a DNA polymerase, such as Klenow fragment and a primer corresponding to the 5′ end of the ligated oligonucleotide. The primer is typically 20-25 bases in length. Methylated dCTP is used for second strand synthesis in order to protect internal EcoRI sites in the cDNA from digestion during the cloning process. 
     Following second strand synthesis, the full-length cDNAs are cloned into a phagemid vector, such as pBlueScript™ (Stratagene). The ends of the full-length cDNAs are blunted with T4 DNA polymerase (Biolabs) and the cDNA is digested with EcoRI. Since methylated dCTP is used during cDNA synthesis, the EcoRI site present in the tag is the only hemi-methylated site; hence the only site susceptible to EcoRI digestion. In some instances, to facilitate subcloning, an Hind III adapter is added to the 3′ end of full-length cDNAs. 
     The full-length cDNAs are then size fractionated using either exclusion chromatography (AcA, Biosepra) or electrophoretic separation which yields 3 to 6 different fractions. The full-length cDNAs are then directionally cloned either into pBlueScript™ using either the EcoRI and SmaI restriction sites or, when the Hind III adapter is present in the full-length cDNAs, the EcoRI and Hind III restriction sites. The ligation mixture is transformed, preferably by electroporation, into bacteria, which are then propagated under appropriate antibiotic selection. 
     Clones containing the oligonucleotide tag attached to full-length cDNAs are selected as follows. 
     The plasmid cDNA libraries made as described above are purified (e.g. by a column available from Qiagen). A positive selection of the tagged clones is performed as follows. Briefly, in this selection procedure, the plasmid DNA is converted to single stranded DNA using phage F1 gene II endonuclease in combination with an exonuclease (Chang et al.,  Gene  127:95 (1993)) such as exonuclease III or T7 gene 6 exonuclease. The resulting single stranded DNA is then purified using paramagnetic beads as described by Fry et al.,  Biotechniques  13: 124 (1992). Here the single stranded DNA is hybridized with a biotinylated oligonucleotide having a sequence corresponding to the 3′ end of the oligonucleotide tag. Preferably, the primer has a length of 20-25 bases. Clones including a sequence complementary to the biotinylated oligonucleotide are selected by incubation with streptavidin coated magnetic beads followed by magnetic capture. After capture of the positive clones, the plasmid DNA is released from the magnetic beads and converted into double stranded DNA using a DNA polymerase such as ThermoSequenase™ (obtained from Amersham Pharmacia Biotech). Alternatively, protocols such as the Gene Trapper™ kit (Gibco BRL) can be used. The double stranded DNA is then transformed, preferably by electroporation, into bacteria. The percentage of positive clones having the 5′ tag oligonucleotide is typically estimated to be between 90 and 98% from dot blot analysis. 
     Following transformation, the libraries are ordered in microtiter plates and sequenced. The  Arabidopsis  library was deposited at the American Type Culture Collection on Jan. 7, 2000 as “ E - coli  liba 010600” under the accession number PTA-1161. 
     B. Example 2: Southern Hybridizations 
     The SDFs of the invention can be used in Southern hybridizations as described above. The following describes extraction of DNA from nuclei of plant cells, digestion of the nuclear DNA and separation by length, transfer of the separated fragments to membranes, preparation of probes for hybridization, hybridization and detection of the hybridized probe. 
     The procedures described herein can be used to isolate related polynucleotides or for diagnostic purposes. Moderate stringency hybridization conditions, as defined above, are described in the present example. These conditions result in detection of hybridization between sequences having at least 70% sequence identity. As described above, the hybridization and wash conditions can be changed to reflect the desired percenatge of sequence identity between probe and target sequences that can be detected. 
     In the following procedure, a probe for hybridization is produced from two PCR reactions using two primers from genomic sequence of  Arabidopsis thaliana . As described above, the particular template for generating the probe can be any desired template. 
     The first PCR product is assessed to validate the size of the primer to assure it is of the expected size. Then the product of the first PCR is used as a template, with the same pair of primers used in the first PCR, in a second PCR that produces a labeled product used as the probe. 
     Fragments detected by hybridization, or other bands of interest, can be isolated from gels used to separate genomic DNA fragments by known methods for further purification and/or characterization. 
     Buffers for nuclear DNA extraction 
     
         
         1. 10×HB 
       
    
     
       
         
           
               
               
               
             
               
                   
               
               
                   
                 1000 ml 
                   
               
               
                   
               
             
            
               
                   
               
            
           
           
               
               
               
               
            
               
                 40 mM spermidine 
                 10.2  
                 g 
                 Spermine (Sigma S-2876) and spermidine  
               
               
                   
                   
                   
                 (Sigma S-2501) 
               
               
                 10 mM spermine 
                 3.5  
                 g 
                 Stabilize chromatin and the  
               
               
                   
                   
                   
                 nuclear membrane 
               
               
                 0.1M EDTA 
                 37.2  
                 g 
                 EDTA inhibits nuclease 
               
               
                 (disodium) 
                   
                   
                   
               
               
                 0.1M Tris 
                 12.1  
                 g 
                 Buffer 
               
               
                 0.8M KCl 
                 59.6  
                 g 
                 Adjusts ionic strength for stability  
               
               
                   
                   
                   
                 of nuclei 
               
               
                   
               
            
           
         
       
         
         
           
             Adjust pH to 9.5 with 10 N NaOH. It appears that there is a nuclease present in leaves. Use of pH 9.5 appears to inactivate this nuclease. 
           
         
         2. 2 M sucrose (684 g per 1000 ml)
       Heat about half the final volume of water to about 50° C. Add the sucrose slowly then bring the mixture to close to final volume; stir constantly until it has dissolved. Bring the solution to volume.   
     
         3. Sarkosyl solution (lyses nuclear membranes) 
       
    
     
       
         
           
               
               
               
             
               
                   
                   
               
               
                   
                   
                 1000 ml 
               
               
                   
                   
               
             
            
               
                   
                 N-lauroyl sarcosine (Sarkosyl) 
                 20.0 g 
               
               
                   
                 0.1M Tris 
                 12.1 g 
               
               
                   
                 0.04M EDTA (Disodium) 
                 14.9 g 
               
               
                   
                   
               
            
           
         
       
         
         
           
             Adjust the pH to 9.5 after all the components are dissolved and bring up to the proper volume. 
           
         
         4. 20% TRITON® X-100
       80 ml TRITON® X-100   320 ml 1×HB (w/o β-ME and PMSF)   Prepare in advance; TRITON® takes some time to dissolve
 
A. Procedure
   
     
         1. Prepare 1× “H” buffer (keep ice-cold during use) 
       
    
     
       
         
           
               
               
               
             
               
                   
                   
               
               
                   
                   
                 1000 ml 
               
               
                   
                   
               
             
            
               
                   
                 10× HB 
                 100 ml 
               
               
                   
                 2M sucrose 
                 250 ml a non-ionic osmoticum  
               
               
                   
                 Water 
                 634 ml 
               
               
                   
                   
               
            
           
         
       
         
         
           
             Added just before use: 
           
         
       
    
     
       
         
           
               
               
             
               
                   
               
             
            
               
                 100 mM PMSF* 
                 10 ml a protease inhibitor; protects nuclear 
               
               
                   
                 membrane proteins 
               
               
                 β-mercaptoethanol 
                 1 ml inactivates nuclease by reducing 
               
               
                   
                 disulfide bonds 
               
               
                   
               
               
                 *100 mM PMSF (phenyl methyl sulfonyl fluoride, Sigma P-7626) (add 0.0875 g to 5 ml 100% ethanol) 
               
            
           
         
       
         
         2. Homogenize the tissue in a blender (use 300-400 ml of 1×HB per blender). Be sure that you use 5-10 ml of HB buffer per gram of tissue. Blenders generate heat so be sure to keep the homogenate cold. It is necessary to put the blenders in ice periodically. 
         3. Add the 20% TRITON® X-100 (25 ml per liter of homogenate) and gently stir on ice for 20 min. This lyses plastid, but not nuclear, membranes. 
         4. Filter the tissue suspension through several nylon filters into an ice-cold beaker. The first filtration is through a 250-micron membrane; the second is through an 85-micron membrane; the third is through a 50-micron membrane; and the fourth is through a 20-micron membrane. Use a large funnel to hold the filters. Filtration can be sped up by gently squeezing the liquid through the filters. 
         5. Centrifuge the filtrate at 1200×g for 20 min. at 4° C. to pellet the nuclei. 
         6. Discard the dark green supernatant. The pellet will have several layers to it. One is starch; it is white and gritty. The nuclei are gray and soft. In the early steps, there may be a dark green and somewhat viscous layer of chloroplasts.
       Wash the pellets in about 25 ml cold H buffer (with TRITON® X-100) and resuspend by swirling gently and pipetting. After the pellets are resuspended.   Pellet the nuclei again at 1200-1300×g. Discard the supernatant.   Repeat the wash 3-4 times until the supernatant has changed from a dark green to a pale green. This usually happens after 3 or 4 resuspensions. At this point, the pellet is typically grayish white and very slippery. The TRITON® X-100 in these repeated steps helps to destroy the chloroplasts and mitochondria that contaminate the prep.   Resuspend the nuclei for a final time in a total of 15 ml of H buffer and transfer the suspension to a sterile 125 ml Erlenmeyer flask.   
     
         7. Add 15 ml, dropwise, cold 2% Sarkosyl, 0.1 M Tris, 0.04 M EDTA solution (pH 9.5) while swirling gently. This lyses the nuclei. The solution will become very viscous. 
         8. Add 30 grams of CsCl and gently swirl at room temperature until the CsCl is in solution. The mixture will be gray, white and viscous. 
         9. Centrifuge the solution at 11,400×g at 4° C. for at least 30 min. The longer this spin is, the firmer the protein pellicle. 
         10. The result is typically a clear green supernatant over a white pellet, and (perhaps) under a protein pellicle. Carefully remove the solution under the protein pellicle and above the pellet. Determine the density of the solution by weighing 1 ml of solution and add CsCl if necessary to bring to 1.57 g/ml. The solution contains dissolved solids (sucrose etc) and the refractive index alone will not be an accurate guide to CsCl concentration. 
         11. Add 20 μl of 10 mg/ml EtBr per ml of solution. 
         12. Centrifuge at 184,000×g for 16 to 20 hours in a fixed-angle rotor. 
         13. Remove the dark red supernatant that is at the top of the tube with a plastic transfer pipette and discard. Carefully remove the DNA band with another transfer pipette. The DNA band is usually visible in room light; otherwise, use a long wave UV light to locate the band. 
         14. Extract the ethidium bromide with isopropanol saturated with water and salt. Once the solution is clear, extract at least two more times to ensure that all of the EtBr is gone. Be very gentle, as it is very easy to shear the DNA at this step. This extraction may take a while because the DNA solution tends to be very viscous. If the solution is too viscous, dilute it with TE. 
         15. Dialyze the DNA for at least two days against several changes (at least three times) of TE (10 mM Tris, 1 mM EDTA, pH 8) to remove the cesium chloride. 
         16. Remove the dialyzed DNA from the tubing. If the dialyzed DNA solution contains a lot of debris, centrifuge the DNA solution at least at 2500×g for 10 min. and carefully transfer the clear supernatant to a new tube. Read the A260 concentration of the DNA. 
         17. Assess the quality of the DNA by agarose gel electrophoresis (1% agarose gel) of the DNA. Load 50 ng and 100 ng (based on the OD reading) and compare it with known and good quality DNA. Undigested lambda DNA and a lambda-HindIII-digested DNA are good molecular weight makers.
 
Protocol for Digestion of Genomic DNA
 
Protocol:
 
         1. The relative amounts of DNA for different crop plants that provide approximately a balanced number of genome equivalent is given in Table 3. Note that due to the size of the wheat genome, wheat DNA will be underrepresented. Lambda DNA provides a useful control for complete digestion. 
         2. Precipitate the DNA by adding 3 volumes of 100% ethanol. Incubate at −20° C. for at least two hours. Yeast DNA can be purchased and made up at the necessary concentration, therefore no precipitation is necessary for yeast DNA. 
         3. Centrifuge the solution at 11,400×g for 20 min. Decant the ethanol carefully (be careful not to disturb the pellet). Be sure that the residual ethanol is completely removed either by vacuum desiccation or by carefully wiping the sides of the tubes with a clean tissue. 
         4. Resuspend the pellet in an appropriate volume of water. Be sure the pellet is fully resuspended before proceeding to the next step. This may take about 30 min. 
         5. Add the appropriate volume of 10× reaction buffer provided by the manufacturer of the restriction enzyme to the resuspended DNA followed by the appropriate volume of enzymes. Be sure to mix it properly by slowly swirling the tubes. 
         6. Set-up the lambda digestion-control for each DNA that you are digesting. 
         7. Incubate both the experimental and lambda digests overnight at 37° C. Spin down condensation in a microfuge before proceeding. 
         8. After digestion, add 2 μl of loading dye (typically 0.25% bromophenol blue, 0.25% xylene cyanol in 15% Ficoll or 30% glycerol) to the lambda-control digests and load in 1% TPE-agarose gel (TPE is 90 mM Tris-phosphate, 2 mM EDTA, pH 8). If the lambda DNA in the lambda control digests are completely digested, proceed with the precipitation of the genomic DNA in the digests. 
         9. Precipitate the digested DNA by adding 3 volumes of 100% ethanol and incubating in −20° C. for at least 2 hours (preferably overnight).
       EXCEPTION:  Arabidopsis  and yeast DNA are digested in an appropriate volume; they don&#39;t have to be precipitated.   
     
         10. Resuspend the DNA in an appropriate volume of TE (e.g., 22 μl×50 blots=1100 μl) and an appropriate volume of 10× loading dye (e.g., 2.4 μl×50 blots=120 μl). Be careful in pipetting the loading dye—it is viscous. Be sure you are pipetting the correct volume. 
       
    
                     TABLE 3                  Some guide points in digesting genomic DNA.                                             Genome                       Equivalent to 2   Amount           Genome   Size Relative to   μg  Arabidopsis     of DNA       Species   Size     Arabidopsis     DNA   per blot                                                   Arabidopsis     120    Mb     1×      1×   2    μg         Brassica     1,100    Mb    9.2×   0.54×   10    μg       Corn   2,800    Mb   23.3×   0.43×   20   μg       Cotton   2,300    Mb   19.2×   0.52×   20    μg       Oat   11,300    Mb     94×   0.11×   20   μg       Rice   400    Mb    3.3×   0.75×   5   μg       Soybean   1,100    Mb    9.2×   0.54×   10   μg       Sugarbeet   758    Mb    6.3×    0.8×   10    μg       Sweetclover   1,100    Mb    9.2×   0.54×   10    μg       Wheat   16,000    Mb    133×   0.08×   20    μg       Yeast   15    Mb   0.12×      1×   0.25    μg                    
Protocol for Southern Blot Analysis
 
     The digested DNA samples are electrophoresed in 1% agarose gels in 1×TPE buffer. Low voltage; overnight separations are preferred. The gels are stained with EtBr and photographed.
     1. For blotting the gels, first incubate the gel in 0.25 N HCl (with gentle shaking) for about 15 min.   2. Then briefly rinse with water. The DNA is denatured by 2 incubations. Incubate (with shaking) in 0.5 M NaOH in 1.5 M NaCl for 15 min.   3. The gel is then briefly rinsed in water and neutralized by incubating twice (with shaking) in 1.5 M Tris pH 7.5 in 1.5 M NaCl for 15 min.   4. A nylon membrane is prepared by soaking it in water for at least 5 min, then in 6×SSC for at least 15 min. before use. (20×SSC is 175.3 g NaCl, 88.2 g sodium citrate per liter, adjusted to pH 7.0.)   5. The nylon membrane is placed on top of the gel and all bubbles in between are removed. The DNA is blotted from the gel to the membrane using an absorbent medium, such as paper toweling and 6×SCC buffer. After the transfer, the membrane may be lightly brushed with a gloved hand to remove any agarose sticking to the surface.   6. The DNA is then fixed to the membrane by UV crosslinking and baking at 80° C. The membrane is stored at 4° C. until use.
 
B. Protocol for PCR Amplification of Genomic Fragments in  Arabidopsis  
 
Amplification Procedures:
   

     1. Mix the following in a 0.20 ml PCR tube or 96-well PCR plate: 
     
       
         
           
               
               
               
             
               
                   
               
               
                 Volume 
                 Stock 
                 Final Amount or Conc. 
               
