Patent Publication Number: US-2020291435-A1

Title: Gene-modified microorganism for producing 3-hydroxyadipic acid, alpha-hydromuconic acid, and/or adipic acid, and production method for said chemical products

Description:
TECHNICAL FIELD 
     The present invention relates to a genetically modified microorganism in which a nucleic acid encoding a polypeptide involved in the production of a substance of interest is introduced or expression of the polypeptide is enhanced, and to a method of producing the substance by using the microorganism. 
     BACKGROUND ART 
     3-Hydroxyadipic acid (IUPAC name: 3-hydroxyhexanedioic acid), α-hydromuconic acid (IUPAC name: (E)-hex-2-enedioic acid), and adipic acid (IUPAC name: hexanedioic acid) are dicarboxylic acids containing six carbon atoms. These dicarboxylic acids can be used as raw materials for the production of polyesters by polymerization with polyhydric alcohols or as raw materials for the production of polyamides by polymerization with polyfunctional amines. Additionally, these dicarboxylic acids can be used as raw materials for polyamides by themselves by adding ammonia to the end of these dicarboxylic acids and converting the resultants to lactams. 
     Examples of the literature relating to the biosynthesis of 3-hydroxyadipic acid using a non-naturally occurring microorganism include Patent Document 1 in which 3-hydroxyadipic acid (3-hydroxyadipate) is described as a metabolic intermediate produced by the microorganism in the pathway of biosynthesis of 1,3-butadiene from succinyl-CoA. 
     Examples of the literature relating to the biosynthesis of α-hydromuconic acid using a non-naturally occurring microorganism include Patent Document 2 in which α-hydromuconic acid (2,3-dehydroadipate) is described as a metabolic intermediate produced by the microorganism in the pathway of biosynthesis of trans,trans-muconic acid from succinyl-CoA. 
     Examples of the literature relating to the biosynthesis of adipic acid using a microorganism include Patent Document 3 in which the reverse adipate-degradation pathway is described as a pathway to produce adipic acid from succinyl-CoA. 
     It is described that all the biosynthesis pathways described in Patent Documents 1 to 3 proceed through an enzymatic reaction that reduces 3-oxoadipyl-CoA to 3-hydroxyadipyl-CoA. 
     PRIOR ART DOCUMENTS 
     Patent Documents 
     
         
         Patent Document 1: JP 2013-535203 A 
         Patent Document 2: US 2011/0124911 A1 
         Patent Document 3: JP 2011-515111 A 
       
    
     SUMMARY OF THE INVENTION 
     Problems to be Solved by the Invention 
     Patent Documents 1 and 2 describe the metabolic pathways that can produce 3-hydroxyadipic acid and α-hydromuconic acid in the microorganisms, but not anything about interruption of the metabolic pathways to secrete 3-hydroxyadipic acid and α-hydromuconic acid into culture medium. Moreover, the prior studies described in Patent Documents 1 to 3 have not examined whether or not 3-hydroxyadipic acid, α-hydromuconic acid, or adipic acid can be actually produced by using the non-naturally occurring microorganisms in which a nucleic acid encoding an enzyme that catalyzes a reaction to reduce 3-oxoadipyl-CoA to 3-hydroxyadipyl-CoA is introduced. Accordingly, it is not known whether the enzyme that catalyzes a reaction to reduce 3-oxoadipyl-CoA to 3-hydroxyadipyl-CoA, as described in Patent Documents 1 to 3, also exhibits excellent activity in the production of 3-hydroxyadipic acid, α-hydromuconic acid, and/or adipic acid. 
     Accordingly, an object of the present invention is to provide a genetically modified microorganism in which a nucleic acid encoding an enzyme that exhibits excellent activity in a 3-oxoadipyl-CoA reduction reaction is introduced or expression of the enzyme is enhanced, and a method of producing a substance by using the modified microorganism. 
     Means for Solving the Problem 
     The inventors intensively studied to achieve the above-described object and consequently found that a group of polypeptides with high similarities in amino acid sequences exhibit an excellent catalytic activity for a reaction to reduce 3-oxoadipyl-CoA to 3-hydroxyadipyl-CoA, to complete the present invention. 
     That is, the present invention provides the following: 
     (1) A genetically modified microorganism in which a nucleic acid encoding any one of polypeptides described in (a) to (c) below is introduced or expression of the polypeptide is enhanced:
 
(a) a polypeptide composed of an amino acid sequence represented by any one of SEQ ID NOs: 1 to 6 and 213;
 
(b) a polypeptide composed of the same amino acid sequence as that represented by any one of SEQ ID NOs: 1 to 6 and 213, except that one or several amino acids are substituted, deleted, inserted, and/or added, and having an enzymatic activity that catalyzes a reaction to reduce 3-oxoadipyl-CoA to 3-hydroxyadipyl-CoA;
 
(c) a polypeptide composed of an amino acid sequence with a sequence identity of not less than 70% to the sequence represented by any one of SEQ ID NOs: 1 to 6 and 213 and having an enzymatic activity that catalyzes a reaction to reduce 3-oxoadipyl-CoA to 3-hydroxyadipyl-CoA.
 
(2) The genetically modified microorganism according to (1), wherein the polypeptide described in either (b) or (c) comprises a region with an amino acid sequence represented by SEQ ID NO: 212.
 
(3) The genetically modified microorganism according to (2), wherein the amino acid sequence represented by SEQ ID NO: 212 comprises a phenylalanine or leucine residue as the 13th amino acid residue from the N terminus, a leucine or glutamine residue as the 15th amino acid residue from the N terminus, a lysine or asparagine residue as the 16th amino acid residue from the N terminus, a glycine or serine residue as the 17th amino acid residue from the N terminus, a proline or arginine residue as the 19th amino acid residue from the N terminus, and preferably a leucine, methionine, or valine residue as the 21st amino acid residue from the N terminus.
 
(4) The genetically modified microorganism according to any one of (1) to (3), which is a genetically modified microorganism selected from the group consisting of the genera  Escherichia, Serratia, Hafnia , and  Pseudomonas.  
 
(5) The genetically modified microorganism according to any one of (1) to (4), which has an ability to generate 3-oxoadipyl-CoA and coenzyme A from acetyl-CoA and succinyl-CoA; and an ability to generate 3-hydroxyadipic acid from 3-hydroxyadipyl-CoA.
 
(6) The genetically modified microorganism according to any one of (1) to (4), which has an ability to generate 3-oxoadipyl-CoA and coenzyme A from acetyl-CoA and succinyl-CoA: an ability to generate 2,3-dehydroadipyl-CoA from 3-hydroxyadipyl-CoA: and an ability to generate α-hydromuconic acid from 2,3-dehydroadipyl-CoA.
 