               
                   
               
             
            
               
                   
               
            
           
           
               
               
               
               
               
            
               
                 0.5  
                 μl 
                 ~10 ng/μl genomic DNA 1   
                 5  
                 ng 
               
            
           
           
               
               
               
               
            
               
                 2.5  
                 μl 
                 10× PCR buffer 
                 20 mM Tris, 50 mM KCl 
               
            
           
           
               
               
               
               
               
            
               
                 0.75  
                 μl 
                 50 mM MgCl 2   
                 1.5  
                 mM 
               
               
                 1  
                 μl 
                 10 pmol/μl Primer 1 (Forward) 
                 10  
                 pmol 
               
               
                 1  
                 μl 
                 10 pmol/μl Primer 2 (Reverse) 
                 10  
                 pmol 
               
               
                 0.5  
                 μl 
                 5 mM dNTPs 
                 0.1  
                 mM 
               
               
                 0.1 
                 μl 
                 5 units/μl Platinum Taq ™ (Life 
                 1  
                 units 
               
               
                   
                   
                 Technologies, Gaithersburg, MD) 
                   
                   
               
               
                   
                   
                 DNA Polymerase 
                   
                   
               
            
           
           
               
               
               
               
            
               
                 (to 25 μl) 
                 Water 
                   
                   
               
               
                   
               
               
                   1   Arabidopsis  DNA is used in the present experiment, but the procedure is a general one. 
               
            
           
         
       
     
     2. The template DNA is amplified using a Perkin Elmer 9700 PCR machine: 
     1) 94° C. for 10 min. followed by 
     
       
         
           
               
               
               
               
             
               
                   
                   
               
               
                   
                 2) 5 cycles: 
                 3) 5 cycles: 
                 4) 25 cycles: 
               
               
                   
                   
               
             
            
               
                   
                 94° C.-30 sec 
                 94° C.-30 sec 
                 94° C.-30 sec 
               
               
                   
                 62° C.-30 sec 
                 58° C.-30 sec 
                 53° C.-30 sec 
               
               
                   
                 72° C.-3 min 
                 72° C.-3 min 
                 72° C.-3 min 
               
               
                   
                   
               
            
           
         
       
     
     5) 72° C. for 7 min. Then the reactions are stopped by chilling to 4° C. 
     The procedure can be adapted to a multi-well format if necessary. 
     Quantification and Dilution of PCR Products: 
     
         
         1. The product of the PCR is analyzed by electrophoresis in a 1% agarose gel. A linearized plasmid DNA can be used as a quantification standard (usually at 50, 100, 200, and 400 ng). These will be used as references to approximate the amount of PCR products. HindIII-digested Lambda DNA is useful as a molecular weight marker. The gel can be run fairly quickly; e.g., at 100 volts. The standard gel is examined to determine that the size of the PCR products is consistent with the expected size and if there are significant extra bands or smeary products in the PCR reactions. 
         2. The amounts of PCR products can be estimated on the basis of the plasmid standard. 
         3. For the small number of reactions that produce extraneous bands, a small amount of DNA from bands with the correct size can be isolated by dipping a sterile 10-μl tip into the band while viewing though a UV Transilluminator. The small amount of agarose gel (with the DNA fragment) is used in the labeling reaction.
 
C. Protocol for PCR-Dig-Labeling of DNA
 
Solutions:
       Reagents in PCR reactions (diluted PCR products, 10×PCR Buffer, 50 mM MgCl 2 , 5 U/μl Platinum Taq Polymerase, and the primers)   10×dNTP+DIG-11-dUTP [1:5]: (2 mM dATP, 2 mM dCTP, 2 mM dGTP, 1.65 mM dTTP, 0.35 mM DIG-11-dUTP)   10×dNTP+DIG-11-dUTP [1:10]: (2 mM dATP, 2 mM dCTP, 2 mM dGTP, 1.81 mM dTTP, 0.19 mM DIG-11-dUTP)   10×dNTP+DIG-11-dUTP [1:15]: (2 mM dATP, 2 mM dCTP, 2 mM dGTP, 1.875 mM dTTP, 0.125 mM DIG-11-dUTP)   TE buffer (10 mM Tris, 1 mM EDTA, pH 8)   Maleate buffer: In 700 ml of deionized distilled water, dissolve 11.61 g maleic acid and 8.77 g NaCl. Add NaOH to adjust the pH to 7.5. Bring the volume to 1 L. Stir for 15 min. and sterilize.   10% blocking solution: In 80 ml deionized distilled water, dissolve 1.16 g maleic acid. Next, add NaOH to adjust the pH to 7.5. Add 10 g of the blocking reagent powder (Boehringer Mannheim, Indianapolis, Ind., Cat. no. 1096176). Heat to 60° C. while stirring to dissolve the powder. Adjust the volume to 100 ml with water. Stir and sterilize.   1% blocking solution: Dilute the 10% stock to 1% using the maleate buffer.   Buffer 3 (100 mM Tris, 100 mM NaCl, 50 mM MgCl 2 , pH9.5). Prepared from autoclaved solutions of 1M Tris pH 9.5, 5 M NaCl, and 1 M MgCl 2  in autoclaved distilled water.
 
Procedure:
   
     
         1. PCR reactions are performed in 25 μl volumes containing: 
       
    
     
       
         
           
               
               
               
             
               
                   
                   
               
             
            
               
                   
                 PCR buffer 
                 1× 
               
               
                   
                 MgCl 2   
                 1.5 mM 
               
               
                   
                 10× dNTP + DIG-11-dUTP 
                 1× (please see the note below) 
               
               
                   
                 Platinum Taq ™ Polymerase 
                 1 unit 
               
               
                   
                 10 pg probe DNA 
                   
               
               
                   
                 10 pmol primer 1 
               
               
                   
                   
               
               
                   
                 Note: 
                   
               
               
                   
                   
                 Use for:  
               
               
                   
                 10× dNTP + DIG-11-dUTP (1:5)  
                 &lt;1 kb 
               
               
                   
                 10× dNTP + DIG-11-dUTP (1:10) 
                 1 kb to 1.8 kb 
               
               
                   
                 10× dNTP + DIG-11-dUTP (1:15) 
                 &gt;1.8 kb 
               
            
           
         
       
         
         2. The PCR reaction uses the following amplification cycles:
       1) 94° C. for 10 min.   
     
       
    
     
       
         
           
               
               
               
               
             
               
                   
                   
               
               
                   
                 2) 5 cycles: 
                 3) 5 cycles: 
                 4) 25 cycles: 
               
               
                   
                   
               
             
            
               
                   
                 95° C.-30 sec 
                 95° C.-30 sec 
                 95° C.-30 sec 
               
               
                   
                 61° C.-1 min 
                 59° C.-1 min 
                 51° C.-1 min 
               
               
                   
                 73° C.-5 min 
                 75° C.-5 min 
                 73° C.-5 min 
               
               
                   
                   
               
            
           
         
       
         
         5) 72° C. for 8 min. The reactions are terminated by chilling to 4° C. (hold). 
         3. The products are analyzed by electrophoresis—in a 1% agarose gel, comparing to an aliquot of the unlabelled probe starting material. 
         4. The amount of DIG-labeled probe is determined as follows:
       Make serial dilutions of the diluted control DNA in dilution buffer (TE: 10 mM Tris and 1 mM EDTA, pH 8) as shown in the following table:   
     
       
    
     
       
         
           
               
               
               
             
               
                   
               
               
                 DIG-labeled control 
                   
                 Final Conc. 
               
               
                 DNA starting conc. 
                 Stepwise Dilution 
                 (Dilution Name) 
               
               
                   
               
             
            
               
                   
               
            
           
           
               
               
               
               
               
            
               
                 5  
                 ng/μl 
                 1 μl in 49 μl TE 
                 100  
                 pg/μl (A) 
               
               
                 100  
                 pg/μl (A) 
                 25 μl in 25 μl TE 
                 50  
                 pg/μl (B) 
               
               
                 50  
                 pg/μl (B) 
                 25 μl in 25 μl TE 
                 25  
                 pg/μl (C) 
               
               
                 25  
                 pg/μl (C) 
                 20 μl in 30 μl TE 
                 10  
                 pg/μl (D) 
               
               
                   
               
            
           
         
       
         
         
           
             a. Serial deletions of a DIG-labeled standard DNA ranging from 100 pg to 10 pg are spotted onto a positively charged nylon membrane, marking the membrane lightly with a pencil to identify each dilution. 
             b. Serial dilutions (e.g., 1:50, 1:2500, 1:10,000) of the newly labeled DNA probe are spotted. 
             c. The membrane is fixed by UV crosslinking. 
             d. The membrane is wetted with a small amount of maleate buffer and then incubated in 1% blocking solution for 15 min at room temp. 
             e. The labeled DNA is then detected using alkaline phosphatase conjugated anti-DIG antibody (Boehringer Mannheim, Indianapolis, Ind., cat. no. 1093274) and an NBT substrate according to the manufacture&#39;s instruction. 
             f. Spot intensities of the control and experimental dilutions are then compared to estimate the concentration of the PCR-DIG-labeled probe.
 
D. Prehybridization and Hybridization of Southern Blots
 
Solutions:
 
             100% Formamide purchased from Gibco 
             20×SSC (IX=0.15 M NaCl, 0.015 M Na 3 citrate) 
             per L: 175 gNaCl
           87.5 g Na 3 citrate.2H2O   
         
             20% Sarkosyl (N-lauroyl-sarcosine) 
             20% SDS (sodium dodecyl sulphate) 
             10% Blocking Reagent: In 80 ml deionized distilled water, dissolve 1.16 g maleic acid. Next, add NaOH to adjust the pH to 7.5. Add 10 g of the blocking reagent powder. Heat to 60° C. while stirring to dissolve the powder. Adjust the volume to 100 ml with water. Stir and sterilize.
 
Prehybridization Mix:
 
           
         
       
    
                                                     Final       Volume               Concentration   Components   (per 100 ml)   Stock                                                                 50%   Formamide   50    ml   100%            5×   SSC   25    ml   20×           0.1%   Sarkosyl   0.5    ml   20%           0.02%    SDS   0.1    ml   20%             2%   Blocking Reagent   20    ml   10%               Water   4.4    ml                        
General Procedures:
     1. Place the blot in a heat-sealable plastic bag and add an appropriate volume of prehybridization solution (30 ml/100 cm 2 ) at room temperature. Seal the bag with a heat sealer, avoiding bubbles as much as possible. Lay down the bags in a large plastic tray (one tray can accommodate at least 4-5 bags). Ensure that the bags are lying flat in the tray so that the prehybridization solution is evenly distributed throughout the bag. Incubate the blot for at least 2 hours with gentle agitation using a waver shaker.   2. Denature DIG-labeled DNA probe by incubating for 10 min. at 98° C. using the PCR machine and immediately cool it to 4° C.   3. Add probe to prehybridization solution (25 ng/ml; 30 ml=750 ng total probe) and mix well but avoid foaming. Bubbles may lead to background.   4. Pour off the prehybridization solution from the hybridization bags and add new prehybridization and probe solution mixture to the bags containing the membrane.   5. Incubate with gentle agitation for at least 16 hours.   6. Proceed to medium stringency post-hybridization wash:
       Three times for 20 min. each with gentle agitation using 1×SSC, 1% SDS at 60° C.   All wash solutions must be prewarmed to 60° C. Use about 100 ml of wash solution per membrane.   To avoid background keep the membranes fully submerged to avoid drying in spots; agitate sufficiently to avoid having membranes stick to one another.   
       7. After the wash, proceed to immunological detection and CSPD development.
 
E. Procedure for Immunological Detection with Cspd
 
Solutions:
   Buffer 1: Maleic acid buffer (0.1 M maleic acid, 0.15 M NaCl; adjusted to pH 7.5 with NaoH)   Washing buffer: Maleic acid buffer with 0.3% (v/v) Tween 20.   Blocking stock solution 10% blocking reagent in buffer 1. Dissolve (10× concentration): blocking reagent powder (Boehringer Mannheim, Indianapolis, Ind., cat. no. 1096176) by constantly stirring on a 65° C. heating block or heat in a microwave, autoclave and store at 4° C.   Buffer 2   (1× blocking solution): Dilute the stock solution 1:10 in Buffer 1.   Detection buffer: 0.1 M Tris, 0.1 M NaCl, pH 9.5
 
Procedure:
   1. After the post-hybridization wash the blots are briefly rinsed (1-5 min.) in the maleate washing buffer with gentle shaking.   2. Then the membranes are incubated for 30 min. in Buffer 2 with gentle shaking.   3. Anti-DIG-AP conjugate (Boehringer Mannheim, Indianapolis, Ind., cat. no. 1093274) at 75 mU/ml (1:10,000) in Buffer 2 is used for detection. 75 ml of solution can be used for 3 blots.   4. The membrane is incubated for 30 min. in the antibody solution with gentle shaking.   5. The membrane are washed twice in washing buffer with gentle shaking. About 250 mls is used per wash for 3 blots.   6. The blots are equilibrated for 2-5 min in 60 ml detection buffer.   7. Dilute CSPD (1:200) in detection buffer. (This can be prepared ahead of time and stored in the dark at 4° C.).
       The following steps must be done individually. Bags (one for detection and one for exposure) are generally cut and ready before doing the following steps.   
       8. The blot is carefully removed from the detection buffer and excess liquid removed without drying the membrane. The blot is immediately placed in a bag and 1.5 ml of CSPD solution is added. The CSPD solution can be spread over the membrane. Bubbles present at the edge and on the surface of the blot are typically removed by gentle rubbing. The membrane is incubated for 5 min. in CSPD solution.   9. Excess liquid is removed and the membrane is blotted briefly (DNA side up) on WHATMAN® 3 MM paper. Do not let the membrane dry completely.   10. Seal the damp membrane in a hybridization bag and incubate for 10 min at 37° C. to enhance the luminescent reaction.   11. Expose for 2 hours at room temperature to X-ray film. Multiple exposures can be taken. Luminescence continues for at least 24 hours and signal intensity increases during the first hours.   

     Example 3: Microarray Experiments and Results 
     1. Sample Tissue Preparation 
     (a) Roots 
     Seeds of  Arabidopsis thaliana  (Ws) were sterilized in full strength bleach for less than 5 min., washed more than 3 times in sterile distilled deionized water and plated on MS agar plates. The plates were placed at 4° C. for 3 nights and then placed vertically into a growth chamber having 16 hr light/8 hr dark cycles, 23° C., 70% relative humidity and ˜11,000 LUX. After 2 weeks, the roots were cut from the agar, flash frozen in liquid nitrogen and stored at −80° C. (EXPT REP: 108439 and 108434) 
     (b) Root Hairless Mutants 
     Plants mutant at the rhl gene locus lack root hairs. This mutation is maintained as a heterozygote. 
     Seeds of  Arabidopsis thaliana  (Landsberg  erecta ) mutated at the rhl gene locus were sterilized using 30% bleach with 1 ul/ml 20% TRITON®-X 100 and then vernalized at 4° C. for 3 days before being plated onto GM agar plates. Plates were placed in growth chamber with 16 hr light/8 hr. dark, 23° C., 14,500-15,900 LUX, and 70% relative humidity for germination and growth. 
     After 7 days, seedlings were inspected for root hairs using a dissecting microscope. Mutants were harvested and the cotyledons removed so that only root tissue remained. Tissue was then flash frozen in liquid nitrogen and stored at −80 C. (EXPT REP: 108433) 
       Arabidopsis thaliana  (Landsberg  erecta ) seedlings grown and prepared as above were used as controls. (EXPT REP: 108433) 
     Alternatively, seeds of  Arabidopsis thaliana  (Landsberg  erecta ), heterozygous for the rhll (root hairless) mutation, were surface-sterilized in 30% bleach containing 0.1% TRITON® X-100 and further rinsed in sterile water. They were then vernalized at 4° C. for 4 days before being plated onto MS agar plates. The plates were maintained in a growth chamber at 24° C. with 16 hr light/8 hr dark for germination and growth. After 10 days, seedling roots that expressed the phenotype (i.e. lacking root hairs) were cut below the hypocotyl junction, frozen in liquid nitrogen and stored at −80° C. Those seedlings with the normal root phenotype (heterozygous or wt) were collected as described for the mutant and used as controls. 
     (c) Rosette Leaves, Stems, and Siliques 
       Arabidopsis thaliana  (Ws) seed was vernalized at 4° C. for 3 days before sowing in Metro-mix soil type 350. Flats were placed in a growth chamber having 16 hr light/8 hr dark, 80% relative humidity, 23° C. and 13,000 LUX for germination and growth. After 3 weeks, rosette leaves, stems, and siliques (see EXPT REP: 108436, 108437 and 108438) were harvested, flash frozen in liquid nitrogen and stored at −80° C. until use. After 4 weeks, siliques (&lt;5 mm, 5-10 mm and &gt;10 mm) were harvested, flash frozen in liquid nitrogen and stored at −80° C. until use. 5 week old whole plants (used as controls) were harvested, flash frozen in liquid nitrogen and kept at −80° C. until RNA was isolated. 
     (d) Trichomes 
       Arabidopsis thaliana  (Colombia glabrous) inflorescences were used as a control and CS8143 (hairy inflorescence ecotype) inflorescences, having increased trichomes, were used as the experimental sample. 
     Approximately 10 μl of each type of seed was sown on a flat of 350 soil (containing 0.03% marathon) and vernalized at 4° C. for 3 days. Plants were then grown at room temperature under florescent lighting. Young inflorescences were collected at 30 days for the control plants and 37 days for the experimental plants. Each inflorescence was cut into one-half inch (½″) pieces, flash frozen in liquid nitrogen and stored at −80° C. until RNA was isolated. 
     (e) Germination 
       Arabidopsis thaliana  seeds (ecotype Ws) were sterilized in bleach and rinsed with sterile water. The seeds were placed in 100 mm petri plates containing soaked autoclaved filter paper. Plates were foil-wrapped and left at 4° C. for 3 nights to vernalize. After cold treatment, the foil was removed and plates were placed into a growth chamber having 16 hr light/8 hr dark cycles, 23° C., 70% relative humidity and ˜11,000 lux. Seeds were collected 1 d (EXPT REP: 108461), 2 d (EXPT REP: 108462), 3 d (EXPT REP: 108463) and 4 d (EXPT REP: 108464) later, flash frozen in liquid nitrogen and stored at −80° C. until RNA was isolated. 
     (f) Shoot Apical Meristem 
       Arabidopsis thaliana  ( Landsberg erecta ) plants mutant at the stm gene locus lack shoot meristems, produce aerial rosettes, have a reduced number of flowers per inflorescence, as well as a reduced number of petals, stamens and carpels, and is female sterile. This mutation is maintained as a heterozygote. 
     Seeds of  Arabidopsis thaliana  ( Landsberg erecta ) mutated at the stm locus were sterilized using 30% bleach with 1 ul/ml 20% TRITON®-X100. The seeds were vernalized at 4° C. for 3 days before being plated onto GM agar plates. Half were then put into a 22° C., 24 hr light growth chamber and half in a 24° C. 16 hr light/8 hr dark growth chamber having 14,500-15,900 LUX, and 70% relative humidity for germination and growth. 
     After 7 days, seedlings were examined for leaf primordia using a dissecting microscope. Presence of leaf primordia indicated a wild type phenotype. Mutants were selected based on lack of leaf primordia. Mutants were then harvested and hypocotyls removed leaving only tissue in the shoot region. Tissue was then flash frozen in liquid nitrogen and stored at −80° C. 
     Control tissue was isolated from 5 day old Landsberg  erecta  seedlings grown in the same manner as above. Tissue from the shoot region was harvested in the same manner as the stm tissue, but only contained material from the 24° C., 16 hr light/8 hr dark long day cycle growth chamber. (EXPT REP: 108453) 
     Seeds of maize hybrid 35A (Pioneer) were sown in water-moistened sand in flats (10 rows, 5-6 seed/row) and covered with clear, plastic lids before being placed in a growth chamber having 16 hr light (25° C.)/8 hr dark (20° C.), 75% relative humidity and 13,000-14,000 LUX. Covered flats were watered every three days for 8 days. Seedlings were carefully removed from the sand and the outer layers of leaf shealth removed. About 2 mm sections were cut and flash frozen in liquid nitrogen prior to storage at −80° C. The tissues above the shoot apices (˜1 cm long) were cut, treated as above and used as control tissue. 
     (g) Abscissic Acid (ABA) 
     Seeds of  Arabidopsis thaliana  (ecotype Wassilewskija) were sown in trays and left at 4° C. for 4 days to vernalize. They were then transferred to a growth chamber having grown 16 hr light/8 hr dark, 13,000 LUX, 70% humidity, and 20° C. and watered twice a week with 1 L of 1× Hoagland&#39;s solution. Approximately 1,000 14 day old plants were spayed with 200-250 mls of 100 μM ABA in a 0.02% solution of the detergent SILWET L-77®. Whole seedlings, including roots, were harvested within a 15 to 20 minute time period at 1 hr and 6 hr after treatment, flash-frozen in liquid nitrogen and stored at −80° C. 
     Seeds of maize hybrid 35A (Pioneer) were sown in water-moistened sand in flats (10 rows, 5-6 seed/row) and covered with clear, plastic lids before being placed in a growth chamber having 16 hr light (25° C.)/8 hr dark (20° C.), 75% relative humidity and 13,000-14,000 LUX. Covered flats were watered every three days for 7 days. Seedlings were carefully removed from the sand and placed in 1-liter beakers with 100 μM ABA for treatment. Control plants were treated with water. After 6 hr and 24 hr, aerial and root tissues were separated and flash frozen in liquid nitrogen prior to storage at −80° C. 
     (h) Auxin Responsive 
     Seeds of  Arabidopsis thaliana  (ecotype Wassilewskija) were sown in trays and left at 4° C. for 4 days to vernalize. They were then transferred to a growth chamber having 16 hr light/8 hr dark, 13,000 LUX, 70% humidity, 20° C. and watered twice a week with 1 L of 1× Hoagland&#39;s solution (recipe recited in Feldmann et al., (1987) Mol. Gen. Genet. 208: 1-9 and described as complete nutrient solution). Approximately 1,000 14 day old plants were spayed with 200-250 mls of 100 μM NAA in a 0.02% solution of the detergent SILWET L-77®. Aerial tissues (everything above the soil line) were harvested within a 15 to 20 minute time period 1 hr and 6 hrs after treatment, flash-frozen in liquid nitrogen and stored at −80° C. 
     Seeds of maize hybrid 35A (Pioneer) were sown in water-moistened sand in flats (10 rows, 5-6 seed/row) and covered with clear, plastic lids before being placed in a growth chamber having 16 hr light (25° C.)/8 hr dark (20° C.), 75% relative humidity and 13,000-14,000 LUX. Covered flats were watered every three days for 7 days. Seedlings were carefully removed from the sand and placed in 1-liter beakers with 100 μM NAA for treatment. Control plants were treated with water. After 6 hr and 24 hr, aerial and root tissues were separated and flash frozen in liquid nitrogen prior to storage at −80° C. 
     (i) Cytokinin 
     Seeds of  Arabidopsis thaliana  (ecotype Wassilewskija) were sown in trays and left at 4° C. for 4 days to vernalize. They were then transferred to a growth chamber having 16 hr light/8 hr dark, 13,000 LUX, 70% humidity, 20° C. temperature and watered twice a week with 1 L of 1× Hoagland&#39;s solution. Approximately 1,000 14 day old plants were spayed with 200-250 mls of 100 μM BA in a 0.02% solution of the detergent SILWET L-77®. Aerial tissues (everything above the soil line) were harvested within a 15 to 20 minute time period 1 hr and 6 hrs after treatment, flash-frozen in liquid nitrogen and stored at −80° C. 
     Seeds of maize hybrid 35A (Pioneer) were sown in water-moistened sand in flats (10 rows, 5-6 seed/row) and covered with clear, plastic lids before being placed in a growth chamber having 16 hr light (25° C.)/8 hr dark (20° C.), 75% relative humidity and 13,000-14,000 LUX. Covered flats were watered every three days for 7 days. Seedlings were carefully removed from the sand and placed in 1-liter beakers with 100 μM BA for treatment. Control plants were treated with water. After 6 hr, aerial and root tissues were separated and flash frozen in liquid nitrogen prior to storage at −80° C. 
     (j) Brassinosteroid Responsive 
     Two separate experiments were performed, one with epi-brassinolide and one with the brassinosteroid biosynthetic inhibitor brassinazole. 
     In the epi-brassinolide experiments, seeds of wild-type  Arabidopsis thaliana  (ecotype Wassilewskija) and the brassinosteroid biosynthetic mutant dwf4-1 were sown in trays and left at 4° C. for 4 days to vernalize. They were then transferred to a growth chamber having 16 hr light/8 hr dark, 11,000 LUX, 70% humidity and 22° C. temperature. Four week old plants were spayed with a 1 μM solution of epi-brassinolide and shoot parts (unopened floral primordia and shoot apical meristems) harvested three hours later. Tissue was flash-frozen in liquid nitrogen and stored at −80° C. (EXPT REP 108480) 
     In the brassinazole experiments, seeds of wild-type  Arabidopsis thaliana  (ecotype Wassilewskija) were grown as described above. Four week old plants were spayed with a 1 μM solution of brassinazole and shoot parts (unopened floral primordia and shoot apical meristems) harvested three hours later. Tissue was flash-frozen in liquid nitrogen and stored at −80° C. (EXPT REP 108481) 
     In addition to the spray experiments, tissue was prepared from two different mutants; (1) a dwf4-1 knock out mutant (EXPT REP: 108478) and (2) a mutant overexpressing the dwf4-1 gene (EXPT REP: 108479). 
     Seeds of wild-type  Arabidopsis thaliana  (ecotype Wassilewskija) and of the dwf4-1 knock out and overexpressor mutants were sown in trays and left at 4° C. for 4 days to vernalize. They were then transferred to a growth chamber having 16 hr light/8 hr dark, 11,000 LUX, 70% humidity and 22° C. temperature. Tissue from shoot parts (unopened floral primordia and shoot apical meristems) was flash-frozen in liquid nitrogen and stored at −80° C. 
     Another experiment was completed with seeds of  Arabidopsis thaliana  (ecotype Wassilewskija) were sown in trays and left at 4° C. for 4 days to vernalize. They were then transferred to a growth chamber. Plants were grown under long-day (16 hr light: 8 hr. dark) conditions, 13,000 LUX light intensity, 70% humidity, 20° C. temperature and watered twice a week with 1 L 1× Hoagland&#39;s solution (recipe recited in Feldmann et al., (1987) Mol. Gen. Genet. 208: 1-9 and described as complete nutrient solution). Approximately 1,000 14 day old plants were spayed with 200-250 mls of 0.1 μM Epi-Brassinolite in 0.02% solution of the detergent SILWET L-77®. At 1 hr. and 6 hrs. after treatment aerial tissues were harvested within a 15 to 20 minute time period and flash-frozen in liquid nitrogen. 
     Seeds of maize hybrid 35A (Pioneer) were sown in water-moistened sand in flats (10 rows, 5-6 seed/row) and covered with clear, plastic lids before being placed in a growth chamber having 16 hr light (25° C.)/8 hr dark (20° C.), 75% relative humidity and 13,000-14,000 LUX. Covered flats were watered every three days for 7 days. Seedlings were carefully removed from the sand and placed in 1-liter beakers with 0.1 μM epi-brassinolide for treatment. Control plants were treated with distilled deionized water. After 24 hr, aerial and root tissues were separated and flash frozen in liquid nitrogen prior to storage at −80° C. 
     (k) Gibberillic Acid 
     Seeds of  Arabidopsis thaliana  (ecotype Wassilewskija) were sown in trays and left at 4° C. for 4 days to vernalize. They were then transferred to a growth chamber having 16 hr light/8 hr. dark, 13,000 LUX, 70% humidity, 20° C. and watered twice a week with 1 L of 1× Hoagland&#39;s solution. Approximately 1,000 14 day old plants were spayed with 200-250 mls of 100 μM gibberillic acid in a 0.02% solution of the detergent SILWET L-77®. At 1 hr. and 6 hrs. after treatment, aerial tissues (everything above the soil line) were harvested within a 15 to 20 minute time period, flash-frozen in liquid nitrogen and stored at −80° C. 
     Alternatively, seeds of  Arabidopsis thaliana  (ecotype Ws) were sown in Metro-mix soil type 350 and left at 4° C. for 3 days to vernalize. They were then transferred to a growth chamber having 16 hr light/8 hr dark, 13,000 LUX, 80% humidity, 20° C. temperature and watered every four days with 1.5 L water. 14 days after germination, plants were sprayed with 100 μM gibberillic acid or with water. Aerial tissues were harvested 1 hr (EXPT REP: 108484), 6 hrs (EXPT REP: 108485), 12 hrs (EXPT REP: 108486), and 24 hrs post-treatment, flash frozen and stored at −80° C. 
     Seeds of maize hybrid 35A (Pioneer) were sown in water-moistened sand in flats (10 rows, 5-6 seed/row) and covered with clear, plastic lids before being placed in a growth chamber having 16 hr light (25° C.)/8 hr dark (20° C.), 75% relative humidity and 13,000-14,000 LUX. Covered flats were watered every three days for 7 days. Seedlings were carefully removed from the sand and placed in 1-liter beakers with 100 μM gibberillic acid for treatment. Control plants were treated with water. After 1 hr, 6 hr and 12 hr, aerial and root tissues were separated and flash frozen in liquid nitrogen prior to storage at −80° C. 
     (l) Nitrogen: High to Low 
     Wild type  Arabidopsis thaliana  seeds (ecotpye Ws) were surface sterilized with 30% CLOROX®, 0.1% TRITON® X-100 for 5 minutes. Seeds were then rinsed with 4-5 exchanges of sterile double distilled deionized water. Seeds were vernalized at 4° C. for 2-4 days in darkness. After cold treatment, seeds were plated on modified 1×MS media (without NH 4 NO 3  or KNO 3 ), 0.5% sucrose, 0.5 g/L MES pH5.7, 1% phytagar and supplemented with KNO 3  to a final concentration of 60 mM (high nitrate modified 1×MS media). Plates were then grown for 7 days in a Percival growth chamber at 22° C. with 16 hr. light/8 hr dark. 
     Germinated seedlings were then transferred to a sterile flask containing 50 mL of high nitrate modified 1×MS liquid media. Seedlings were grown with mild shaking for 3 additional days at 22° C. in 16 hr. light/8 hr dark (in a Percival growth chamber) on the high nitrate modified 1×MS liquid media. 
     After three days of growth on high nitrate modified 1×MS liquid media, seedlings were transferred either to a new sterile flask containing 50 mL of high nitrate modified 1×MS liquid media or to low nitrate modified 1×MS liquid media (containing 20 □M KNO 3 ). Seedlings were grown in these media conditions with mild shaking at 22° C. in 16 hr light/8 hr dark for the appropriate time points and whole seedlings harvested for total RNA isolation via the TRIZOL® method (LifeTech.). The time points used for the microarray experiments were 10 min. (EXPT REP: 108454) and 1 hour (EXPT REP: 108455) time points for both the high and low nitrate modified 1×MS media. 
     Alternatively, seeds that were surface sterilized in 30% bleach containing 0.1% TRITON® X-100 and further rinsed in sterile water, were planted on MS agar, (0.5% sucrose) plates containing 50 mM KNO 3  (potassium nitrate). The seedlings were grown under constant light (3500 LUX) at 22° C. After 12 days, seedlings were transferred to MS agar plates containing either 1 mM KNO 3  or 50 mM KNO 3 . Seedlings transferred to agar plates containing 50 mM KNO 3  were treated as controls in the experiment. Seedlings transferred to plates with 1 mM KNO 3  were rinsed thoroughly with sterile MS solution containing 1 mM KNO 3 . There were ten plates per transfer. Root tissue was collected and frozen in 15 mL Falcon tubes at various time points which included 1 hour, 2 hours, 3 hours, 4 hours, 6 hours, 9 hours, 12 hours, 16 hours, and 24 hours. 
     Maize 35A19 Pioneer hybrid seeds were sown on flats containing sand and grown in a CONVIRON® growth chamber at 25° C., 16 hr light/8 hr dark, ˜13,000 LUX and 80% relative humidity. Plants were watered every three days with double distilled deionized water. Germinated seedlings are allowed to grow for 10 days and were watered with high nitrate modified 1×MS liquid media (see above). On day 11, young corn seedlings were removed from the sand (with their roots intact) and rinsed briefly in high nitrate modified 1×MS liquid media. The equivalent of half a flat of seedlings were then submerged (up to their roots) in a beaker containing either 500 mL of high or low nitrate modified 1×MS liquid media (see above for details). 