(7) The genetically modified microorganism according to any one of (1) to (4), which has an ability to generate 3-oxoadipyl-CoA and coenzyme A from acetyl-CoA and succinyl-CoA; an ability to generate 2,3-dehydroadipyl-CoA from 3-hydroxyadipyl-CoA; an ability to generate adipyl-CoA from 2,3-dehydroadipyl-CoA; and an ability to generate adipic acid from adipyl-CoA.
 
(8) A method of producing 3-hydroxyadipic acid, comprising culturing the genetically modified microorganism according to any one of (1) to (5) in a culture medium containing a carbon source as a material for fermentation.
 
(9) A method of producing α-hydromuconic acid, comprising culturing the genetically modified microorganism according to any one of (1) to (4) and (6) in a culture medium containing a carbon source as a material for fermentation.
 
(10) A method of producing adipic acid, comprising culturing the genetically modified microorganism according to any one of (1) to (4) and (7) in a culture medium containing a carbon source as a material for fermentation.
 
(11) A method of producing one or more substances selected from the group consisting of 3-hydroxyadipic acid. α-hydromuconic acid, and adipic acid, comprising culturing a genetically modified microorganism in a culture medium containing a carbon source as a material for fermentation, wherein a nucleic acid encoding a polypeptide encoded by the 3-hydroxybutyryl-CoA dehydrogenase gene of a microorganism of the genus  Serratia , which forms a gene cluster with 5-aminolevulinic acid synthase gene in the microorganism, is introduced or expression of the polypeptide is enhanced in the genetically modified microorganism.
 
     Effects of the Invention 
     The genetically modified microorganism according to the present invention expresses an enzyme that exhibits excellent activity in a reaction to reduce 3-oxoadipyl-CoA to 3-hydroxyadipyl-CoA and thus is excellent in the production of 3-hydroxyadipic acid. α-hydromuconic acid, and/or adipic acid through production of 3-hydroxyadipyl-CoA. 
     The method of producing a substance according to the present invention uses the genetically modified microorganism which is excellent in the production of 3-hydroxyadipic acid, α-hydromuconic acid, and/or adipic acid through production of 3-hydroxyadipyl-CoA and thus can greatly increase the production of those substances. 
    
    
     
       BRIEF DESCRIPTION OF THE DRAWING 
         FIG. 1  shows a gene cluster constituted by a 3-hydroxybutyryl-CoA dehydrogenase gene and a 5-aminolevulinic acid synthase gene. 
     
    
    
     MODE FOR CARRYING OUT THE INVENTION 
     The microorganism according to the present invention is a genetically modified microorganism in which a nucleic acid encoding any one of the polypeptides described in (a) to (c) below is introduced or expression of the polypeptide is enhanced: 
     (a) a polypeptide composed of an amino acid sequence represented by any one of SEQ ID) NOs: 1 to 6 and 213;
 
(b) a polypeptide composed of the same amino acid sequence as that represented by any one of SEQ ID NOs: 1 to 6 and 213, except that one or several amino acids are substituted, deleted, inserted, and/or added, and having an enzymatic activity that catalyzes the reaction to reduce 3-oxoadipyl-CoA to 3-hydroxyadipyl-CoA;
 
(c) a polypeptide composed of an amino acid sequence with a sequence identity of not less than 70% to the sequence represented by any one of SEQ ID NOs: 1 to 6 and 213 and having an activity to reduce 3-oxoadipyl-CoA to 3-hydroxyadipyl-CoA.
 
     An enzyme that catalyzes the reaction to reduce 3-oxoadipyl-CoA to 3-hydroxyadipyl-CoA is hereinafter referred to as “3-oxoadipyl-CoA reductase” in the specification. Additionally, 3-hydroxyadipic acid may be abbreviated as 3HA, α-hydromuconic acid may be abbreviated as HMA, and adipic acid may be abbreviated as ADA, respectively, in the specification. 
     In the present invention, introduction of a nucleic acid refers to introducing a nucleic acid from outside into a microorganism to give the microorganism an ability to produce a polypeptide encoded by the nucleic acid. The introduction method is not limited to a particular method, and examples of the method that can be used include a method in which the nucleic acid incorporated in an expression vector capable of autonomous replication in a microorganism is introduced into a host microorganism, and a method in which the nucleic acid is integrated into the genome of a microorganism. 
     In the present invention, enhancement of polypeptide expression refers to enhancing the expression of a polypeptide which the microorganism originally has. The method for expression enhancement is not limited to a particular method, and examples of the method include a method in which a nucleic acid encoding the polypeptide is increased in copy number, and a method in which a promoter region or a ribosome-binding sequence upstream of the region coding for the polypeptide is modified. These methods may be carried out individually or in combination. 
     Additionally, one or more nucleic acids may be introduced. Moreover, introduction of a nucleic acid and enhancement of polypeptide expression may be combined. 
     For the polypeptide used in the present invention and composed of the same amino acid sequence as that represented by any one of SEQ ID NOs: 1 to 6 and 213, except that one or several amino acids are substituted, deleted, inserted, and/or added, and having 3-oxoadipyl-CoA reductase activity, the range represented by the phrase “one or several” is preferably 10 or less, more preferably 5 or less, particularly preferably 4 or less, and most preferably one or two. In the case of amino acid substitution, the activity of the original polypeptide is more likely to be maintained when an amino acid(s) is/are replaced by an amino acid(s) with similar properties (so-called conservative substitution). That is, the physiological activity of the original polypeptide is often maintained when the amino acid(s) is/are replaced by an amino acid(s) with similar properties. Thus, the amino acid(s) is/are preferably replaced by an amino acid(s) with similar properties. That is, the 20 amino acids constituting naturally occurring proteins can be divided into groups with similar properties, such as neutral amino acids with a less polar side chain (Gly, Ile, Val, Leu, Ala, Met, Pro), neutral amino acids with a hydrophilic side chain (Asn, Gln, Thr, Ser, Tyr, Cys), acidic amino acids (Asp, Glu), and basic amino acids (Arg, Lys, His), and aromatic amino acids (Phe, Tyr, Trp); it is often the case that substitution between amino acids in the same group does not change the properties of the original polypeptide. 
     For the polypeptide used in the present invention and having an amino acid sequence with a sequence identity of not less than 70% to the sequence represented by any one of SEQ ID NOs: 1 to 6 and 213 and having 3-oxoadipyl-CoA reductase activity, the sequence identity is preferably not less than 80%, more preferably not less than 85%, further preferably not less than 90%, still further preferably not less than 95%, yet further preferably not less than 97%, and even further preferably not less than 99%. 
     In the present invention, the term “sequence identity” means a ratio (percentage) of the number of identical amino acid or nucleotide residues relative to the total number of amino acid or nucleotide residues over the overlapping portion of an amino acid sequence alignment (including an amino acid corresponding to the translation start site) or a nucleotide sequence alignment (including the start codon), which is obtained by aligning two amino acid or nucleotide sequences with or without introduction of gaps for an optimal match, and is calculated by the following formula (1). In the formula (1), the length of a shorter sequence being compared is not less than 400 amino acids; in cases where the length of the shorter sequence is less than 400 amino acids, the sequence identity is not defined. The sequence identity can be easily determined using BLAST (Basic Local Alignment Search Tool), an algorithm widely used in this field. For example, BLAST is publicly available on a website, such as that of NCBI (National Center for Biotechnology Information) or KEGG (Kyoto Encyclopedia of Genes and Genomes), on which the sequence identity can be easily determined using default parameters. Additionally, the sequence identity can also be determined using a similar function implemented in a software program such as Genetyx. 
       Sequence identity (%)=the number of matches (without counting the number of gaps)/the length of a shorter sequence (excluding the terminal gaps)×100  (1)
 
     Sequence identities among the amino acid sequences represented by SEQ ID NOs: 1 to 6 and 213 are calculated using a function of Genetyx (% Identity Matrix) based on the formula (1); the least sequence identity is 71.51% between SEQ ID NOs: 2 and 4, and a sequence identity of not less than 70% is shared at least among the amino acid sequences represented by SEQ ID NOs: 1 to 6 and 213. The results of calculation of sequence identity using Genetyx are presented in Table 1. In Tables 1 to 5 below, the numbers in the leftmost column represent SEQ ID NOs. 
     
       
         
           
               
             
               
                 TABLE 1 
               
               
                   
               
             
            
               
                 [GENETYX: % Identity Matrix] 
               
            
           
           
               
               
               
               
               
               
               
               
            
               
                 [%] 
                 1  Serratia   
                 2  Serratia   
                 3  Serratia   
                 4  Serratia   
                 5  Serratia   
                 6  Serratia   
                 213 Serrat    
               
               
                   
               
               
                 1  Serratia marcescens  ATCC13880 
                 * 
                   
                   
                   
                   
                   
                   
               
               
                 2  Serratia nematodiphila  DSM21420 
                 98.23 
                 * 
                   
                   
                   
                   
                   
               
               
                 3  Serratia plymuthica  NBRC102599 
                 72.10 
                 71.56 
                 * 
                   
                   
                   
                   
               
               
                 4  Serratia proteamaculans  568 
                 72.29 
                 71.51 
                 86.24 
                 * 
                   
                   
                   
               
               
                 5  Serratia ureilytica  Lr5/4 
                 90.76 
                 90.76 
                 72.82 
                 73.28 
                 * 
                   
                   
               
               
                 6  Serratia  sp. BW106 
                 72.29 
                 71.90 
                 87.03 
                 92.33 
                 73.67 
                 * 
                   
               
               
                 213  Serratia liquefaciens  FK01 
                 72.29 
                 71.70 
                 84.67 
                 86.83 
                 73.47 
                 87.81 
                 * 
               
               
                   
               
               
                 [Match Count/Length] 
                 1  Serratia   
                 2  Serratia   
                 3  Serratia   
                 4  Serratia   
                 5  Serratia   
                 6  Serratia   
                 213 Serrat    
               
               
                   
               
               
                 1  Serratia marcescens  ATCC13880 
                 * 
                   
                   
                   
                   
                   
                   
               
               
                 2  Serratia nematodiphila  DSM21420 
                 500/509 
                 * 
                   
                   
                   
                   
                   
               
               
                 3  Serratia plymuthica  NBRC102599 
                 367/509 
                 365/510 
                 * 
                   
                   
                   
                   
               
               
                 4  Serratia proteamaculans  568 
                 368/509 
                 364/509 
                 439/509 
                 * 
                   
                   
                   
               
               
                 5  Serratia ureilytica  Lr5/4 
                 462/509 
                 462/509 
                 371/509 
                 373/509 
                 * 
                   
                   
               
               
                 6  Serratia  sp. BW106 
                 368/509 
                 366/509 
                 443/509 
                 470/509 
                 375/509 
                 * 
                   
               
               
                 213  Serratia liquefaciens  FK01 
                 368/509 
                 365/509 
                 431/509 
                 442/509 
                 374/509 
                 447/509 
                 * 
               
               
                   
               
               
                 *Gaps are not taken into consideration [%]  
               
               
                     indicates data missing or illegible when filed 
               
            
           
         
       
     
     When each of the amino acid sequences represented by SEQ ID NOs: 1 to 6 and 213 as queries was compared using BLASTP to all the amino acid sequences registered in the NCBI amino acid database (non-redundant protein sequences) to determine sequence identities, the sequences with a sequence identity of not less than 70% were all derived from bacteria of the genus  Serratia.    
     All the polypeptides represented by SEQ ID NOs: 1 to 6 and 213 as described above in (a) contain a common sequence 1, composed of 24 amino acid residues and represented by SEQ ID NO: 212, within a region from the 15th to the 38th amino acid residues from the N terminus (hereinafter, an amino acid residue at the n-th position from the N terminus may conveniently be represented by n “a.a.”; for example, the region from the 15th to the 38th amino acid residues from the N terminus may be thus simply represented by “15 to 38 a.a.”). In the common sequence 1, Xaa represents an arbitrary amino acid residue; the 13 a.a. is preferably a phenylalanine or leucine residue; the 15 a.a. is preferably a leucine or glutamine residue; the 16 a.a. is preferably a lysine or asparagine residue; the 17 a.a. is a glycine or serine residue, more preferably glycine residue; the 19 a.a. is preferably a proline or arginine residue, and the 21 a.a. is preferably a leucine, methionine, or valine residue. The common sequence 1 corresponds to the region including the NAD + -binding residue and the surrounding amino acid residues. In the NAD + -binding residues, the 24th amino acid residue in the common sequence 1 is aspartic acid, as described in Biochimie. 2012 February; 94 (2): 471-8., but in the common sequence 1, the residue is asparagine which is characteristic. It is thought that the polypeptides represented by SEQ ID NOs: 1 to 6 and 213 exhibit excellent enzymatic activity as 3-oxoadipyl-CoA reductases due to the presence of the common sequence 1. 
     The polypeptides as described above in (b) and (c) also preferably contain the common sequence 1, composed of 24 amino acid residues and represented by SEQ ID NO: 212, within a region from 1 to 200 a.a. The common sequence is more preferably contained within a region from 1 to 150 a.a., further preferably from 1 to 100 a.a. Specific examples of the polypeptides include those with the amino acid sequences represented by SEQ ID NOs: 7 to 16 and 70 to 138. In the amino acid sequences represented by SEQ ID NOs: 7 to 16 and 70 to 138, the common sequence 1, composed of 24 amino acid residues and represented by SEQ ID NO: 212, is contained within a region from 15 to 38 a.a. The amino acid sequences represented by SEQ ID NOs: 7 to 16 and 70 to 138 have a sequence identity of not less than 90% to the amino acid sequence represented by any one of SEQ ID NOs: 1 to 6 and 213. The results of calculation of sequence identity using Genetyx are presented in Tables 2-1 to 2-3 and Tables 3-1 to 3-3. 
     