     At appropriate time points, seedlings were removed from their respective liquid media, the roots separated from the shoots and each tissue type flash frozen in liquid nitrogen and stored at −80° C. This was repeated for each time point. Total RNA was isolated using the TRIZOL® method (see above) with root tissues only. 
     Corn root tissues isolated at the 4 hr and 16 hr time points were used for the microarray experiments. Both the high and low nitrate modified 1×MS media were used. 
     (m) Nitrogen: Low to High 
       Arabidopsis thaliana  ecotype Ws seeds were sown on flats containing 4 L of a 1:2 mixture of Grace Zonolite vermiculite and soil. Flats were watered with 3 L of water and vernalized at 4° C. for five days. Flats were placed in a CONVIRON® growth chamber having 16 hr light/8 hr dark at 20° C., 80% humidity and 17,450 LUX. Flats were watered with approximately 1.5 L of water every four days. Mature, bolting plants (24 days after germination) were bottom treated with 2 L of either a control (100 mM mannitol pH 5.5) or an experimental (50 mM ammonium nitrate, pH 5.5) solution. Roots, leaves and siliques were harvested separately 30, 120 and 240 minutes after treatment, flash frozen in liquid nitrogen and stored at −80° C. 
     Hybrid maize seed (Pioneer hybrid 35A19) were aerated overnight in deionized water. Thirty seeds were plated in each flat, which contained 4 liters of Grace zonolite vermiculite. Two liters of water were bottom fed and flats were kept in a CONVIRON® growth chamber with 16 hr light/8 hr dark at 20° C. and 80% humidity. Flats were watered with 1 L of tap water every three days. Five day old seedlings were treated as described above with 2 L of either a control (100 mM mannitol pH 6.5) solution or 1 L of an experimental (50 mM ammonium nitrate, pH 6.8) solution. Fifteen shoots per time point per treatment were harvested 10, 90 and 180 minutes after treatment, flash frozen in liquid nitrogen and stored at −80° C. 
     Alternatively, seeds of  Arabidopsis thaliana  (ecotype Wassilewskija) were left at 4° C. for 3 days to vernalize. They were then sown on vermiculite in a growth chamber having 16 hours light/8 hours dark, 12,000-14,000 LUX, 70% humidity, and 20° C. They were bottom-watered with tap water, twice weekly. Twenty-four days old plants were sprayed with either water (control) or 0.6% ammonium nitrate at 4 μL/cm 2  of tray surface. Total shoots and some primary roots were cleaned of vermiculite, flash-frozen in liquid nitrogen and stored at −80° C. 
     (n) Methyl Jasmonate 
     Seeds of  Arabidopsis thaliana  (ecotype Wassilewskija) were sown in trays and left at 4° C. for 4 days to vernalize before being transferred to a growth chamber having 16 hr light/8 hr. dark, 13,000 LUX, 70% humidity, 20° C. temperature and watered twice a week with 1 L of a 1× Hoagland&#39;s solution. Approximately 1,000 14 day old plants were spayed with 200-250 mls of 0.001% methyl jasmonate in a 0.02% solution of the detergent SILWET L-77®. At 1 hr and 6 hrs after treatment, whole seedlings, including roots, were harvested within a 15 to 20 minute time period, flash-frozen in liquid nitrogen and stored at −80° C. 
     Seeds of maize hybrid 35A (Pioneer) were sown in water-moistened sand in flats (10 rows, 5-6 seed/row) and covered with clear, plastic lids before being placed in a growth chamber having 16 hr light (25° C.)/8 hr dark (20° C.), 75% relative humidity and 13,000-14,000 LUX. Covered flats were watered every three days for 7 days. Seedlings were carefully removed from the sand and placed in 1-liter beakers with 0.001% methyl jasmonate for treatment. Control plants were treated with water. After 24 hr, aerial and root tissues were separated and flash frozen in liquid nitrogen prior to storage at −80° C. 
     (O) Salicylic Acid 
     Seeds of  Arabidopsis thaliana  (ecotype Wassilewskija) were sown in trays and left at 4° C. for 4 days to vernalize before being transferred to a growth chamber having 16 hr light/8 hr. dark, 13,000 LUX, 70% humidity, 20° C. temperature and watered twice a week with 1 L of a 1× Hoagland&#39;s solution. Approximately 1,000 14 day old plants were spayed with 200-250 mls of 5 mM salicylic acid (solubilized in 70% ethanol) in a 0.02% solution of the detergent SILWET L-77®. At 1 hr and 6 hrs after treatment, whole seedlings, including roots, were harvested within a 15 to 20 minute time period flash-frozen in liquid nitrogen and stored at −80° C. 
     Alternatively, seeds of wild-type  Arabidopsis thaliana  (ecotype Columbia) and mutant CS3726 were sown in soil type 200 mixed with osmocote fertilizer and Marathon insecticide and left at 4° C. for 3 days to vernalize. Flats were incubated at room temperature with continuous light. Sixteen days post germination plants were sprayed with 2 mM SA, 0.02% SilwettL-77 or control solution (0.02% SilwettL-77. Aerial parts or flowers were harvested 1 hr (EXPT REP: 108471 and 108472), 4 hr (EXPT REP: 108469 and 108470), 6 hr (EXPT REP: 108440) 24 hr (EXPT REP: 108443, 107953 and 107960) and 3 weeks (EXPT REP: 108475, 108476) post-treatment flash frozen and stored at −80° C. 
     Seeds of maize hybrid 35A (Pioneer) were sown in water-moistened sand in flats (10 rows, 5-6 seed/row) and covered with clear, plastic lids before being placed in a growth chamber having 16 hr light (25° C.)/8 hr dark (20° C.), 75% relative humidity and 13,000-14,000 LUX. Covered flats were watered every three days for 7 days. Seedlings were carefully removed from the sand and placed in 1-liter beakers with 2 mM SA for treatment. Control plants were treated with water. After 12 hr and 24 hr, aerial and root tissues were separated and flash frozen in liquid nitrogen prior to storage at −80° C. 
     (P) Wounding 
     Seeds of  Arabidopsis thaliana  (Wassilewskija) were sown in trays and left at 4° C. for three days to vernalize before being transferred to a growth chamber having 16 hr light/8 hr dark, 12,000-14,000 LUX, 70% humidity and 20° C. After 14 days, the leaves were wounded with forceps. Aerial tissues were harvested 1 hour and 6 hours after wounding. Aerial tissues from unwounded plants served as controls. Tissues were flash-frozen in liquid nitrogen and stored at −80° C. 
     Seeds of maize hybrid 35A (Pioneer) were sown in water-moistened sand in flats (10 rows, 5-6 seed/row) and covered with clear, plastic lids before being placed in a growth chamber having 16 hr light (25° C.)/8 hr dark (20° C.), 75% relative humidity and 13,000-14,000 LUX. Covered flats were watered every three days for 7 days. Seedlings were wounded (one leaf nicked by scissors) and placed in 1-liter beakers of water for treatment. Control plants were treated not wounded. After 1 hr and 6 hr aerial and root tissues were separated and flash frozen in liquid nitrogen prior to storage at −80° C. 
     (q) Drought Stress 
     Seeds of  Arabidopsis thaliana  (Wassilewskija) were sown in pots and left at 4° C. for three days to vernalize before being transferred to a growth chamber having 16 hr light/8 hr dark, 150,000-160,000 LUX, 20° C. and 70% humidity. After 14 days, aerial tissues were cut and left to dry on 3 MM WHATMAN® paper in a petri-plate for 1 hour and 6 hours. Aerial tissues exposed for 1 hour and 6 hours to 3 MM WHATMAN® paper wetted with 1× Hoagland&#39;s solution served as controls. Tissues were harvested, flash-frozen in liquid nitrogen and stored at −80° C. 
     Alternatively,  Arabidopsis thaliana  (Ws) seed was vernalized at 4° C. for 3 days before sowing in Metromix soil type 350. Flats were placed in a growth chamber with 23° C., 16 hr light/8 hr. dark, 80% relative humidity, ˜13,000 LUX for germination and growth. Plants were watered with 1-1.5 L of water every four days. Watering was stopped 16 days after germination for the treated samples, but continued for the control samples. Rosette leaves and stems (EXPT REP 108477, 108482 and 108483), flowers (see EXPT REP: 108473, 108474) and siliques were harvested 2 d, 3 d, 4 d, 5 d, 6 d and 7 d (EXPT REP: 108473) after watering was stopped. Tissue was flash frozen in liquid nitrogen and kept at −80° C. until RNA was isolated. Flowers and siliques were also harvested on day 8 from plants that had undergone a 7 d drought treatment followed by 1 day of watering (EXPT REP: 108474). Control plants (whole plants) were harvested after 5 weeks, flash frozen in liquid nitrogen and stored as above. 
     Seeds of maize hybrid 35A (Pioneer) were sown in water-moistened sand in flats (10 rows, 5-6 seed/row) and covered with clear, plastic lids before being placed in a growth chamber having 16 hr light (25° C.)/8 hr dark (20° C.), 75% relative humidity and 13,000-14,000 LUX. Covered flats were watered every three days for 7 days. Seedlings were carefully removed from the sand and placed in empty 1-liter beakers at room temperature for treatment. Control plants were placed in water. After 1 hr, 6 hr, 12 hr and 24 hr aerial and root tissues were separated and flash frozen in liquid nitrogen prior to storage at −80° C. 
     (r) Osmotic Stress 
     Seeds of  Arabidopsis thaliana  (Wassilewskija) were sown in trays and left at 4° C. for three days to vernalize before being transferred to a growth chamber having 16 hr light/8 hr dark, 12,000-14,000 LUX, 20° C., and 70% humidity. After 14 days, the aerial tissues were cut and placed on 3 MM WHATMAN® paper in a petri-plate wetted with 20% PEG (polyethylene glycol-M r  8,000) in 1× Hoagland&#39;s solution. Aerial tissues on 3 MM WHATMAN® paper containing 1× Hoagland&#39;s solution alone served as the control. Aerial tissues were harvested at 1 hour and 6 hours after treatment, flash-frozen in liquid nitrogen and stored at −80° C. 
     Seeds of maize hybrid 35A (Pioneer) were sown in water-moistened sand in flats (10 rows, 5-6 seed/row) and covered with clear, plastic lids before being placed in a growth chamber having 16 hr light (25° C.)/8 hr dark (20° C.), 75% relative humidity and 13,000-14,000 LUX. Covered flats were watered every three days for 7 days. Seedlings were carefully removed from the sand and placed in 1-liter beakers with 20% PEG (polyethylene glycol-M r  8,000) for treatment. Control plants were treated with water. After 1 hr and 6 hr aerial and root tissues were separated and flash frozen in liquid nitrogen prior to storage at −80° C. 
     Seeds of maize hybrid 35A (Pioneer) were sown in water-moistened sand in flats (10 rows, 5-6 seed/row) and covered with clear, plastic lids before being placed in a growth chamber having 16 hr light (25° C.)/8 hr dark (20° C.), 75% relative humidity and 13,000-14,000 LUX. Covered flats were watered every three days for 7 days. Seedlings were carefully removed from the sand and placed in 1-liter beakers with 150 mM NaCl for treatment. Control plants were treated with water. After 1 hr, 6 hr, and 24 hr aerial and root tissues were separated and flash frozen in liquid nitrogen prior to storage at −80° C. 
     (s) Heat Shock Treatment 
     Seeds of  Arabidopsis thaliana  (Wassilewskija) were sown in trays and left at 4° C. for three days to vernalize before being transferred to a growth chamber with 16 hr light/8 hr dark, 12,000-14,000 LUX, 70% humidity and 20° C., fourteen day old plants were transferred to a 42° C. growth chamber and aerial tissues were harvested 1 hr and 6 hr after transfer. Control plants were left at 20° c. and aerial tissues were harvested. Tissues were flashfrozen in liquid nitrogen and stored at −80° c. 
     Seeds of maize hybrid 35A (Pioneer) were sown in water-moistened sand in flats (10 rows, 5-6 seed/row) and covered with clear, plastic lids before being placed in a growth chamber having 16 hr light (25° C.)/8 hr dark (20° C.), 75% relative humidity and 13,000-14,000 LUX. Covered flats were watered every three days for 7 days. Seedlings were carefully removed from the sand and placed in 1-liter beakers containing 42° C. water for treatment. Control plants were treated with water at 25° C. After 1 hr and 6 hr aerial and root tissues were separated and flash frozen in liquid nitrogen prior to storage at −80° C. 
     (t) Cold Shock Treatment 
     Seeds of  Arabidopsis thaliana  (Wassilewskija) were sown in trays and left at 4° C. for three days to vernalize before being transferred to a growth chamber having 16 hr light/8 hr dark, 12,000-14,000 LUX, 20° C. and 70% humidity. Fourteen day old plants were transferred to a 4° C. dark growth chamber and aerial tissues were harvested 1 hour and 6 hours later. Control plants were maintained at 20° C. and covered with foil to avoid exposure to light. Tissues were flash-frozen in liquid nitrogen and stored at −80° C. 
     Seeds of maize hybrid 35A (Pioneer) were sown in water-moistened sand in flats (10 rows, 5-6 seed/row) and covered with clear, plastic lids before being placed in a growth chamber having 16 hr light (25° C.)/8 hr dark (20° C.), 75% relative humidity and 13,000-14,000 LUX. Covered flats were watered every three days for 7 days. Seedlings were carefully removed from the sand and placed in 1-liter beakers containing 4° C. water for treatment. Control plants were treated with water at 25° C. After 1 hr and 6 hr aerial and root tissues were separated and flash frozen in liquid nitrogen prior to storage at −80° C. 
     (u) Oxidative Stress—Hydrogen Peroxide Treatment 
     Seeds of  Arabidopsis thaliana  (Wassilewskija) were sown in trays and left at 4° C. for three days to vernalize. Before being transferred to a growth chamber having 16 hr light/8 hr dark, 12,000-14,000 LUX, 20° C. and 70% humidity. Fourteen day old plants were sprayed with 5 mM H 2 O 2  (hydrogen peroxide) in a 0.02% Silwett L-77 solution. Control plants were sprayed with a 0.02% Silwett L-77 solution. Aerial tissues were harvested 1 hour and 6 hours after spraying, flash-frozen in liquid nitrogen and stored at −80° C. 
     Seeds of maize hybrid 35A (Pioneer) were sown in water-moistened sand in flats (10 rows, 5-6 seed/row) and covered with clear, plastic lids before being placed in a growth chamber having 16 hr light (25° C.)/8 hr dark (20° C.), 75% relative humidity and 13,000-14,000 LUX. Covered flats were watered every three days for 7 days. Seedlings were carefully removed from the sand and placed in 1-liter beakers with 5 mM H 2 O 2  for treatment. Control plants were treated with water. After 1 hr, 6 hr and 24 hr, aerial and root tissues were separated and flash frozen in liquid nitrogen prior to storage at −80° C. 
     (v) Nitric Oxide Treatment 
     Seeds of  Arabidopsis thaliana  (Wassilewskija) were sown in trays and left at 4° C. for three days to vernalize before being transferred to a growth chamber having 16 hr light/8 hr dark, 12,000-14,000 LUX, 20° C. and 70% humidity. Fourteen day old plants were sprayed with 5 mM sodium nitroprusside in a 0.02% Silwett L-77 solution. Control plants were sprayed with a 0.02% Silwett L-77solution. Aerial tissues were harvested 1 hour and 6 hours after spraying, flash-frozen in liquid nitrogen and stored at −80° C. 
     Seeds of maize hybrid 35A (Pioneer) were sown in water-moistened sand in flats (10 rows, 5-6 seed/row) and covered with clear, plastic lids before being placed in a growth chamber having 16 hr light (25° C.)/8 hr dark (20° C.), 75% relative humidity and 13,000-14,000 LUX. Covered flats were watered every three days for 7 days. Seedlings were carefully removed from the sand and placed in 1-liter beakers with 5 mM nitroprusside for treatment. Control plants were treated with water. After 1 hr, 6 hr and 12 hr, aerial and root tissues were separated and flash frozen in liquid nitrogen prior to storage at −80° C. 
     (w) S4 Immature Buds, Inflorescence Meristem 
     Seeds of  Arabidopsis thaliana  (ecotype Wassilewskija) were sown in pots and left at 4° C. for two to three days to vernalize. They were then transferred to a growth chamber. Plants were grown under long-day (16 hr light: 8 hr dark) conditions, 7000-8000 LUX light intensity, 70% humidity, and 22° C. temperature. Inflorescences containing immature floral buds [stages 1-12; Smyth et al., 1990] as well as the inflorescence meristem were harvested and flash frozen in liquid nitrogen. 
     (x) S5 Flowers (Opened) 
     Seeds of  Arabidopsis thaliana  (ecotype Wassilewskija) were sown in pots and left at 4° C. for two to three days to vernalize. They were then transferred to a growth chamber. Plants were grown under long-day (16 hr light: 8 hr dark) conditions, 7000-8000 LUX light intensity, 70% humidity, and 22° C. temperature. Mature, unpollinated flowers [stages 12-14; Smyth et al. 1990] were harvested and flash frozen in liquid nitrogen. 
     (y) S6 Siliques (All Stages) 
     Seeds of  Arabidopsis thaliana  (ecotype Wassilewskija) were sown in pots and left at 4° C. for two to three days to vernalize. They were then transferred to a growth chamber. Plants were grown under long-day (16 hr light: 8 hr dark) conditions, 7000-8000 LUX light intensity, 70% humidity, and 22° C. temperature. Siliques bearing developing seeds containing post fertilization through pre-heart stage [0-72 hours after fertilization (HAF)], heart—through early curled cotyledon stage [72-120 HAF] and late-curled cotyledon stage [&gt;120 HAF] embryos were harvested separately and pooled prior to RNA isolation in a mass ratio of 1:1:1. The tissues were then flash frozen in liquid nitrogen. Description of the stages of  Arabidopsis  embryogenesis used were reviewed by Bowman (1994). 
     (Z)  Arabidopsis  Endosperm 
     Mea/Mea Fruits 0-10 mm 
     Seeds of  Arabidopsis thaliana  heterozygous for the fertilization-independent endosperm1 (fie1) [Ohad et al., 1996; ecotype Landsberg  erecta  (Ler)] were sown in pots and left at 4° C. for two to three days to vernalize. Kiyosue et al. (1999) subsequently determined that fie1 was allelic to the gametophytic maternal effect mutant medea (Grossniklaus et al., 1998). Imbibed seeds were then transferred to a growth chamber. Plants were grown under long-day (16 hr light: 8 hr dark) conditions, 7000-8000 LUX light intensity, 70% humidity, and 22° C. temperature. 1-2 siliques (fruits) bearing developing seeds just prior to dessication[9 days after flowering (DAF)] were selected from each plant and were hand-dissected to identify wild-type, mea/+ heterozygotes, and mea/mea homozygous mutant plants. At this stage, homozygous mea/mea plants produce short siliques that contain &gt;70% aborted seed and can be distinguished from those produced by wild-type (100% viable seed) and mea/+heterozygous (50% viable seed) plants (Ohad et al., 1996; Grossniklaus et al., 1998; Kiyosue et al., 1999). Siliques 0-10 mm in length containing developing seeds 0-9 DAF produced by homozygous mea/mea plants were harvested and flash frozen in liquid nitrogen. 
     Pods 0-10 mm (Control Tissue for Sample 70) 
     Seeds of  Arabidopsis thaliana  heterozygous for the fertilization-independent endosperm1 (fie1) [Ohad et al, 1996; ecotype Landsberg  erecta  (Ler)] were sown in pots and left at 4° C. for two to three days to vernalize. Kiyosue et al. (1999) subsequently determined that fie1 was allelic to the gametophytic maternal effect mutant medea (Grossniklaus et al., 1998). Imbibed seeds were then transferred to a growth chamber. Plants were grown under long-day (16 hr light: 8 hr dark) conditions, 7000-8000 LUX light intensity, 70% humidity, and 22° C. temperature. 1-2 siliques (fruits) bearing developing seeds just prior to dessication[9 days after flowering (DAF)] were selected from each plant and were hand-dissected to identify wild-type, mea/+heterozygotes, and mea/mea homozygous mutant plants. At this stage, homozygous mea/mea plants produce short siliques that contain &gt;70% aborted seed and can be distinguished from those produced by wild-type (100% viable seed) and mea/+heterozygous (50% viable seed) plants (Ohad et al., 1996; Grossniklaus et al., 1998; Kiyosue et al., 1999). Siliques 0-10 mm in length containing developing seeds 0-9 DAF produced by segregating wild-type plants were opened and the seeds removed. The remaining tissues (pods minus seed) were harvested and flash frozen in liquid nitrogen. 
     (aa)  Arabidopsis  Seeds 
     Fruits (pod+seed) 0-5 mm Seeds of  Arabidopsis thaliana  (ecotype Wassilewskija) were sown in pots and left at 4° C. for two to three days to vernalize. They were then transferred to a growth chamber. Plants were grown under long-day (16 hr light: 8 hr dark) conditions, 7000-8000 LUX light intensity, 70% humidity, and 22° C. temperature. 3-4 siliques (fruits) bearing developing seeds were selected from at least 3 plants and were hand-dissected to determine what developmental stage(s) were represented by the enclosed embryos. Description of the stages of  Arabidopsis  embryogenesis used in this determination were summarized by Bowman (1994). Silique lengths were then determined and used as an approximate determinant for embryonic stage. Siliques 0-5 mm in length containing post fertilization through pre-heart stage [0-72 hours after fertilization (HAF)] embryos were harvested and_flash frozen in liquid nitrogen. 
     Fruits(Pod+Seed) 5-10 mm 
     Seeds of  Arabidopsis thaliana  (ecotype Wassilewskija) were sown in pots and left at 4° C. for two to three days to vernalize. They were then transferred to a growth chamber. Plants were grown under long-day (16 hr light: 8 hr dark) conditions, 7000-8000 LUX light intensity, 70% humidity, and 22° C. temperature. 3-4 siliques (fruits) bearing developing seeds were selected from at least 3 plants and were hand-dissected to determine what developmental stage(s) were represented by the enclosed embryos. Description of the stages of  Arabidopsis  embryogenesis used in this determination were summarized by Bowman (1994). Silique lengths were then determined and used as an approximate determinant for embryonic stage. Siliques 5-10 mm in length containing heart-through early upturned-U-stage [72-120 hours after fertilization (HAF)] embryos were harvested and flash frozen in liquid nitrogen. 
     Fruits(Pod+Seed)&gt;10 mm 
     Seeds of  Arabidopsis thaliana  (ecotype Wassilewskija) were sown in pots and left at 4° C. for two to three days to vernalize. They were then transferred to a growth chamber. Plants were grown under long-day (16 hr light: 8 hr dark) conditions, 7000-8000 LUX light intensity, 70% humidity, and 22° C. temperature. 3-4 siliques (fruits) bearing developing seeds were selected from at least 3 plants and were hand-dissected to determine what developmental stage(s) were represented by the enclosed embryos. Description of the stages of  Arabidopsis  embryogenesis used in this determination were summarized by Bowman (1994). Silique lengths were then determined and used as an approximate determinant for embryonic stage. Siliques &gt;10 mm in length containing green, late upturned-U-stage [&gt;120 hours after fertilization (HAF)-9 days after flowering (DAF)] embryos were harvested and flash frozen in liquid nitrogen. 
     Green Pods 5-10 mm (Control Tissue for Samples 72-74) 
     Seeds of  Arabidopsis thaliana  (ecotype Wassilewskija) were sown in pots and left at 4° C. for two to three days to vernalize. They were then transferred to a growth chamber. Plants were grown under long-day (16 hr light: 8 hr dark) conditions, 7000-8000 LUX light intensity, 70% humidity, and 22° C. temperature. 3-4 siliques (fruits) bearing developing seeds were selected from at least 3 plants and were hand-dissected to determine what developmental stage(s) were represented by the enclosed embryos. Description of the stages of  Arabidopsis  embryogenesis used in this determination were summarized by Bowman (1994). Silique lengths were then determined and used as an approximate determinant for embryonic stage. Green siliques 5-10 mm in length containing developing seeds 72-120 hours after fertilization (HAF)] were opened and the seeds removed. The remaining tissues (green pods minus seed) were harvested and flash frozen in liquid nitrogen. 
     Green Seeds from Fruits &gt;10 mm 
     Seeds of  Arabidopsis thaliana  (ecotype Wassilewskija) were sown in pots and left at 4° C. for two to three days to vernalize. They were then transferred to a growth chamber. Plants were grown under long-day (16 hr light: 8 hr dark) conditions, 7000-8000 LUX light intensity, 70% humidity, and 22° C. temperature. 3-4 siliques (fruits) bearing developing seeds were selected from at least 3 plants and were hand-dissected to determine what developmental stage(s) were represented by the enclosed embryos. Description of the stages of  Arabidopsis  embryogenesis used in this determination were summarized by Bowman (1994). Silique lengths were then determined and used as an approximate determinant for embryonic stage. Green siliques &gt;10 mm in length containing developing seeds up to 9 days after flowering (DAF)] were opened and the seeds removed and harvested and flash frozen in liquid nitrogen. 
     Brown Seeds from Fruits &gt;10 mm 
     Seeds of  Arabidopsis thaliana  (ecotype Wassilewskija) were sown in pots and left at 4° C. for two to three days to vernalize. They were then transferred to a growth chamber. Plants were grown under long-day (16 hr light: 8 hr dark) conditions, 7000-8000 LUX light intensity, 70% humidity, and 22° C. temperature. 3-4 siliques (fruits) bearing developing seeds were selected from at least 3 plants and were hand-dissected to determine what developmental stage(s) were represented by the enclosed embryos. Description of the stages of  Arabidopsis  embryogenesis used in this determination were summarized by Bowman (1994). Silique lengths were then determined and used as an approximate determinant for embryonic stage. Yellowing siliques &gt;10 mm in length containing brown, dessicating seeds &gt;11 days after flowering (DAF)] were opened and the seeds removed and harvested and flash frozen in liquid nitrogen. 
     Green/Brown Seeds from Fruits &gt;10 mm 
     Seeds of  Arabidopsis thaliana  (ecotype Wassilewskija) were sown in pots and left at 4° C. for two to three days to vernalize. They were then transferred to a growth chamber. Plants were grown under long-day (16 hr light: 8 hr dark) conditions, 7000-8000 LUX light intensity, 70% humidity, and 22° C. temperature. 3-4 siliques (fruits) bearing developing seeds were selected from at least 3 plants and were hand-dissected to determine what developmental stage(s) were represented by the enclosed embryos. Description of the stages of  Arabidopsis  embryogenesis used in this determination were summarized by Bowman (1994). Silique lengths were then determined and used as an approximate determinant for embryonic stage. Green siliques &gt;10 mm in length containing both green and brown seeds &gt;9 days after flowering (DAF)] were opened and the seeds removed and harvested and flash frozen in liquid nitrogen. 
     Mature Seeds (24 Hours after Imbibition) 
     Mature dry seeds of  Arabidopsis thaliana  (ecotype Wassilewskija) were sown onto moistened filter paper and left at 4° C. for two to three days to vernalize. Imbibed seeds were then transferred to a growth chamber [16 hr light: 8 hr dark conditions, 7000-8000 LUX light intensity, 70% humidity, and 22° C. temperature], the emerging seedlings harvested after 48 hours and flash frozen in liquid nitrogen. 
     Mature Seeds (Dry) 
     Seeds of  Arabidopsis thaliana  (ecotype Wassilewskija) were sown in pots and left at 4° C. for two to three days to vernalize. They were then transferred to a growth chamber. Plants were grown under long-day (16 hr light: 8 hr dark) conditions, 7000-8000 LUX light intensity, 70% humidity, and 22° C. temperature and taken to maturity. Mature dry seeds are collected, dried for one week at 28° C., and vernalized for one week at 4° C. before used as a source of RNA. 
     Ovules 
     Seeds of  Arabidopsis thaliana  heterozygous for pistillata (pi) [ecotype Landsberg  erecta  (Ler)] were sown in pots and left at 4° C. for two to three days to vernalize. They were then transferred to a growth chamber. Plants were grown under long-day (16 hr light: 8 hr dark) conditions, 7000-8000 LUX light intensity, 76% humidity, and 24° C. temperature. Inflorescences were harvested from seedlings about 40 days old. The inflorescences were cut into small pieces and incubated in the following enzyme solution (pH 5) at room temperature for 0.5-1 hr.: 0.2% pectolyase Y-23, 0.04% pectinase, 5 mM MES, 3% Sucrose and MS salts (1900 mg/l KNO 3 , 1650 mg/l NH 4 NO 3 , 370 mg/l MgSO 4 .7H 2 O, 170 mg/l KH 2 PO 4 , 440 mg/l CaCl 2 .2H 2 O, 6.2 mg/l H 2 BO 3 , 15.6 mg/l MnSO 4 .4H 2 O, 8.6 mg/l ZnSO 4 .7H 2 O, 0.25 mg/l NaMoO 4 .2H 2 O, 0.025 mg/l CuCO 4 .5H 2 O, 0.025 mg/l CoCl 2 .6H 2 O, 0.83 mg/l KI, 27.8 mg/l FeSO 4 .7H 2 O, 37.3 mg/l Disodium EDTA, pH 5.8). At the end of the incubation the mixture of inflorescence material and enzyme solution was passed through a size 60 sieve and then through a sieve with a pore size of 125 μm. Ovules greater than 125 μm in diameter were collected, rinsed twice in B5 liquid medium (2500 mg/l KNO 3 , 250 mg/l MgSO 4 .7H 2 O, 150 mg/l NaH2PO4.H 2 O, 150 mg/l CaCl 2 .2H 2 O, 134 mg/l (NH4)2CaCl 2 .SO 4 , 3 mg/l H 2 BO 3 , 10 mg/l MnSO 4 .4H 2 O, 2ZnSO 4 .7H 2 O, 0.25 mg/l NaMoO 4 .2H 2 O, 0.025 mg/l CuCO 4 .5H 2 O, 0.025 mg/l CoCl 2 .6H 2 O, 0.75 mg/l KI, 40 mg/l EDTA sodium ferric salt, 20 g/l sucrose, 10 mg/l Thiamine hydrochloride, 1 mg/l Pyridoxine hydrochloride, 1 mg/l Nicotinic acid, 100 mg/l myo-inositol, pH 5.5)), rinsed once in deionized water and flash frozen in liquid nitrogen. The supernatant from the 125 μm sieving was passed through subsequent sieves of 50 μm and 32 μm. The tissue retained in the 32 μm sieve was collected and mRNA prepared for use as a control. 
     (Bb) Herbicide Treatment 
       Arabidopsis thaliana  (Ws) seeds were sterilized for 5 min. with 30% bleach, 50 μl TRITON® in a total volume of 50 ml. Seeds were vernalized at 4° C. for 3 days before being plated onto GM agar plates at a density of about 144 seeds per plate. Plates were incubated in a Percival growth chamber having 16 hr light/8 hr dark, 80% relative humidity, 22° C. and 11,000 LUX for 14 days. 
     Plates were sprayed (˜0.5 mls/plate) with water, Finale (1.128 g/L), GLEAN® (1.88 g/L), ROUNDUP® (0.01 g/L) or Trimec (0.08 g/L). Tissue was collected and flash frozen in liquid nitrogen at the following time points: 0, 1, 2, 4 (EXPT REP: 107871 (Finale), 107881 (GLEAN®), 107896 (ROUNDUP) and 107886 (Trimec)), 8, 12(EXPT REP: 108467 (Finale), 108468 (GLEAN®), 108465 (ROUNDUP) and 108466, 107891 (Trimec)), and 24 hours. Frozen tissue was stored at −80° C. prior to RNA isolation. 
     (cc) Ap2 
     Seeds of  Arabidopsis thaliana  (ecotype Landesberg  erecta ) and floral mutant  apetala 2 (Jofuku et al., 1994, Plant Cell 6:1211-1225) were sown in pots and left at 4° C. for two to three days to vernalize. They were then transferred to a growth chamber. Plants were grown under long-day (16 hr light, 8 hr dark) conditions 7000-8000 LUX light intensity, 70% humidity and 22° C. temperature. Inflorescences containing immature floral buds (stages 1-7; Bowman, 1994) as well as the inflorescence meristem were harvested and flashfrozen. Polysomal polyA+ RNA was isolated from tissue according to Cox and Goldberg, 1988). 
     (dd) Protein Degradation 
       Arabidopsis thaliana  (ecotype Ws) wild-type and 13B12-1 (homozygous) mutant seed were sown in pots containing Metro-mix 350 soil and incubated at 4° C. for four days. Vernalized seeds were germinated in the greenhouse (16 hr light/8 hr dark) over a 7 day period. Mutant seedlings were sprayed with 0.02% (active ingredient) Finale to confirm their transgenic standing. Plants were grown until the mutant phenotype (either multiple pistils in a single flower and/or multiple branching per node) was apparent. Young inflorescences immediately forming from the multiple-branched stems were cut and flash frozen in liquid nitrogen. Young inflorescences from wild-type plants grown in parallel and under identical conditions were collected as controls. All collected tissue was stored at −80° C. until RNA isolation. (EXPT REP 108451) 
     (ee) Root tips 
     Seeds of  Arabidopsis thaliana  (ecotye Ws) were placed on MS plates and vernalized at 4° C. for 3 days before being placed in a 25° C. growth chamber having 16 hr light/8 hr dark, 70% relative humidty and about 3 W/m 2 . After 6 days, young seedlings were transferred to flasks containing B5 liquid medium, 1% sucrose and 0.05 mg/l indole-3-butyric acid. Flasks were incubated at room temperature with 100 rpm agitation. Media was replaced weekly. After three weeks, roots were harvested and incubated for 1 hr with 2% pectinase, 0.2% cellulase, pH 7 before straining through a #80 (Sigma) sieve. The root body material remaining on the sieve (used as the control) was flash frozen and stored at −80° C. until use. The material that passed through the #80 sieve was strained through a #200 (Sigma) sieve and the material remaining on the sieve (root tips) was flash frozen and stored at −80° C. until use. Approximately 10 mg of root tips were collected from one flask of root culture. 
     Seeds of maize hybrid 35A (Pioneer) were sown in water-moistened sand in flats (10 rows, 5-6 seed/row) and covered with clear, plastic lids before being placed in a growth chamber having 16 hr light (25° C.)/8 hr dark (20° C.), 75% relative humidity and 13,000-14,000 LUX. Covered flats were watered every three days for 8 days. Seedlings were carefully removed from the sand and the root tips (˜2 mm long) were removed and flash frozen in liquid nitrogen prior to storage at −80° C. The tissues above the root tips (˜1 cm long) were cut, treated as above and used as control tissue. 
     (ff) rt1 
     The rt1 allele is a variation of rt1 rootless1 and is recessive. Plants displaying the rt1 phenotype have few or no secondary roots. 
     Seed from plants segregating for rt1 were sown on sand and placed in a growth chamber having 16 hr light/8 hr dark, 13,000 LUX, 70% humidity and 20° C. temperature. Plants were watered every three days with tap water. Eleven (11) day old seedlings were carefully removed from the sand, keeping the roots intact. rt1-type seedlings were separated from their wild-type counterparts and the root tissue isolated. Root tissue from normal seedlings (control) and rt1 mutants were flash frozen in liquid nitrogen and stored at −80° C. until use. 
     (Gg) Imbibed Seed 
     Seeds of maize hybrid 35A (Pioneer) were sown in water-moistened sand in covered flats (10 rows, 5-6 seed/row) and covered with clear, plastic lids before being placed in a growth chamber having 16 hr light (25° C.)/8 hr dark (20° C.), 75% relative humidity and 13,000-14,000 LUX. One day after sowing, whole seeds were flash frozen in liquid nitrogen prior to storage at −80° C. Two days after sowing, embryos and endosperm were isolated and flash frozen in liquid nitrogen prior to storage at −80° C. On days 3-6, aerial tissues, roots and endosperm were isolated and flash frozen in liquid nitrogen prior to storage at −80° C. 
     (hh) Rough Sheath2-R (rs2-R) Mutants (1400-6/S-17) 
     This experiment was conducted to identify abnormally expressed genes in the shoot apex of rough sheath2-R (rs2-R) mutant plants. rs2 encodes a myb domain DNA binding protein that functions in repression of several shoot apical meristem expressed homeobox genes. Two homeobox gene targets are known for rs2 repression, rough sheath1, liguleless 3. The recessive loss of function phenotype of rs2-R homozygous plants is described in Schneeberger et al. 1998 Development 125: 2857-2865. 
     The seed stock genetically segregates 1:1 for rs2-R/rs2-R:rs2-R/+ 
     Preparation of tissue samples: 160 seedlings pooled from 2 and 3 week old plants grown in sand. Growth conditions; CONVIRON® #107 @ 12 hr days/12 hr night, 25° C., 75% humidity. Shoot apex was dissected to include leaf three and older. (Pictures available upon request). 
     1) rough sheath2-R homozygous (mutant) shoot apex 
     2) rough sheath2-R heterozygous (wt, control) shoot apex 
     (ii) Leaf Mutant 3642: 
     Mutant 3642 is a recessive mutation that causes abnormal leaf development. The leaves of mutant 3642 plants are characterized by leaf twisting and irregular leaf shape. Mutant 3642 plants also exhibit abnormally shaped floral organs which results in reduced fertility. 
     Seed segregating for the mutant phenotype was sown in Metro-mix 350 soil and grown in a CONVIRON® growth chamber with watering by sub-irrigation twice a week. Environmental conditions were set at 20 degrees Celsius, 70% humidity with an 8 hour day, 16 hour night light regime. Plants were harvested after 4 weeks of growth and the entire aerial portion of the plant was harvested and immediately frozen in liquid nitrogen and stored at −80 C. Mutant phenotype plants were harvested separately from normal phenotype plants, which serve as the control tissue. 
     (jj) Flowers (Green, White or Buds) 
     Approximately 10 □l of  Arabidopsis thaliana  seeds (ecotype Ws) were sown on 350 soil (containing 0.03% marathon) and vernalized at 4 C for 3 days. Plants were then grown at room temperature under fluorescent lighting until flowering. Flowers were harvested after 28 days in three different categories. Buds that had not opened at all and were completely green were categorized as “flower buds” (also referred to as green buds by the investigator). Buds that had started to open, with white petals emerging slightly were categorized as “green flowers” (also referred to as white buds by the investigator). Flowers that had opened mostly (with no silique elongation) with white petals completely visible were categorized as “white flowers” (also referred to as open flowers by the investigator). Buds and flowers were harvested with forceps, flash frozen in liquid nitrogen and stored at −80 C until RNA was isolated. 