       
         
           
               
             
               
                 TABLE 2-1 
               
             
            
               
                   
               
               
                 [GENETYX: % Identity Matrix] 
               
            
           
           
               
               
               
               
               
               
               
               
            
               
                 [%] 
                 1  Serratia   
                 2  Serratia   
                 3  Serratia   
                 4  Serratia   
                 5  Serratia   
                 6  Serratia   
                 213 Serrat    
               
               
                   
               
            
           
           
               
               
               
               
               
               
               
               
            
               
                 1  Serratia marcescens  ATCC13880 
                 * 
                   
                   
                   
                   
                   
                   
               
               
                 2  Serratia nematodiphila  DSM21420 
                 98.23 * 
                   
                   
                   
                   
                   
                   
               
               
                 3  Serratia plymuthica  NBRC102599 
                 72.1 
                 71.51 * 
                   
                   
                   
                   
                   
               
               
                 4  Serratia proteamaculans  568 
                 72.29 
                 71.51 
                 86.24 * 
                   
                   
                   
                   
               
               
                 5  Serratia ureilytica  Lr5/4 
                 90.76 
                 90.76 
                 72.88 
                 73.28 * 
                   
                   
                   
               
               
                 6  Serratia  sp. BW106 
                 72.29 
                 71.9 
                 87.03 
                 92.33 
                 73.67 * 
                   
                   
               
               
                 213  Serratia liquefaciens  FK01 
                 72.29 
                 71.7 
                 84.67 
                 86.83 
                 73.47 
                 87.81 * 
                   
               
               
                 7  Serratia  sp. S119 
                 94.89 
                 94.3 
                 72.88 
                 72.49 
                 91.55 
                 73.08 
                 72.88 
               
               
                 8  Serratia  sp. YD25 
                 92.33 
                 92.33 
                 72.49 
                 72.49 
                 93.51 
                 72.69 
                 72.88 
               
               
                 9  Serratia  sp. FS14 
                 98.62 
                 99.6 
                 71.7 
                 71.7 
                 91.15 
                 72.1 
                 72.1 
               
               
                 10  Serratia  sp. HMSC15F11 
                 94.89 
                 94.3 
                 73.28 
                 73.28 
                 91.35 
                 73.47 
                 73.47 
               
               
                 11  Serratia  sp. JKS000199 
                 90.76 
                 90.76 
                 72.69 
                 73.08 
                 99.41 
                 73.47 
                 73.28 
               
               
                 12  Serratia  sp. TEL 
                 90.56 
                 90.56 
                 72.88 
                 73.28 
                 99.8 
                 73.67 
                 73.47 
               
               
                 13  Serratia  sp. ISTD04 
                 90.56 
                 90.56 
                 72.49 
                 73.08 
                 99.41 
                 73.47 
                 73.28 
               
               
                 14  Serratia  sp. SCBI 
                 90.76 
                 90.76 
                 72.88 
                 73.28 
                 99.6 
                 73.47 
                 73.47 
               
               
                 15  Serratia  sp. S4 
                 72.1 
                 71.31 
                 86.44 
                 98.62 
                 73.08 
                 91.94 
                 86.64 
               
               
                 16  Serratia  sp. C-1 
                 72.49 
                 71.9 
                 98.03 
                 86.05 
                 73.28 
                 86.64 
                 84.08 
               
               
                 70  Serratia marcescens  532 
                 99.8 
                 98.03 
                 72.29 
                 72.1 
                 90.56 
                 72.1 
                 72.1 
               
               
                 71  Serratia marcescens   
                 99.6 
                 97.83 
                 72.1 
                 72.29 
                 90.37 
                 72.1 
                 72.29 
               
               
                 2880STDY5683033 
                   
                   
                   
                   
                   
                   
                   
               
               
                 72  Serratia marcescens  WW4 
                 98.42 
                 99.41 
                 71.9 
                 71.9 
                 90.96 
                 72.29 
                 71.9 
               
               
                 73  Serratia marcescens  K27 
                 98.23 
                 99.21 
                 71.31 
                 71.31 
                 90.96 
                 71.7 
                 71.7 
               
               
                 74  Serratia marcescens  280 
                 98.42 
                 99.41 
                 71.7 
                 71.7 
                 90.96 
                 72.1 
                 72.1 
               
               
                 75  Serratia marcescens  19F 
                 98.42 
                 99.41 
                 71.51 
                 71.7 
                 90.96 
                 72.1 
                 72.1 
               
               
                 76  Serratia marcescens  1185 
                 98.23 
                 99.6 
                 71.31 
                 71.31 
                 90.37 
                 71.7 
                 71.51 
               
               
                   
               
               
                 * Gaps are not taken into consideration 
               
               
                     indicates data missing or illegible when filed 
               
            
           
         
       
     
     
       
         
           
               
               
               
               
               
               
               
               
             
               
                 TABLE 2-2 
               
               
                   
               
             
            
               
                 77  Serratia marcescens  S217 
                 98.23 
                 99.21 
                 71.31 
                 71.51 
                 90.96 
                 71.9 
                 71.9 
               
               
                 78  Serratia marcescens  KHCo-24B 
                 98.03 
                 99.8 
                 71.31 
                 71.31 
                 90.56 
                 71.7 
                 71.9 
               
               
                 79  Serratia marcescens  Z6 
                 98.03 
                 99.01 
                 71.7 
                 71.9 
                 90.56 
                 72.29 
                 71.9 
               
               
                 80  Serratia marcescens  546 
                 97.83 
                 99.21 
                 71.51 
                 71.7 
                 90.37 
                 72.1 
                 71.7 
               
               
                 81  Serratia nematodiphila  MB307 
                 98.03 
                 99.8 
                 71.31 
                 71.51 
                 90.56 
                 71.9 
                 71.7 
               
               
                 82  Serratia marcescens  VGH107 
                 98.03 
                 99.01 
                 71.31 
                 71.51 
                 90.56 
                 71.9 
                 71.9 
               
               
                 83  Serratia marcescens  MCB 
                 95.48 
                 95.28 
                 72.29 
                 72.69 
                 91.15 
                 72.88 
                 72.69 
               
               
                 84  Serratia marcescens  AH0650 
                 95.67 
                 95.48 
                 72.29 
                 72.69 
                 90.76 
                 73.28 
                 72.69 
               
               
                 85  Serratia marcescens  UMH12 
                 95.48 
                 95.28 
                 72.1 
                 72.49 
                 90.56 
                 73.08 
                 72.49 
               
               
                 86  Serratia  sp. OMLW3 
                 95.48 
                 95.28 
                 72.29 
                 72.49 
                 90.76 
                 73.28 
                 72.69 
               
               
                 87  Serratia marcescens  UMH11 
                 95.28 
                 95.08 
                 72.1 
                 72.69 
                 90.56 
                 73.47 
                 72.49 
               
               
                 88  Serratia marcescens  UMH1 
                 95.08 
                 94.89 
                 72.29 
                 72.49 
                 90.17 
                 73.08 
                 72.29 
               
               
                 89  Serratia marcescens  2880STDY5683020 
                 95.48 
                 94.89 
                 73.08 
                 72.69 
                 92.14 
                 73.28 
                 73.08 
               
               
                 90  Serratia marcescens  99 
                 95.48 
                 94.69 
                 73.28 
                 72.88 
                 91.55 
                 73.67 
                 73.28 
               
               
                 91  Serratia marcescens  374 
                 94.89 
                 94.69 
                 72.29 
                 72.29 
                 90.17 
                 73.08 
                 72.29 
               
               
                 92  Serratia marcescens  2880STDY5683036 
                 95.28 
                 94.49 
                 73.08 
                 72.69 
                 91.35 
                 73.47 
                 73.08 
               
               
                 93  Serratia marcescens  2880STDY5683034 
                 95.28 
                 94.69 
                 73.08 
                 72.69 
                 91.94 
                 73.28 
                 73.08 
               
               
                 94  Serratia marcescens  2880STDY5682892 
                 95.28 
                 94.69 
                 73.28 
                 72.88 
                 91.94 
                 73.47 
                 73.28 
               
               
                 95  Serratia marcescens  SM39 
                 95.08 
                 94.49 
                 73.28 
                 72.69 
                 92.14 
                 73.28 
                 73.28 
               
               
                 96  Serratia marcescens  189 
                 95.08 
                 94.49 
                 73.28 
                 72.88 
                 92.14 
                 73.47 
                 73.28 
               
               
                 97  Serratia marcescens  SMB2099 
                 95.08 
                 94.49 
                 73.47 
                 72.69 
                 91.74 
                 73.67 
                 73.47 
               
               
                 98  Serratia marcescens  2880STDY5682862 
                 94.89 
                 94.3 
                 73.47 
                 72.88 
                 91.55 
                 73.47 
                 73.47 
               
               
                 99  Serratia marcescens  SE4145 
                 94.89 
                 94.3 
                 73.08 
                 72.49 
                 91.94 
                 73.08 
                 73.08 
               
               
                 100  Serratia marcescens  2880STDY5682876 
                 95.08 
                 94.49 
                 73.28 
                 72.88 
                 91.74 
                 73.47 
                 73.28 
               
               
                 101  Serratia marcescens  709 
                 95.08 
                 94.49 
                 73.08 
                 72.69 
                 91.74 
                 73.28 
                 73.08 
               
               
                 102  Serratia marcescens  MGH136 
                 94.89 
                 94.3 
                 72.88 
                 72.49 
                 91.94 
                 73.08 
                 72.88 
               
               
                 103  Serratia marcescens  2880STDY5682884 
                 94.69 
                 94.1 
                 72.88 
                 72.49 
                 91.74 
                 73.08 
                 73.08 
               
               
                 104  Serratia marcescens  D-3 
                 95.08 
                 94.49 
                 73.08 
                 72.69 
                 91.74 
                 73.28 
                 73.08 
               
               
                 105  Serratia marcescens  2880STDY5682957 
                 94.89 
                 94.3 
                 72.88 
                 72.69 
                 91.55 
                 73.28 
                 72.88 
               
               
                 106  Serratia marcescens  YDC563 
                 94.69 
                 94.1 
                 72.88 
                 72.69 
                 91.35 
                 73.28 
                 72.88 
               
               
                 107  Serratia marcescens  2880STDY5683035 
                 94.89 
                 94.3 
                 73.08 
                 72.69 
                 91.55 
                 73.28 
                 73.08 
               
               
                   
               
            
           
         
       
     
     
       
         
           
               
               
               
               
               
               
               
               
             
               
                 TABLE 2-3 
               
               
                   
               
             
            
               
                 108  Serratia marcescens  2880STDY5682930 
                 94.69 
                 94.1 
                 72.88 
                 72.49 
                 91.35 
                 73.08 
                 72.88 
               
               
                 109  Serratia marcescens  790 
                 94.49 
                 94.3 
                 73.28 
                 72.88 
                 91.35 
                 73.47 
                 73.28 
               
               
                 110  Serratia marcescens  UMH5 
                 93.51 
                 92.92 
                 72.69 
                 72.88 
                 90.37 
                 72.69 
                 72.49 
               
               
                 111  Serratia marcescens  2880STDY5682988 
                 93.32 
                 92.73 
                 72.69 
                 72.88 
                 90.17 
                 72.69 
                 72.49 
               
               
                 112  Serratia marcescens  945154301 
                 94.89 
                 94.3 
                 73.28 
                 73.28 
                 91.35 
                 73.67 
                 73.47 
               
               
                 113  Serratia marcescens  at10508 
                 94.69 
                 94.1 
                 73.47 
                 73.47 
                 91.15 
                 73.67 
                 73.67 
               
               
                 114  Serratia marcescens  ML2637 
                 94.49 
                 93.9 
                 73.28 
                 73.47 
                 90.96 
                 73.67 
                 73.67 
               
               
                 115  Serratia marcescens  SM1978 
                 94.3 
                 93.71 
                 73.28 
                 73.28 
                 90.76 
                 73.67 
                 73.67 
               
               
                 116  Serratia marcescens  PWN146 
                 dehydroge 
                 93.51 
                 72.88 
                 72.88 
                 90.96 
                 72.88 
                 73.28 
               
               
                 117  Serratia marcescens  H1q 
                 92.53 
                 92.53 
                 72.49 
                 72.49 
                 93.51 
                 72.69 
                 73.08 
               
               
                 118  Serratia marcescens  UMH6 
                 91.15 
                 91.15 
                 72.69 
                 73.08 
                 99.6 
                 73.47 
                 73.28 
               
               
                 119  Serratia nematodiphila  WCU338 
                 91.15 
                 91.15 
                 72.69 
                 73.08 
                 99.41 
                 73.47 
                 73.28 
               
               
                 120  Serratia  sp. OLEL1 
                 90.96 
                 90.96 
                 72.88 
                 73.28 
                 99.8 
                 73.67 
                 73.47 
               
               
                 121  Serratia marcescens  7209 
                 90.96 
                 90.96 
                 72.49 
                 72.88 
                 99.41 
                 73.28 
                 73.08 
               
               
                 122  Serratia marcescens  sicaria (Ss1) 
                 90.96 
                 90.96 
                 72.69 
                 73.08 
                 99.41 
                 73.28 
                 73.28 
               