     2. Microarray Hybridization Procedures 
     Microarray technology provides the ability to monitor mRNA transcript levels of thousands of genes in a single experiment. These experiments simultaneously hybridize two differentially labeled fluorescent cDNA pools to glass slides that have been previously spotted with cDNA clones of the same species. Each arrayed cDNA spot will have a corresponding ratio of fluorescence that represents the level of disparity between the respective mRNA species in the two sample pools. Thousands of polynucleotides can be spotted on one slide, and each experiment generates a global expression pattern. 
     Coating Slides 
     The microarray consists of a chemically coated microscope slide, referred herein as a “chip” with numerous polynucleotide samples arrayed at a high density. The poly-L-lysine coating allows for this spotting at high density by providing a hydrophobic surface, reducing the spreading of spots of DNA solution arrayed on the slides. Glass microscope slides (Gold Seal #3010 manufactured by Gold Seal Products, Portsmouth, N.H., USA) were coated with a 0.1% W/V solution of Poly-L-lysine (Sigma, St. Louis, Mo.) using the following protocol: 
     1. Slides were placed in slide racks (Shandon Lipshaw #121). The racks were then put in chambers (Shandon Lipshaw #121). 
     2. Cleaning solution was prepared: 
     70 g NaOH was dissolved in 280 mL ddH2O. 
     420 mL 95% ethanol was added. The total volume was 700 mL (=2×350 mL); it was stirred until completely mixed. 
     If the solution remained cloudy, ddH 2 O was added until clear. 
     3. The solution was poured into chambers with slides; the chambers were covered with glass lids. The solution was mixed on an orbital shaker for 2 hr. 
     4. The racks were quickly transferred to fresh chambers filled with ddH 2 O. They were rinsed vigorously by plunging racks up and down. 
     Rinses were repeated 4× with fresh ddH 2 O each time, to remove all traces of NaOH-ethanol. 
     5. Polylysine solution was prepared: 
     0 mL poly-L-lysine+70 mL tissue culture PBS in 560 mL water, using plastic graduated cylinder and beaker. 
     6. Slides were transferred to polylysine solution and shaken for 1 hr. 
     7. The rack was transferred to a fresh chambers filled with ddH 2 O. It was plunged up and down 5× to rinse. 
     8. The slides were centrifuged on microtiter plate carriers (paper towels were placed below the rack to absorb liquid) for 5 min. @ 500 rpm. The slide racks were transferred to empty chambers with covers. 
     9. Slide racks were dried in a 45 C oven for 10 min. 
     10. The slides were stored in a closed plastic slide box. 
     11. Normally, the surface of lysine coated slides was not very hydrophobic immediately after this process, but became increasingly hydrophobic with storage. A hydrophobic surface helped ensure that spots didn&#39;t run together while printing at high densities. After they aged for 10 days to a month the slides were ready to use. However, coated slides that have been sitting around for long periods of time were usually too old to be used. This was because they developed opaque patches, visible when held to the light, and these resulted in high background hybridization from the fluorescent probe. 
     Alternativey, precoated glass slides were purchased from TeleChem Internation, Inc. (Sunnyvale, Calif., 94089; catalog number SMM-25, Superamine substrates). 
     PCR Amplification of cDNA Clone Inserts 
     Polynucleotides were amplified from  Arabidopsis  cDNA clones using insert specific probes. The resulting 100 uL PCR reactions were purified with QIAQUICK® 96 PCR purification columns (Qiagen, Valencia, Calif., USA) and eluted in 30 uL of 5 mM Tris. 8.5 uL of the elution were mixed with 1.5 uL of 20×SSC to give a final spotting solution of DNA in 3×SSC. The concentrations of DNA generated from each clone varied between 10-100 ng/ul, but were usually about 50 ng/ul. 
     Arraying of PCR Products on Glass Slides 
     PCR products from cDNA clones were spotted onto the poly-L-Lysine coated glass slides using an arrangement of quill-tip pins (ChipMaker 3 spotting pins; Telechem, International, Inc., Sunnyvale, Calif., USA) and a robotic arrayer (PixSys 3500, Cartesian Technologies, Irvine, Calif., USA). Around 0.5 nl of a prepared PCR product was spotted at each location to produce spots with approximately 100 um diameters. Spot center-to-center spacing was from 180 urn to 210 um depending on the array. Printing was conducted in a chamber with relative humidity set at 50%. 
     Slides containing maize sequences were purchased from Agilent Technology (Palo Alto, Calif. 94304). 
     Post-Processing of Slides 
     After arraying, slides were processed through a series of steps—rehydration, UV crosslinking, blocking and denaturation—required prior to hybridization. Slides were rehydrated by placing them over a beaker of warm water (DNA face down), for 2-3 sec, to distribute the DNA more evenly within the spots, and then snap dried on a hot plate (DNA side, face up). The DNA was then cross-linked to the slides by UV irradiation (60-65 mJ; 2400 Stratalinker, Stratagene, La Jolla, Calif., USA). 
     Following this a blocking step was performed to modify remaining free lysine groups, and hence minimize their ability to bind labeled probe DNA. To achieve this the arrays were placed in a slide rack. An empty slide chamber was left ready on an orbital shaker. The rack was bent slightly inwards in the middle, to ensure the slides would not run into each other while shaking. The blocking solution was prepared as follows: 
     3×350-ml glass chambers (with metal tops) were set to one side, and a large round Pyrex dish with dH 2 O was placed ready in the microwave. At this time, 15 ml sodium borate was prepared in a 50 ml conical tube. 
     6-g succinic anhydride was dissolved in approx. 325-350 mL 1-methyl-2-pyrrolidinone. Rapid addition of reagent was crucial. 
     a. Immediately after the last flake of the succinic anhydride dissolved, the 15-mL sodium borate was added. 
     b. Immediately after the sodium borate solution mixed in, the solution was poured into an empty slide chamber. 
     c. The slide rack was plunged rapidly and evenly in the solution. It was vigorously shaken up and down for a few seconds, making sure slides never left the solution. 
     d. It was mixed on an orbital shaker for 15-20 min. Meanwhile, the water in the Pyrex dish (enough to cover slide rack) was heated to boiling. 
     Following this, the slide rack was gently plunge in the 95 C water (just stopped boiling) for 2 min. Then the slide rack was plunged 5× in 95% ethanol. The slides and rack were centrifuged for 5 min. @ 500 rpm. The slides were loaded quickly and evenly onto the carriers to avoid streaking. The arrays were used immediately or store in slide box. 
     The Hybridization process began with the isolation of mRNA from the two tissues (see “Isolation of total RNA” and “Isolation of mRNA”, below) in question followed by their conversion to single stranded cDNA (see “Generation of probes for hybridization”, below). The cDNA from each tissue was independently labeled with a different fluorescent dye and then both samples were pooled together. This final differentially labeled cDNA pool was then placed on a processed microarray and allowed to hybridize (see “Hybridization and wash conditions”, below). 
     Isolation of Total RNA 
     Approximately 1 g of plant tissue was ground in liquid nitrogen to a fine powder and transferred into a 50-ml centrifuge tube containing 10 ml of TRIZOL® reagent. The tube was vigorously vortexed for 1 min and then incubated at room temperature for 10-20 min. on an orbital shaker at 220 rpm. Two ml of chloroform was added to the tube and the solution vortexed vigorously for at least 30-sec before again incubating at room temperature with shaking. The sample was then centrifuged at 12,000×g (10,000 rpm) for 15-20 min at 4° C. The aqueous layer was removed and mixed by inversion with 2.5 ml of 1.2 M NaCl/0.8 M Sodium Citrate and 2.5 ml of isopropyl alcohol added. After a 10 min. incubation at room temperature, the sample was centrifuged at 12,000×g (10,000 rpm) for 15 min at 4° C. The pellet was washed with 70% ethanol, re-centrifuged at 8,000 rpm for 5 min and then air dried at room temperature for 10 min. The resulting total RNA was dissolved in either TE (10 mM Tris-HCl, 1 mM EDTA, pH 8.0) or DEPC (diethylpyrocarbonate) treated deionized water (RNAse-free water). For subsequent isolation of mRNA using the Qiagen kit, the total RNA pellet was dissolved in RNAse-free water. 
     Isolation of mRNA 
     mRNA was isolated using the Qiagen OLIGOTEX® mRNA Spin-Column protocol (Qiagen, Valencia, Calif.). Briefly, 500 μl OBB buffer (20 mM Tris-Cl, pH 7.5, 1 M NaCl, 2 mM EDTA, 0.2% SDS) was added to 500 μl of total RNA (0.5-0.75 mg) and mixed thoroughly. The sample was first incubated at 70° C. for 3 min, then at room temperature for 10 minutes and finally centrifuged for 2 min at 14,000-18,000×g. The pellet was resuspended in 400 μl OW2 buffer (10 mM Tris-Cl, pH 7.5, 150 mM NaCl, 1 mM EDTA) by vortexing, the resulting solution placed on a small spin column in a 1.5 ml RNase-free microcentrifuge tube and centrifuged for 1 min at 14,000-18,000×g. The spin column was transferred to a new 1.5 ml RNase-free microcentrifuge tube and washed with 400 μl of OW2 buffer. To release the isolated mRNA from the resin, the spin column was again transferred to a new RNase-free 1.5 ml microcentrifuge tube, 20-100 μl 70° C. OEB buffer (5 mM Tris-Cl, pH 7.5) added and the resin resuspended in the resulting solution via pipetting. The mRNA solution was collected after centrifuging for 1 min at 14,000-18,000×g. 
     Alternatively, mRNA was isolated using the Stratagene Poly(A) Quik mRNA Isolation Kit (Startagene, La Jolla, Calif.). Here, up to 0.5 mg of total RNA (maximum volume of 1 ml) was incubated at 65° C. for 5 minutes, snap cooled on ice and 0.1× volumes of 10× sample buffer (10 mM Tris-HCl (pH 7.5), 1 mM EDTA (pH 8.0) 5 M NaCl) added. The RNA sample was applied to a prepared push column and passed through the column at a rate of ˜1 drop every 2 sec. The solution collected was reapplied to the column and collected as above. 200 μl of high salt buffer (10 mM Tris-HCl (pH 7.5), 1 mM EDTA, 0.5 NaCl) was applied to the column and passed through the column at a rate of ˜1 drop every 2 sec. This step was repeated and followed by three low salt buffer (10 mM Tris-HCl (pH 7.5), 1 mM EDTA, 0.1 M NaCl) washes preformed in a similar manner. mRNA was eluted by applying to the column four separate 200 μl aliquots of elution buffer (10 mM Tris-HCl (pH 7.5), 1 mM EDTA) preheated to 65° C. Here, the elution buffer was passed through the column at a rate of 1 drop/sec. The resulting mRNA solution was precipitated by adding 0.1× volumes of 10× sample buffer, 2.5 volumes of ice-cold 100% ethanol, incubating overnight at −20° C. and centrifuging at 14,000-18,000×g for 20-30 min at 4° C. The pellet was washed with 70% ethanol and air dried for 10 min. at room temperature before resuspension in RNase-free deionized water. 
     Preparation of Yeast Controls 
     Plasmid DNA was isolated from the following yeast clones using Qiagen filtered maxiprep kits (Qiagen, Valencia, Calif.): YAL022c(Fun26), YAL031c(Fun21), YBRO32w, YDL131w, YDL182w, YDL194w, YDL196w, YDR050c and YDR116c. Plasmid DNA was linearized with either BsrBI (YAL022c(Fun26), YAL031c(Fun21), YDL131w, YDL182w, YDL194w, YDL196w, YDR050c) or AflIII (YBRO32w, YDR116c) and isolated. 
     In Vitro Transcription of Yeast Clones 
     The following solution was incubated at 37° C. for 2 hours: 17 μl of isolated yeast insert DNA (1 μg), 20 μl 5× buffer, 10 l 100 mM DTT, 2.5 μl (100 U) RNasin, 20 μl 2.5 mM (ea.) rNTPs, 2.7 μl (40 U) SP6 polymerase and 27.8 μl RNase-free deionized water. 2 μl (2 U) Ampli DNase I was added and the incubation continued for another 15 min. 10 μl 5M NH 4 OAC and 100 μl phenol:chloroform:isoamyl alcohol (25:24:1) were added, the solution vortexed and then centrifuged to separate the phases. To precipitate the RNA, 250 μl ethanol was added and the solution incubated at −20° C. for at least one hour. The sample was then centrifuged for 20 min at 4° C. at 14,000-18,000×g, the pellet washed with 500 μl of 70% ethanol, air dried at room temperature for 10 min and resuspended in 100 μl of RNase-free deionized water. The precipitation procedure was then repeated. 
     Alternatively, after the two-hour incubation, the solution was extracted with phenol/chloroform once before adding 0.1 volume 3M sodium acetate and 2.5 volumes of 100% ethanol. The solution was centrifuged at 15,000 rpm, 4° C. for 20 minutes and the pellet resuspended in RNase-free deionized water. The DNase I treatment was carried out at 37° C. for 30 minutes using 2 U of Ampli DNase I in the following reaction condition: 50 mM Tris-HCl (pH 7.5), 10 mM MgCl 2 . The DNase I reaction was then stopped with the addition of NH 4 OAC and phenol:chloroform:isoamyl alcohol (25:24:1), and RNA isolated as described above. 
     0.15-2.5 ng of the in vitro transcript RNA from each yeast clone were added to each plant mRNA sample prior to labeling to serve as positive (internal) probe controls. 
     Generation of Probes for Hybridization 
     Generation of Labeled Probes for Hybridization from First-Strand cDNA 
     Hybridization probes were generated from isolated mRNA using an Atlas™ Glass Fluorescent Labeling Kit (Clontech Laboratories, Inc., Palo Alto, Calif., USA). This entails a two step labeling procedure that first incorporates primary aliphatic amino groups during cDNA synthesis and then couples fluorescent dye to the cDNA by reaction with the amino functional groups. Briefly, 5 μg of oligo(dT) 18  primer d(TTTTTTTTTTTTTTTTTTV) (SEQ ID NO:200517) was mixed with Poly A+mRNA (1.5-2 μg mRNA isolated using the Qiagen OLIGOTEX® mRNA Spin-Column protocol or—the Stratagene Poly(A) Quik mRNA Isolation protocol (Stratagene, La Jolla, Calif., USA)) in a total volume of 25 μl. The sample was incubated in a thermocycler at 70° C. for 5 min, cooled to 48° C. and 10 μl of 5×cDNA Synthesis Buffer (kit supplied), 5 μl 10×dNTP mix (dATP, dCTP, dGTP, dTTP and aminoallyl-dUTP; kit supplied), 7.5 μl deionized water and 2.5 μl MMLV Reverse Transcriptase (500 U) added. The reaction was then incubated at 48° C. for 30 minutes, followed by 1 hr incubation at 42° C. At the end of the incubation the reaction was heated to 70° C. for 10 min, cooled to 37° C. and 0.5 μl (5 U) RNase H added, before incubating for 15 min at 37° C. The solution was vortexed for 1 min after the addition of 0.5 μl 0.5 M EDTA and 5 μl of QuickClean Resin (kit supplied) then centrifuged at 14,000-18,000×g for 1 min. After removing the supernatant to a 0.45 μm spin filter (kit supplied), the sample was again centrifuged at 14,000-18,000×g for 1 min, and 5.5 μl 3 M sodium acetate and 137.5 μl of 100% ethanol added to the sample before incubating at −20° C. for at least 1 hr. The sample was then centrifuged at 14,000-18,000×g at 4° C. for 20 min, the resulting pellet washed with 500 μl 70% ethanol, air-dried at room temperature for 10 min and resuspended in 10 μl of 2× fluorescent labeling buffer (kit provided). 10 μl each of the fluorescent dyes Cy3 and Cy5 (Amersham Pharmacia (Piscataway, N.J., USA); prepared according to Atlas™ kit directions of Clontech) were added and the sample incubated in the dark at room temperature for 30 min. 
     The fluorescently labeled first strand cDNA was precipitated by adding 2 μl 3M sodium acetate and 50 μl 100% ethanol, incubated at −20° C. for at least 2 hrs, centrifuged at 14,000-18,000×g for 20 min, washed with 70% ethanol, air-dried for 10 min and dissolved in 100 of water. 
     Alternatively, 3-4 μg mRNA, 2.5 (˜8.9 ng of in vitro translated mRNA) μl yeast control and 3 μg oligo dTV (TTTTTTTTTTTTTTTTTT(A/C/G); SEQ ID NO:200518) were mixed in a total volume of 24.7 μl. The sample was incubated in a thermocycler at 70° C. for 10 min. before chilling on ice. To this, 8 μl of 5× first strand buffer (SuperScript II RNase H—Reverse Transcriptase kit from Invitrogen (Carlsbad, Calif. 92008); cat no. 18064022), 0.8° C. of aa-dUTP/dNTP mix (50×; 25 mM dATP, 25 mM dGTP, 25 mM dCTP, 15 mM dTTP, 10 mM aminoallyl-dUTP), 4 μl of 0.1 M DTT and 2.5 μl (500 units) of Superscript R.T.II enzyme (Stratagene) were added. The sample was incubated at 42° C. for 2 hours before a mixture of 10° C. of 1M NaOH and 10° C. of 0.5 M EDTA were added. After a 15 minute incubation at 65° C., 25 μl of 1 M Tris pH 7.4 was added. This was mixed with 450 μl of water in a Microcon 30 column before centrifugation at 11,000×g for 12 min. The column was washed twice with 450 (centrifugation at 11,000 g, 12 min.) before eluting the sample by inverting the Microcon column and centrifuging at 11,000×g for 20 seconds. Sample was dehydrated by centrifugation under vacuum and stored at −20° C. 
     Each reaction pellet was dissolved in 9 μl of 0.1 M carbonate buffer (0.1 M sodium carbonate and sodium bicarbonate, pH=8.5-9) and 4.5 μl of this placed in two microfuge tubes. 4.5 μl of each dye (in DMSO) were added and the mixture incubated in the dark for 1 hour. 4.5 μl of 4 M hydroxylamine was added and again incubated in the dark for 15 minutes. 
     Regardless of the method used for probe generation, the probe was purified using a Qiagen PCR cleanup kit (Qiagen, Valencia, Calif., USA), and eluted with 100 ul EB (kit provided). The sample was loaded on a Microcon YM-30 (Millipore, Bedford, Mass., USA) spin column and concentrated to 4-5 ul in volume. Probes for the maize microarrays were generated using the Fluorescent Linear Amplification Kit (cat. No. G2556A) from Agilent Technologies (Palo Alto, Calif.). 
     Hybridization and Wash Conditions 
     The following Hybridization and Washing Condition were developed: 
     Hybridization Conditions: 
     Labeled probe was heated at 95° C. for 3 min and chilled on ice. Then 25 □L of the hybridization buffer which was warmed at 42 C was added to the probe, mixing by pipetting, to give a final concentration of: 
     50% formamide 
     