               
                 123  Serratia  sp. OLFL2 
                 90.76 
                 90.76 
                 72.69 
                 73.08 
                 99.6 
                 73.47 
                 73.28 
               
               
                 124  Serratia marcescens  BIDMC 81 
                 90.76 
                 90.76 
                 72.88 
                 73.28 
                 99.6 
                 73.67 
                 73.47 
               
               
                 125  Serratia marcescens  BIDMC 50 
                 90.76 
                 90.76 
                 72.69 
                 73.08 
                 99.21 
                 73.47 
                 73.28 
               
               
                 126  Serratia marcescens  UMH7 
                 90.56 
                 90.56 
                 72.88 
                 73.28 
                 99.8 
                 73.67 
                 73.47 
               
               
                 127  Serratia marcescens  RSC-14 
                 90.56 
                 90.56 
                 72.88 
                 73.47 
                 99.21 
                 73.87 
                 73.67 
               
               
                 128  Serratia marcescens  SM03 
                 92.33 
                 92.33 
                 72.29 
                 72.29 
                 93.51 
                 72.49 
                 72.88 
               
               
                 129  Serratia marcescens  90-166 
                 90.17 
                 89.78 
                 72.49 
                 73.47 
                 96.66 
                 73.67 
                 73.08 
               
               
                 130  Serratia marcescens  UMH2 
                 90.76 
                 90.76 
                 72.88 
                 73.28 
                 99.21 
                 73.67 
                 73.47 
               
               
                 131  Serratia plymuthica  AS9 
                 72.49 
                 71.9 
                 96.66 
                 85.06 
                 73.47 
                 86.05 
                 83.69 
               
               
                 132  Serratia plymuthica  tumat 205 
                 72.69 
                 72.1 
                 98.03 
                 86.24 
                 73.47 
                 86.64 
                 84.28 
               
               
                 133  Serratia plymuthica  A30 
                 72.29 
                 71.7 
                 98.82 
                 85.65 
                 72.88 
                 86.44 
                 84.08 
               
               
                 134  Serratia plymuthica  4Rx13 
                 72.29 
                 71.7 
                 97.83 
                 85.85 
                 73.08 
                 86.44 
                 84.28 
               
               
                 135  Serratia plymuthica  V4 
                 72.29 
                 71.7 
                 98.42 
                 85.85 
                 73.08 
                 86.44 
                 84.28 
               
               
                 136  Serratia plymuthica  3Rp8 
                 72.29 
                 71.7 
                 98.62 
                 86.05 
                 73.08 
                 86.64 
                 84.08 
               
               
                 137  Serratia proteamaculans  MFPA44A14 
                 72.29 
                 71.9 
                 87.03 
                 92.53 
                 73.28 
                 98.82 
                 87.22 
               
               
                 138  Serratia plymuthica  A153 
                 72.1 
                 71.51 
                 99.21 
                 86.05 
                 72.88 
                 86.64 
                 84.47 
               
               
                   
               
            
           
         
       
     
     
       
         
           
               
               
               
               
               
               
               
               
             
               
                 TABLE 3-1 
               
               
                   
               
               
                 [Match Count/Length] 
                 1  Serratia   
                 2  Serratia   
                 3  Serratia   
                 4  Serratia   
                 5  Serratia   
                 6  Serratia   
                 213 Serrat    
               
               
                   
               
             
            
               
                 1  Serratia marcescens  ATCC13880 
                 * 
                   
                   
                   
                   
                   
                   
               
               
                 2  Serratia nematodiphila  DSM21420 
                 500/509 
                 * 
                   
                   
                   
                   
                   
               
               
                 3  Serratia plymuthica  NBRC102599 
                 367/509 
                 364/509 
                 * 
                   
                   
                   
                   
               
               
                 4  Serratia proteamaculans  568 
                 368/509 
                 364/509 
                 439/509 
                 * 
                   
                   
                   
               
               
                 5  Serratia ureilytica  Lr5/4 
                 462/509 
                 462/509 
                 371/509 
                 373/509 
                 * 
                   
                   
               
               
                 6  Serratia  sp. BW106 
                 368/509 
                 366/509 
                 443/509 
                 470/509 
                 375/509 
                 * 
                   
               
               
                 213  Serratia liquefaciens  FK01 
                 368/509 
                 365/509 
                 431/509 
                 442/509 
                 374/509 
                 447/509 
                 * 
               
               
                 7  Serratia  sp. S119 
                 483/509 
                 480/509 
                 371/509 
                 369/509 
                 466/509 
                 372/509 
                 371/509 
               
               
                 8  Serratia  sp. YD25 
                 470/509 
                 470/509 
                 369/509 
                 369/509 
                 476/509 
                 370/509 
                 371/509 
               
               
                 9  Serratia  sp. FS14 
                 502/509 
                 507/509 
                 365/509 
                 365/509 
                 464/509 
                 367/509 
                 367/509 
               
               
                 10  Serratia  sp. HMSC15F11 
                 483/509 
                 480/509 
                 373/509 
                 373/509 
                 465/509 
                 374/509 
                 374/509 
               
               
                 11  Serratia  sp. JKS000199 
                 462/509 
                 462/509 
                 370/509 
                 372/509 
                 506/509 
                 374/509 
                 373/509 
               
               
                 12  Serratia  sp. TEL 
                 461/509 
                 461/509 
                 371/509 
                 373/509 
                 508/509 
                 375/509 
                 374/509 
               
               
                 13  Serratia  sp. ISTD04 
                 461/509 
                 461/509 
                 369/509 
                 372/509 
                 506/509 
                 374/509 
                 373/509 
               
               
                 14  Serratia  sp. SCBI 
                 462/509 
                 462/509 
                 371/509 
                 373/509 
                 507/509 
                 374/509 
                 374/509 
               
               
                 15  Serratia  sp. S4 
                 367/509 
                 363/509 
                 440/509 
                 502/509 
                 372/509 
                 468/509 
                 441/509 
               
               
                 16  Serratia  sp. C-1 
                 369/509 
                 366/509 
                 499/509 
                 438/509 
                 373/509 
                 441/509 
                 428/509 
               
               
                 70  Serratia marcescens  532 
                 508/509 
                 499/509 
                 368/509 
                 367/509 
                 461/509 
                 367/509 
                 367/509 
               
               
                 71  Serratia marcescens   
                 507/509 
                 498/509 
                 367/509 
                 368/509 
                 460/509 
                 367/509 
                 368/509 
               
               
                 2880STDY5683033 
                   
                   
                   
                   
                   
                   
                   
               
               
                 72  Serratia marcescens  WW4 
                 501/509 
                 506/509 
                 366/509 
                 366/509 
                 463/509 
                 368/509 
                 366/509 
               