         
         
           
             4×SSC 
             0.03% SDS
 
5×Denhardt&#39;s solution
 
             0.1 μg/ml single-stranded salmon sperm DNA 
           
         
       
    
     The probe was kept at 42 C. Prior to the hybridization, the probe was heated for 1 more min., added to the array, and then covered with a glass cover slip. Slides were placed in hybridization chambers (Telechem, Sunnyvale, Calif.) and incubated at 42° C. overnight. 
     Washing Conditions: 
     A. Slides were washed in 1×SSC+0.03% SDS solution at room temperature for 5 minutes, 
     B. Slides were washed in 0.2×SSC at room temperature for 5 minutes, 
     C. Slides were washed in 0.05×SSC at room temperature for 5 minutes. 
     After A, B, and C, slides were spun at 800×g for 2 min. to dry. They were then scanned. 
     Maize microarrays were hybridized according to the instructions included Fluorescent Linear Amplification Kit (cat. No. G2556A) from Agilent Technologies (Palo Alto, Calif.). 
     Scanning of Slides 
     The chips were scanned using a ScanArray 3000 or 5000 (General Scanning, Watertown, Mass., USA). The chips were scanned at 543 and 633 nm, at 10 um resolution to measure the intensity of the two fluorescent dyes incorporated into the samples hybridized to the chips. 
     Data Extraction and Analysis 
     The images generated by scanning slides consisted of two 16-bit TIFF images representing the fluorescent emissions of the two samples at each arrayed spot. These images were then quantified and processed for expression analysis using the data extraction software Imagene™ (Biodiscovery, Los Angeles, Calif., USA). Imagene output was subsequently analyzed using the analysis program Genespring™ (Silicon Genetics, San Carlos, Calif., USA). In Genespring, the data was imported using median pixel intensity measurements derived from Imagene output. Background subtraction, ratio calculation and normalization were all conducted in Genespring. Normalization was achieved by breaking the data in to 32 groups, each of which represented one of the 32 pin printing regions on the microarray. Groups consist of 360 to 550 spots. Each group was independently normalized by setting the median of ratios to one and multiplying ratios by the appropriate factor. 
     The results of the microarray experiments are reported in the MA_DIFF Table as described above in the section entitled “Brief Description of the Individual Tables”. 
     Example 4: AFLP Experiments and Results 
     Production of Samples 
     mRNA was prepared from 27 plant tissues. Based on preliminary cDNA-AFLP analysis with a few primer combinations, 11 plant tissues and/or pooled samples were selected. Samples were selected to give the greatest representation of unique band upon electrophoresis. The final 11 samples or pooled samples used in the cDNA-AFLP analysis were: 
     
       
         
           
               
               
               
             
               
                   
                   
               
             
            
               
                   
                 S1 
                 Dark adapted seedlings 
               
               
                   
                 S2 
                 Roots/Etiolated Seedlings 
               
               
                   
                 S3 
                 Mature leaves, soil grown 
               
               
                   
                 S4 
                 Immature buds, inflorescence meristem 
               
               
                   
                 S5 
                 Flowers opened 
               
               
                   
                 S6 
                 Siliques, all stages 
               
               
                   
                 S7 
                 Senescing leaves (just beginning to yellow) 
               
               
                   
                 S8 
                 Callus Inducing medium 
               
               
                   
                   
                 Callus shoot induction 
               
               
                   
                   
                 Callus root induction 
               
               
                   
                 S9 
                 Wounding 
               
               
                   
                   
                 Methyl-jasmonate-treated 
               
               
                   
                 S10 
                 Oxidative stress 
               
               
                   
                   
                 Drought stress 
               
               
                   
                   
                 Oxygen Stress-flooding 
               
               
                   
                 S11 
                 Heat treated light grown seedling 
               
               
                   
                   
                 Cold treated light grown seedlings 
               
               
                   
                   
               
            
           
         
       
     
     cDNA from each of the 11 samples was digested with two restriction endonucleases, namely TaqI and MseI. TagI and MseI adapters were then ligated to the restriction enzyme fragments. Using primers to these adapters that were specific in sequence (i.e. without extensions), the restriction fragments were subjected to cycles of non-radioactive pre-amplification. 
     Selective PCR 
     In order to limit the number of fragments or bands on each lane of the AFLP gel, fragments were subjected to another round of selective radioactive polymerase chain amplification. The TaqI primers used in this amplification were 5′-labelled with P 33 . For these amplifications, the TaqI primers had two extra nucleotides at their 3′ end and the MseI primers had three extra nucleotides at their 3′ end. This resulted in 16 primer designs for the TagI primer and 64 primer designs for the MseI primer. Altogether, this gave rise to a total of 1024 primer designs. Fragments generated in this selective amplification protocol were run with labeled molecular weight markers on polyacrylamide gels to separate fragments in the size range of 100-600 nucleotides. 
     Following gel electrophoresis, profiles were analyzed with a phosphoimager. From these images, electronic files, giving the mobilities of all bands on the gels and their intensities in each of the samples, were compiled. 
     All unique bands were cut out of the gels. The gel pieces were placed in 96 well plates for elution and their plate designation was linked to their electrophoretic mobilities recorded in the electronic files. The eluted fragments were then subjected to another round of amplification, this time using reamplification primers (see below). After amplification, DNA fragments were sequenced. 
     A computer database was established linking the mobilities of all the bands observed on the cDNA-AFLP gels with the sequence of the correspondingly isolated fragment. The sequence allowed for identification of the gene from which the cDNA-AFLP fragment was derived, allowing for a linkage of band mobility with the transcript of a specific gene. Also linked to the band mobilities were their intensities recorded for each of the eleven samples used in constructing the database. 
     This cDNA-AFLP analysis with TaqIMseI and 1024 primer combinations was repeated using the enzymes NlaIII in place of TaqI, and Csp6I in place of MseI. 
     Using the Database for the Transcript Profiling of Experimental Samples 
     Experimental Samples were subjected to cDNA-AFLP as described above, resulting in electronic files recording band mobilities and intensities. Through use of the database established above, band mobilities could be linked to specific cDNAs, and therefore genes. Furthermore, the linkage with the intensities in the respective samples allowed for the quantification of specific cDNAs in these samples, and thus the relative concentration of specific transcripts in the samples, indicating the level to which specific genes were expressed. 
                    Reamplification primers       99G24       (SEQ ID NO: 200519)       CGCCAGGGTTTTCCCAGTCACGAC| ACGACTCACT |gatgagtcctgagt       M13 forward        +10     MseI + 0               aa|               99G20       (SEQ ID NO: 200520)       AGCGGATAACAATTTCACACAGGA| CACACTGGTA |tagactgcgtaccg       M13 reverse       +10      TaqI +0               ga|            
Purification of the Reamplifiction Reaction Before Sequencing
 
5 μl reamplification reaction
 
0.25 μl 10×PCR buffer
 
0.33 μl Shrimp Alkaline Phosphatase (Amersham Life Science)
 
0.033 μl Exonuclease I (USB)
 
0.297 μl SAP dilution buffer
 
1.59 μl MQ
 
7.5 μl total
 
30′ 37° C.
 
10′ 80° C.
 
4° C.
 
Sample Preparation
 
     S1: Dark Adapted Seedlings: 
     Seeds of  Arabidopsis thaliana  (wassilewskija) were sown in pots and left at 4° C. for two to three days to vernalize. They were transferred to a growth chamber after three days. The intensity of light in the growth chamber was 7000-8000 LUX, temperature was 22° C., with 16 h light and 8 h dark. After 8 days, the seedlings were foil-wrapped and harvested after two days. 
     S2: Roots/Etiolated Seedlings: 
     Seeds of  Arabidopsis thaliana  (wassilewskija) were germinated on solid germination media (1×MS salts, 1×MS vitamins, 20 g/L sucrose, 50 mg/L MES pH 5.8) in the dark. Tissues were harvested 14 days later. 
     S3: Mature Leaves, Soil Grown: 
     Seeds of  Arabidopsis thaliana  (wassilewskija) were sown in pots and left at 4° C. for two to three days to vernalize. They were transferred to a growth chamber after three days. The intensity of light in the growth chamber was 7000-8000 LUX, temperature was 22° C., with 16 h light and 8 h dark. Leaves were harvested 17 days later from plants that had not yet bolted. 
     S4: Immature buds, Inflorescence Meristem: 
     Seeds of  Arabidopsis thaliana  (wassilewskija) were sown in pots and left at 4° C. for two to three days to vernalize. They were transferred to a growth chamber after three days. The intensity of light in the growth chamber was 7000-8000 LUX, temperature was 22° C., with 16 h light and 8 h dark. 
     S5: Flowers, Opened: 
     Seeds of  Arabidopsis thaliana  (wassilewskija) were sown in pots and left at 4° C. for two to three days to vernalize. They were transferred to a growth chamber after three days. The intensity of light in the growth chamber was 7000-8000 LUX, temperature was 22° C., with 16 h light and 8 h dark. 
     S6: Siliques, all Stages: 
     Seeds of  Arabidopsis thaliana  (wassilewskija) were sown in pots and left at 4° C. for two to three days to vernalize. They were transferred to a growth chamber after three days. The intensity of light in the growth chamber was 7000-8000 LUX, temperature was 22° C., with 16 h light and 8 h dark. 
     S7: Senescing Leaves (Just Beginning to Yellow): 
     Seeds of  Arabidopsis thaliana  (wassilewskija) were sown in pots and left at 4° C. for two to three days to vernalize. They were transferred to a growth chamber after three days. The intensity of light in the growth chamber was 7000-8000 LUX, temperature was 22° C., with 16 h light and 8 h dark. When the plant had leaves that were less than 50% yellow, the leaves that were just beginning to yellow were harvested. 
     S8: Callus Inducing Medium: 
     Seeds of  Arabidopsis thaliana  (wassilewskija) were surface sterilized (1 min-75% Ethanol, 6 min-bleach 100%+Tween 20, rinse) and incubated on MS medium containing 2,4-Dichlorophenoxyacetic acid (2,4-D) 1 mg/l and Kinetin 1 mg/l in the dark for 3 weeks to generate primary callus. 
     Hypocotyls and roots of the seedling were swollen after a week after incubation in this callus induction medium and subsequently callus was initiated from these swollen areas. 
     Callus Shoot Induction: 
     Primary calluses were transferred to the fresh callus induction medium for another 2 weeks growth to generate secondary callus. Secondary callus were transferred to shoot induction medium containing MS basal medium and Benzyladenine (BA) 2 mg/l and Naphthaleneacetic acid (NAA)) 0.1 mg/l for 2 weeks growth in the light before it was harvested and frozen and sent to Keygene. Many shoot meristems were observed under the microscope. 
     Callus Root Induction: 
     Secondary calluses were transferred to root induction medium containing MS basal medium, sucrose 1% and Indolebutyric acid (IBA) 0.05 mg/l in the dark. Many root primordia were observed under microscope after 10 days in the root induction medium. Those callus tissue were harvested and frozen and sent to Keygene. 
     S9: Wounding: 
     Seeds of  Arabidopsis thaliana  (wassilewskija) were sown in pots and left at 4° C. for two to three days to vernalize. They were transferred to a growth chamber after three days. The intensity of light in the growth chamber was 7000-8000 LUX, temperature was 22° C., with 16 h light and 8 h dark. After 20 days, leaves of plants were wounded with pliers. Wounded leaves were harvested 1 hour and 4 hours after wounding. 
     Methyl Jasmonate Treatment: 
     Seeds of  Arabidopsis thaliana  (wassilewskija) were sown in pots and left at 4° C. for two to three days to vernalize. They were transferred to a growth chamber after three days. The intensity of light in the growth chamber was 7000-8000 LUX, temperature was 22° C., with 16 h light and 8 h dark. After 13 days, plants were sprayed with 0.001% methyl jasmonate. Leaves were harvested 1.5 hours and 6 hours after spraying 
     S10: Oxidative Stress: 
     Seeds of  Arabidopsis thaliana  (wassilewskija) were sown in pots and left at 4° C. for two to three days to vernalize. They were transferred to a growth chamber after three days. The intensity of light in the growth chamber was 7000-8000 LUX, temperature was 22° C., with 16 h light and 8 h dark. After 24 days, a few leaves were inoculated with a mixture of 2.5 mM D-glucose, 2.5 U/mL glucose oxidase in 20 mM sodium phosphate buffer pH 6.5. After an hour, 3 hours, or 5 hours after inoculation, whole plant, except for the inoculated leaves, was harvested. This sample was mixed with sample from plants that were sitting in full sun (152,000 LUX) for 2 hours or four hours. 
     Drought Stress: 
     Seeds of  Arabidopsis thaliana  (wassilewskija) were sown in pots and left at 4° C. for two to three days to vernalize. They were transferred to a growth chamber after three days. The intensity of light in the growth chamber was 7000-8000 LUX, temperature was 22° C., with 16 h light and 8 h dark. After 20 days, aerial tissues were harvested and left to dry in 3 MM WHATMAN® paper for 1 hour or 4 hours. 
     Oxygen Stress: 
     Seeds of  Arabidopsis thaliana  (wassilewskija) were sown in pots and left at 4° C. for two to three days to vernalize. They were transferred to a growth chamber after three days. The intensity of light in the growth chamber was 7000-8000 LUX, temperature was 22° C., with 16 h light and 8 h dark. After 21 days, the plant was flooded by immersing its pot in a beaker of tap water. After 6 days, the upper tissues were harvested. 
     S11: Heat-Treated Light Grown Seedlings: 
     Seeds of  Arabidopsis thaliana  (wassilewskija) were sown in pots and left at 4° C. for two to three days to vernalize. They were transferred to a growth chamber after three days. The intensity of light in the growth chamber was 7000-8000 LUX, temperature was 22° C., with 16 h light and 8 h dark. Over a 5 hour period, the temperature was raised to 42° C. at the rate of approximately 4° C. per hour. After 1 hour at 42° C., the aerial tissues were collected. This sample was mixed with an equal volume of sample that went through a heat-recovery treatment namely bringing down the temperature to 22° C. from 42° C. over a 5 hour period at the rate of 4° C. per hour. 
     Cold-Treated Light Grown Seedlings: 
     Seeds of  Arabidopsis thaliana  (wassilewskija) were sown in pots and left at 4° C. for two to three days to vernalize. They were transferred to a growth chamber after three days. The intensity of light in the growth chamber was 7000-8000 LUX, temperature was 22° C., with 16 h light and 8 h dark. After 18 days, the plant was transferred to 4° C. for an hour before the aerial tissues were harvested. This sample was mixed with aerial tissues from another plant that was transferred to 4° C. for 27 hours before being harvested. 
     Analysis of Data: 
     Intensity: 
     The intensity of the band corresponds to the value in each lane marked S1, S2 etc. 
     P-Values: 
     The data shows P-values of each of the samples 1-11. P-values are calculated using the following formula 2*(1−NORMDIST(ABS(Sx−AVERAGE(of S1 to S11, not including Sx))/STDEV (of S1 to S11 not including Sx),0,1,TRUE)) using Excel functions. 
     The equivalent mathematical formula of P-value is as follows: 
     
       
         
           
             
               ∫ 
               
                 
                   φ 
                   ⁡ 
                   
                     ( 
                     x 
                     ) 
                   
                 
                 ⁢ 
                 
                   ⅆ 
                   x 
                 
               
             
             , 
             
               integrated 
               ⁢ 
               
                   
               
               ⁢ 
               from 
               ⁢ 
               
                   
               
               ⁢ 
               a 
               ⁢ 
               
                   
               
               ⁢ 
               to 
               ⁢ 
               
                   
               
               ⁢ 
               ∞ 
             
             , 
             
               
 
             
             ⁢ 
             
               where 
               ⁢ 
               
                   
               
               ⁢ 
               
                 φ 
                 ⁡ 
                 
                   ( 
                   x 
                   ) 
                 
               
               ⁢ 
               
                   
               
               ⁢ 
               is 
               ⁢ 
               
                   
               
               ⁢ 
               a 
               ⁢ 
               
                   
               
               ⁢ 
               normal 
               ⁢ 
               
                   
               
               ⁢ 
               distribution 
               ⁢ 
               
                 : 
               
             
           
         
       
       
         
           
             
               where 
               ⁢ 
               
                   
               
               ⁢ 
               a 
             
             = 
             
               
                  
                 
                   Sx 
                   - 
                   μ 
                 
                  
               
               _ 
             
           
         
       
       
         
           
             
               σ 
               ⁡ 
               
                 ( 
                 
                   
                     S 
                     ⁢ 
                     
                         
                     
                     ⁢ 
                     1 
                     ⁢ 
                     
                         
                     
                     ⁢ 
                     … 
                     ⁢ 
                     
                         
                     
                     ⁢ 
                     S 
                     ⁢ 
                     
                         
                     
                     ⁢ 
                     11 
                   
                   , 
                   
                     not 
                     ⁢ 
                     
                         
                     
                     ⁢ 
                     including 
                     ⁢ 
                     
                         
                     
                     ⁢ 
                     Sx 
                   
                 
                 ) 
               
             
             ; 
           
         
       
       
         
           
             
               where 
               ⁢ 
               
                   
               
               ⁢ 
               μ 
             
             = 
             
               is 
               ⁢ 
               
                   
               
               ⁢ 
               the 
               ⁢ 
               
                   
               
               ⁢ 
               average 
               ⁢ 
               
                   
               
               ⁢ 
               of 
               ⁢ 
               
                   
               
               ⁢ 
               the 
               ⁢ 
               
                   
               
               ⁢ 
               intensities 
               ⁢ 
               
                   
               
               ⁢ 
               of 
               ⁢ 
               
                   
               
               ⁢ 
               all 
               ⁢ 
               
                   
               
               ⁢ 
               samples 
             
           
         
       
       
         
           
             
               except 
               ⁢ 
               
                   
               
               ⁢ 
               Sx 
             
             , 
             
               
 
             
             ⁢ 
             
               = 
               
                 
                   
                     ( 
                     
                       ∑ 
                       
                         S 
                         ⁢ 
                         
                             
                         
                         ⁢ 
                         1 
                         ⁢ 
                         
                             
                         
                         ⁢ 
                         … 
                         ⁢ 
                         
                             
                         
                         ⁢ 
                         Sn 
                       
                     
                     ) 
                   
                   - 
                   Sx 
                 
                 
                   n 
                   - 
                   1 
                 
               
             
           
         
       
         
         
           
             where σ(S1 . . . S11, not including Sx)=the standard deviation of all sample intensities except Sx.
 
Results:
 
           
         
       
    
     The results are shown in the MA_diff tables. 
     Example 5: Transformation of Carrot Cells 
     Transformation of plant cells can be accomplished by a number of methods, as described above. Similarly, a number of plant genera can be regenerated from tissue culture following transformation. Transformation and regeneration of carrot cells as described herein is illustrative. 
     Single cell suspension cultures of carrot ( Daucus carota ) cells are established from hypocotyls of cultivar Early Nantes in B 5  growth medium (O. L. Gamborg et al.,  Plant Physiol.  45:372 (1970)) plus 2,4-D and 15 mM CaCl 2  (B 5 -44 medium) by methods known in the art. The suspension cultures are subcultured by adding 10 ml of the suspension culture to 40 ml of B 5 -44 medium in 250 ml flasks every 7 days and are maintained in a shaker at 150 rpm at 27° C. in the dark. 
     The suspension culture cells are transformed with exogenous DNA as described by Z. Chen et al.  Plant Mol. Bio.  36:163 (1998). Briefly, 4-days post-subculture cells are incubated with cell wall digestion solution containing 0.4 M sorbitol, 2% driselase, 5 mM MES (2-EN-Morpholino] ethanesulfonic acid) pH 5.0 for 5 hours. The digested cells are pelleted gently at 60×g for 5 min. and washed twice in W5 solution containing 154 mM NaCl, 5 mM KCl, 125 mM CaCl 2  and 5 mM glucose, pH 6.0. The protoplasts are suspended in MC solution containing 5 mM MES, 20 mM CaCl 2 , 0.5 M mannitol, pH 5.7 and the protoplast density is adjusted to about 4×10 6  protoplasts per ml. 
     15-60 μg of plasmid DNA is mixed with 0.9 ml of protoplasts. The resulting suspension is mixed with 40% polyethylene glycol (MW 8000, PEG 8000), by gentle inversion a few times at room temperature for 5 to 25 min. Protoplast culture medium known in the art is added into the PEG-DNA-protoplast mixture. Protoplasts are incubated in the culture medium for 24 hour to 5 days and cell extracts can be used for assay of transient expression of the introduced gene. Alternatively, transformed cells can be used to produce transgenic callus, which in turn can be used to produce transgenic plants, by methods known in the art. See, for example, Nomura and Komamine, Plt. Phys. 79:988-991 (1985), Identification and Isolation of Single Cells that Produce Somatic Embryos in Carrot Suspension Cultures. 
     Example 6: Phenotype Screens and Results 
     A. Triparental Mating and Vacuum Infiltration Transformation of Plants 
     Standard laboratory techniques are as described in Sambrook et al. (1989) unless otherwise stated. Single colonies of  Agrobacterium  C58C1Rif,  E. coli  helper strain HB 101 and the  E. coli  strain containing the transformation construct to be mobilized into  Agrobacterium  were separately inoculated into appropriate growth media and stationary cultures produced. 100 μl of each of the three cultures were mixed gently, plated on YEB (5 g Gibco beef extract, 1 g Bacto yeast extract, 1 g Bacto peptone, 5 g sucrose, pH 7.4) solid growth media and incubated overnight at 28° C. The bacteria from the triparental mating were collected in 2 ml of lambda buffer (20 mM Tris (pH 7.5), 100 mM NaCl, 10 mM MgCl 2 ) and serial dilutions made. An aliquot of the each dilution was then plated and incubated for 2 days at 28° C. on YEB plates supplemented with 100 μg/ml rifampicin and 100 μg/ml carbenicillin for calculation of the number of acceptor cells and on YEB plates supplemented with 100 μg/ml rifampicin, 100 μg/ml carbenicillin and 100 μg/ml spectinomycin for selection of transconjugant cells. The cointegrate structure of purified transconjugants was verified via Southern blot hybridization. 
     A transconjugant culture was prepared for vacuum infiltration by inoculating 1 ml of a stationary culture arising from a single colony into liquid YEB media and incubating at 28° C. for approximately 20 hours with shaking (220 rpm) until the OD taken at 600 nm was 0.8-1.0. The culture was then pelleted (8000 rpm, 10 min, 4° C. in a Sorvall SLA 3000 rotor) and the bacteria resuspended in infiltration medium (0.5×MS salts, 5% w/v sucrose, 10 μg/l BAP, 200 μl/l SILWET L-77®, pH 5.8) to a final OD 600  of 1.0. This prepared transconjugant culture was used within 20 minutes of preparation. 
     Wild-type plants for vacuum infiltration were grown in 4-inch pots containing Metromix 200 and Osmocote. Briefly, seeds of  Arabidopsis thaliana  (ecotype Wassilewskija) were sown in pots and left at 4° C. for two to four days to vernalize. They were then transferred to 22-25° C. and grown under long-day (16 hr light: 8 hr dark) conditions, sub-irrigated with water. After bolting, the primary inflorescence was removed and, after four to eight days, the pots containing the plants were inverted in the vacuum chamber to submerge all of the plants in the prepared transconjugant culture. Vacuum was drawn for two minutes before pots were removed, covered with plastic wrap and incubated in a cool room under darkness or very low light for one to two days. The plastic wrap was then removed, the plants returned to their previous growing conditions and subsequently produced (T1) seed collected. 
     B. Selection of T-DNA Insertion Lines 
     Approximately 10,750 seeds from the initial vacuum infiltrated plants were sown per flat of Metromix 350 soil. Flats were vernalized for four to five days at 4° C. before being transferred to 2-25° C. and grown under long-day (16 hr light: 8 hr dark) conditions, sub-irrigated with water. Approximately seven to ten days after germination, the (T1) seedlings were sprayed with 0.02% Finale herbicide (AgrEvo). After another five to seven days, herbicide treatment was repeated. Herbicide resistant T1 plants were allowed to self-pollinate and T2 seed were collected from each individual. In the few cases where the T1 plant produced few seed, the T2 seed was planted in bulk, the T2 plants allowed to self-pollinate and T3 seed collected. 
     C. Phenotype Screening 
     Approximately 40 seed from each T2 (or T3) line were planted in a 4-inch pot containing either Sunshine mix or Metromix 350 soil. Pots were vernalized for four to five days at 4° C. before being transferred to 22-25° C. and grown under long-day (16 hr light: 8 hr dark) conditions, sub-irrigated with water. A first phenotype screen was conducted by visually inspecting the seedlings five to seven days after germination and aberrant phenotypes noted. Plants were then sprayed with Finale herbicide within four days (i.e. about seven to nine days after germination). The second visual screen was conducted on surviving T2 (or T3) plants about sixteen to seventeen days after germination and the final screen was conducted after the plants had bolted and formed siliques. Here, the third and fourth green siliques were collected and aberrant phenotypes noted. The Knock-in and Knock-out Tables contain descriptions of identified phenotypes. 
     Alternative, seed were surface sterilized and transferred to agar solidified medium containing Murashige and Skoog salts (1×), 1% sucrose (wt/v) pH 5.7 before autoclaving. Seed were cold treated for 48 hours and transferred to long days [16 hours light and 8 hours dark], 25° C. Plants were screened at 5 and 10 days. 
     In another screen, seed were surface sterilized and transferred to agar solidified medium containing Murashige and Skoog salts (1×), and combinations of various nitrogen and sucrose amounts as specified below:
         Medium 1: no sucrose, 20.6 mM NH 4 NO 3 , 18.8 mM KNO 3 ;   Medium 2: 0.5% sucrose, 20.6 mM NH 4 NO3, 18.8 mM KNO 3 ;   Medium 3: 3% sucrose, 20.6 mM NH 4 NO 3 , 18.8 mM KNO 3 ;   Medium 4: no sucrose, 20.6 □M NH 4 NO 3 , 18.8 □M KNO 3 ;   Medium 5: 0.5% sucrose, 20.6 □M NH 4 NO 3 , 18.8 □M KNO 3 ; and   Medium 6: 3% sucrose, 20.6 □M NH 4 NO 3 , 18.8 □M KNO 3 .       

     The 0.5% sucrose was the control concentration for the sucrose. The low nitrogene, 20.6 □M NH 4 NO 3 , 18.8 □M KNO 3 , is the control for the nitrogen. Seed were cold treated for 48 hours and transferred to long days [16 hours light and 8 hours dark], 25° C. Plants were screened at 2, 5, and 10 days. 
     D. TAIL-PCR and Fragment Sequencing 
     Rosette leaves were collected from each putative mutant and crushed between parafilm and FTA paper (Life Technologies). Two 2 mm 2  hole punches were isolated from each FTA sample and washed according to the manufacturer&#39;s instructions by vortexing with 200 ul of the provided FTA purification reagent. The FTA reagent was removed and the washing procedure repeated two more times. The sample was then washed twice with 200 ul of FTA TE (10 mM Tris, 0.1 mM EDTA, pH 8.0) and vortexing prior to PCR. 
     Primers used for TAIL-PCR are as follows: 
     
       
         
           
               
               
            
               
                   
                 AD2: 
               
               
                   
                 (SEQ ID NO: 200521) 
               
               
                   
                 5′ NGTCGASWGANAWGAA 3′ (128-fold degeneracy) 
               
               
                   
                   
               
               
                   
                 S = G or C, W = A or T, and N = A, G, C, or T 
               
               
                   
                   
               
               
                   
                 LB1: 
               
               
                   
                 (SEQ ID NO: 200522) 
               
               
                   
                 5′ GTTTAACTGCGGCTCAACTGTCT 3′ 
               
               
                   
                   
               
               
                   
                 LB2: 
               
               
                   
                 (SEQ ID NO: 200523) 
               
               
                   
                 5′ CCCATAGACCCTTACCGCTTTAGTT 3′ 
               
               
                   
                   
               
               
                   
                 LB3: 
               
               
                   
                 (SEQ ID NO: 200524) 
               
               
                   
                 5′ GAAAGAAAAAGAGGTATAACTGGTA 3′ 
               
            
           
         
       
     
     The extent to which the left and right borders of the T-DNA insert were intact was measured for each line by PCR. The following components were mixed for PCR: 1 2 mm 2  FTA sample, 38.75 μl distilled water, 5 μl 10× Platinum PCR buffer (Life Technologies), 2 μl 50 mM MgCl 2 , 1 μl 10 mM dNTPs, 1 μl 10 μM primer LB1 (or RB1 for analysis of the right border), 1 μl 10 μM primer LB3R (or RB3R for analysis of the right border) and 1.25 U Platinum Taq (Life Technologies). Cycling conditions were: 94° C., 10 sec.; thirty cycles of 94° C., 1 sec.—54° C., 1 sec.—72° C., 1 sec.; 72° C., 4 sec. The expected band size for an intact left border is bp, while an intact right border generates a by band. 
     Fragments containing left or right border T-DNA sequence and adjacent genomic DNA sequence were obtained via PCR. First product PCR reactions use the following reaction mixture: 1 2 mm 2  FTA sample, 12.44 μl distilled water, 2 μl 10× Platinum PCR buffer (Life Technologies), 0.6 μl 50 mM MgCl 2 , 0.4 μl 10 mM dNTPs, 0.4 μl 10 μM primer LB1 (or RB1 for analysis of the right border), 3 μl 20 μM primer AD2 and 0.8 U Platinum Taq (Life Technologies). Cycling conditions for these reactions were: 93° C., 1 min.; 95° C., 1 min.; three cycles of 94° C., 45 sec.—62° C., 1 min.—72° C., 2.5 min.; 94° C., 45 sec.; 25° C., 3 min.; ramp to 72° C. in 3 min.; 72° C., 2.5 min.; fourteen cycles of 94° C., 20 sec.—68° C., 1 min.—72° C., 2.5 min.—94° C., 20 sec.; −68° C., 1 min.—72° C., 2.5 min.—94° C., 20 sec.—44° C., 1 min.—72° C., 2.5 min.; 72° C., 5 min.; end; ˜4.5 hrs. For second product PCR reactions 1 μl of a 1:50 dilution of the first PCR product reaction was mixed with 13.44 μl distilled water, 2 μl 10× Platinum PCR buffer (Life Technologies), 0.6 μl 50 mM MgCl 2 , 0.4 μl 10 mM dNTPs, 0.4 μl 10 μM primer LB2 (or RB2 for analysis of the right border), 2 μl 20 μM primer AD2 and 0.8 U Platinum Taq (Life Technologies). Second product cycling conditions were: eleven cycles of 94° C., 20 sec.—64° C., 1 min.—72° C., 2.5 min.—94° C., 20 sec.—64° C., 1 min.—72° C., 2.5 min.—94° C., 20 sec.—44° C., 1 min.; 72° C., 5 min.; end; ˜3 hrs. Third product PCR reactions were prepared by first diluting 2 μl of the second PCR product with 98 μl of distilled water and then adding 1 μl of the dilution to 13.44 μl distilled water, 2 μl 10× Platinum PCR buffer (Life Technologies), 0.6 μl 50 mM MgCl 2 , 0.4 μl 10 mM dNTPs, 0.4 μl 10 μM primer LB3 (or RB3 for analysis of the right border), 2 μl 20 μM primer AD2 and 0.8 U Platinum Taq (Life Technologies). Third product cycling conditions were: twenty cycles of 94° C., 38 sec.—44° C., 1 min.—72° C., 2.5 min.; 72° C., 5 min.; end; ˜2 hrs. Aliquots of the first, second and third PCR products were electrophoresed on 1% TAE (40 mM Tris-acetate, 1 mM EDTA) to determine their size. 
     Reactions were purified prior to sequencing by conducting a final PCR reaction. Here, 0.25 μl Platinum PCR Buffer (Life Technologies), 0.1 μl 50 mM MgCl 2 , 3.3 U SAP shrimp alkaline phosphatase, 0.33 U Exonuclease and 1.781 μl distilled water were added to a 5 μl third product and the reaction cycled at 37° C., 30 min.; 80° C., 10 min.; 4° C. indefinitely. Di-deoxy “Big Dye” sequencing was conducted on Perkin-Elmer 3700 or 377 machines. 
     Knock-in Experiments 
     For the following examples, a two-component system was constructed in a plant to ectopically express the desired cDNA. 
     First, a plant was generated by inserting a sequence encoding a transcriptional activator downstream of a desired promoter, thereby creating a first component where the desired promoter facilitates expression of the activator generated a plant. The first component also is referred to as the activator line. 
     Next, the second component is constructed by linking a desired cDNA to a sequence that the transcriptional activator can bind to and facilitate expression of the desired cDNA. The second component can be inserted into the activator line by transformation. Alternatively, the second component can be inserted into a separate plant, also referred to as the target line. Then, the target and activator lines can be crossed to generate progeny that have both components. 
     Two component lines were generated by both means. 
     Part I—from Crosses 
     Target lines containing cDNA constructs are generated using the  Agrobacterium -mediated transformation. Selected target lines are genetically crossed to activation lines (or promoter lines). Generally, the promoter lines used are as described above. Evaluation of phenotypes is done on the resulting F1 progenies. 
     Part II—From Type I Supertransformation 
     Promoter activation lines (generally Vascular/Ovule/Young Seed/Embryo line, Seed/Epidermls/Ovary/Fruit line, Roots/Shoots/Ovule line, and Vasculature/Meristem are transformed with cDNA constructs using the  Agrobacterium  mediated transformation. Selected transformants (and their progenies) are evaluated for changes in phenotypes. The table for the knock-in of the Type I supertransformation comprises the following information
         Clone ID,   Pfam,   Gemini ID   Trans. Unique ID (which indicates what promoter activation line was transformed   S Ratio: segregation ratio after the transformed plants are selected for the marker.   Assay   Stage: phenotype was observed   Feature: Where the phenotype was observed   Phenotype   P Ratio: phenotype ratio   Comments
 
Part III—From Type II Supertransformation
       

     Target lines generated using the procedure mentioned in Part I are transformed with T-DNA construct containing constitutive promoter. Selected transformants (and their progenies) are evaluated for changes in phenotypes. 
     An additional deposit of an  E. coli  Library,  E. coli  LibA021800, was made at the American Type Culture Collection in Manassas, Va., USA on Feb. 22, 2000 to meet the requirements of Budapest Treaty for the international recognition of the deposit of microorganisms. This deposit was assigned ATCC accession no. PTA-1411. 
     Additionaly, ATCC Library deposits; PTA-1161, PTA-1411 and PTA-2007 were made at the American Type Culture Collection in Manassas, Va., USA on; Jan. 7, 2000, Feb. 23, 2000 and Jun. 8, 2000 respectively, to meet the requirements of Budapest Treaty for the international recognition of the deposit of microorganisms. 
     The invention being thus described, it will be apparent to one of ordinary skill in the art that various modifications of the materials and methods for practicing the invention can be made. Such modifications are to be considered within the scope of the invention as defined by the following claims. 
     Each of the references from the patent and periodical literature cited herein is hereby expressly incorporated in its entirety by such citation.