               
                 73  Serratia marcescens  K27 
                 500/509 
                 505/509 
                 363/509 
                 363/509 
                 463/509 
                 365/509 
                 365/509 
               
               
                 74  Serratia marcescens  280 
                 501/509 
                 506/509 
                 365/509 
                 365/509 
                 463/509 
                 367/509 
                 367/509 
               
               
                 75  Serratia marcescens  19F 
                 501/509 
                 506/509 
                 364/509 
                 365/509 
                 463/509 
                 367/509 
                 367/509 
               
               
                 76  Serratia marcescens  1185 
                 500/509 
                 507/509 
                 363/509 
                 363/509 
                 460/509 
                 365/509 
                 364/509 
               
               
                   
               
               
                     indicates data missing or illegible when filed 
               
            
           
         
       
     
     
       
         
           
               
               
               
               
               
               
               
               
             
               
                 TABLE 3-2 
               
               
                   
               
             
            
               
                 77  Serratia marcescens  S217 
                 500/509 
                 505/509 
                 363/509 
                 364/509 
                 463/509 
                 366/509 
                 366/509 
               
               
                 78  Serratia marcescens  KHCo-24B 
                 499/509 
                 508/509 
                 363/509 
                 363/509 
                 461/509 
                 365/509 
                 366/509 
               
               
                 79  Serratia marcescens  Z6 
                 499/509 
                 504/509 
                 365/509 
                 366/509 
                 461/509 
                 368/509 
                 366/509 
               
               
                 80  Serratia marcescens  546 
                 498/509 
                 505/509 
                 364/509 
                 365/509 
                 460/509 
                 367/509 
                 365/509 
               
               
                 81  Serratia nematodiphila  MB307 
                 499/509 
                 508/509 
                 363/509 
                 364/509 
                 461/509 
                 366/509 
                 365/509 
               
               
                 82  Serratia marcescens  VGH107 
                 499/509 
                 504/509 
                 363/509 
                 364/509 
                 461/509 
                 366/509 
                 366/509 
               
               
                 83  Serratia marcescens  MCB 
                 486/509 
                 485/509 
                 368/509 
                 370/509 
                 464/509 
                 371/509 
                 370/509 
               
               
                 84  Serratia marcescens  AH0650 
                 487/509 
                 486/509 
                 368/509 
                 370/509 
                 462/509 
                 373/509 
                 370/509 
               
               
                 85  Serratia marcescens  UMH12 
                 486/509 
                 485/509 
                 367/509 
                 369/509 
                 461/509 
                 372/509 
                 369/509 
               
               
                 86  Serratia  sp. OMLW3 
                 486/509 
                 485/509 
                 368/509 
                 369/509 
                 462/509 
                 373/509 
                 370/509 
               
               
                 87  Serratia marcescens  UMH1 1 
                 485/509 
                 484/509 
                 367/509 
                 370/509 
                 461/509 
                 374/509 
                 369/509 
               
               
                 88  Serratia marcescens  UMH1 
                 484/509 
                 483/509 
                 368/509 
                 369/509 
                 459/509 
                 372/509 
                 368/509 
               
               
                 89  Serratia marcescens  2880STDY5683020 
                 486/509 
                 483/509 
                 372/509 
                 370/509 
                 469/509 
                 373/509 
                 372/509 
               
               
                 90  Serratia marcescens  99 
                 486/509 
                 482/509 
                 373/509 
                 371/509 
                 466/509 
                 375/509 
                 373/509 
               
               
                 91  Serratia marcescens  374 
                 483/509 
                 482/509 
                 368/509 
                 368/509 
                 459/509 
                 372/509 
                 368/509 
               
               
                 92  Serratia marcescens  2880STDY5683036 
                 485/509 
                 481/509 
                 372/509 
                 370/509 
                 465/509 
                 374/509 
                 372/509 
               
               
                 93  Serratia marcescens  2880STDY5683034 
                 485/509 
                 482/509 
                 372/509 
                 370/509 
                 468/509 
                 373/509 
                 372/509 
               
               
                 94  Serratia marcescens  2880STDY5682892 
                 485/509 
                 482/509 
                 373/509 
                 371/509 
                 468/509 
                 374/509 
                 373/509 
               
               
                 95  Serratia marcescens  SM39 
                 484/509 
                 481/509 
                 373/509 
                 370/509 
                 469/509 
                 373/509 
                 373/509 
               
               
                 96  Serratia marcescens  189 
                 484/500 
                 481/509 
                 373/509 
                 371/509 
                 469/509 
                 374/509  
                 373/509 
               
               
                 97  Serratia marcescens  SMB2099 
                 484/509 
                 481/509 
                 374/509 
                 370/509 
                 467/509 
                 375/509 
                 374/509 
               
               
                 98  Serratia marcescens  2880STDY5682862 
                 483/509 
                 480/509 
                 374/509 
                 371/509 
                 466/509 
                 374/509 
                 374/509 
               
               
                 99  Serratia marcescens  SE4145 
                 483/509 
                 480/509 
                 372/509 
                 369/509 
                 468/509 
                 372/509 
                 372/509 
               
               
                 100  Serratia marcescens  2880STDY5682876 
                 484/509 
                 481/509 
                 373/509 
                 371/509 
                 467/509 
                 374/509 
                 373/509 
               
               
                 101  Serratia marcescens  709 
                 484/509 
                 481/509 
                 372/509 
                 370/509 
                 467/509 
                 373/509 
                 372/509 
               
               
                 102  Serratia marcescens  MGH136 
                 483/509 
                 480/509 
                 371/509 
                 369/509 
                 468/509 
                 372/509 
                 371/509 
               
               
                 103  Serratia marcescens  2880STDY5682884 
                 482/509 
                 479/509 
                 371/509 
                 369/509 
                 467/509 
                 372/509 
                 372/509 
               
               
                 104  Serratia marcescens  D-3 
                 484/509 
                 481/509 
                 372/509 
                 370/509 
                 467/509 
                 373/509 
                 372/509 
               
               
                 105  Serratia marcescens  2880STDY5682957 
                 483/509 
                 480/509 
                 371/509 
                 370/509 
                 466/509 
                 373/509 
                 371/509 
               
               
                 106  Serratia marcescens  YDC563 
                 482/509 
                 479/509 
                 371/509 
                 370/509 
                 465/509 
                 373/509 
                 371/509 
               
               
                 107  Serratia marcescens  2880STDY5683035 
                 483/509 
                 480/509 
                 372/509 
                 370/509 
                 466/509 
                 373/509 
                 372/509 
               
               
                   
               
            
           
         
       
     
     
       
         
           
               
               
               
               
               
               
               
               
             
               
                 TABLE 3-3 
               
               
                   
               
             
            
               
                 108  Serratia marcescens  2880STDY5682930 
                 482/509 
                 479/509 
                 371/509 
                 369/509 
                 465/509 
                 372/509 
                 371/509 
               
               
                 109  Serratia marcescens  790 
                 481/509 
                 480/509 
                 373/509 
                 371/509 
                 465/509 
                 374/509 
                 373/509 
               
               
                 110  Serratia marcescens  UMH5 
                 476/509 
                 473/509 
                 370/509 
                 371/509 
                 460/509 
                 370/509 
                 369/509 
               
               
                 111  Serratia marcescens  2880STDY5682988 
                 475/509 
                 472/509 
                 370/509 
                 371/509 
                 459/509 
                 370/509 
                 369/509 
               
               
                 112  Serratia marcescens  945154301 
                 483/509 
                 480/509 
                 373/509 
                 373/509 
                 465/509 
                 375/509 
                 374/509 
               
               
                 113  Serratia marcescens  at10508 
                 482/509 
                 479/509 
                 374/509 
                 374/509 
                 464/509 
                 375/509 
                 375/509 
               
               
                 114  Serratia marcescens  ML2637 
                 481/509 
                 478/509 
                 373/509 
                 374/509 
                 463/509 
                 375/509 
                 375/509 
               
               
                 115  Serratia marcescens  SM1978 
                 480/509 
                 477/509 
                 373/509 
                 373/509 
                 462/509 
                 375/509 
                 375/509 
               
               
                 116  Serratia marcescens  PWN146 
                 dehydroge 
                 476/509 
                 371/509 
                 371/509 
                 463/509 
                 371/509 
                 373/509 
               
               
                 117  Serratia marcescens  H1q 
                 471/509 
                 471/509 
                 369/509 
                 369/509 
                 476/509 
                 370/509 
                 372/509 
               
               
                 118  Serratia marcescens  UMH6 
                 464/509 
                 464/509 
                 370/509 
                 372/509 
                 507/509 
                 374/509 
                 373/509 
               
               
                 119  Serratia nematodiphila  WCU338 
                 464/509 
                 464/509 
                 370/509 
                 372/509 
                 506/509 
                 374/509 
                 373/509 
               
               
                 120  Serratia  sp. OLEL1 
                 463/509 
                 462/509 
                 371/509 
                 373/509 
                 58/509 
                 375/509 
                 374/509 
               
               
                 121  Serratia marcescens  7209 
                 463/509 
                 463/509 
                 369/509 
                 371/509 
                 506/509 
                 373/509 
                 372/509 
               
               
                 122  Serratia marcescens  sicaria (Ss1) 
                 463/509 
                 463/509 
                 370/509 
                 372/509 
                 506/509 
                 373/509 
                 373/509 
               
               
                 123  Serratia  sp. OLFL2 
                 462/509 
                 462/509 
                 370/509 
                 372/509 
                 507/509 
                 374/509 
                 373/509 
               
               
                 124  Serratia marcescens  BIDMC 81 
                 462/509 
                 462/509 
                 371/509 
                 373/509 
                 507/509 
                 375/509 
                 374/509 
               
               
                 125  Serratia marcescens  BIDMC 50 
                 462/509 
                 462/509 
                 370/509 
                 372/509 
                 505/509 
                 374/509 
                 373/509 
               
               
                 126  Serratia marcescens  UMH7 
                 461/509 
                 461/509 
                 371/509 
                 373/509 
                 508/509 
                 375/509 
                 374/509 
               
               
                 127  Serratia marcescens  RSC-14 
                 461/509 
                 461/509 
                 371/509 
                 374/509 
                 505/509 
                 376/509 
                 375/509 
               
               
                 128  Serratia marcescens  SM03 
                 470/509 
                 470/509 
                 368/509 
                 368/509 
                 476/509 
                 369/509 
                 371/509 
               
               
                 129  Serratia marcescens  90-166 
                 459/509 
                 457/509 
                 369/509 
                 374/509 
                 492/509 
                 375/509 
                 372/509 
               
               
                 130  Serratia marcescens  UMH2 
                 462/509 
                 462/509 
                 371/509 
                 373/509 
                 505/509 
                 375/509 
                 374/509 
               
               
                 131  Serratia plymuthica  AS9 
                 369/509 
                 366/509 
                 492/509 
                 433/509 
                 374/509 
                 438/509 
                 426/509 
               
               
                 132  Serratia plymuthica  tumat 205 
                 370/509 
                 367/509 
                 499/509 
                 439/509 
                 374/509 
                 441/509 
                 429/509 
               
               
                 133  Serratia plymuthica  A30 
                 368/509 
                 365/509 
                 503/509 
                 436/509 
                 371/509 
                 440/509 
                 428/509 
               
               
                 134  Serratia plymuthica  4Rx13 
                 368/509 
                 365/509 
                 498/509 
                 437/509 
                 372/509 
                 440/509 
                 429/509 
               
               
                 135  Serratia plymuthica  V4 
                 368/509 
                 365/509 
                 501/509 
                 437/509 
                 372/509 
                 440/509 
                 429/509 
               
               
                 136  Serratia plymuthica  3Rp8 
                 368/509 
                 365/509 
                 502/509 
                 438/509 
                 372/509 
                 441/509 
                 428/509 
               
               
                 137  Serratia proteamaculans  MFPA44A14 
                 368/509 
                 366/509 
                 443/509 
                 471/509 
                 373/509 
                 503/509 
                 444/509 
               
               
                 138  Serratia plymuthica  A153 
                 367/509 
                 364/509 
                 505/509 
                 438/509 
                 371/509 
                 441/509 
                 430/509 
               
               
                   
               
            
           
         
       
     
     The nucleic acids encoding the polypeptides described in (a) to (c) according to the present invention may contain an additional sequence that encodes a peptide or protein added to the original polypeptides at the N terminus and/or the C terminus. Examples of such a peptide or protein can include secretory signal sequences, translocation proteins, binding proteins, tag peptides applicable for purification, and fluorescent proteins. Among those peptides or proteins, a peptide or protein with a desired function can be selected depending on the purpose and added to the polypeptides of the present invention by those skilled in the art. It should be noted that the amino acid sequence of such a peptide or protein is not included in the calculation of sequence identity. 
     The nucleic acids encoding the polypeptides represented by SEQ ID NOs: 1 to 16, 70 to 138, and 213 are not particularly limited, provided that those nucleic acids are composed of nucleotide sequences which can be translated into the amino acid sequences represented by SEQ ID NOs: 1 to 16 and 70 to 138, and the nucleotide sequences can be determined by considering a set of codons (standard genetic code) corresponding to each amino acid. In this respect, the nucleotide sequences may be redesigned using codons that are frequently used by a host microorganism used in the present invention. 
     Specific examples of the nucleotide sequences of the nucleic acids that encode the polypeptides with the amino acid sequences represented by SEQ ID NOs: 1 to 16, 70 to 138, and 213 include the nucleotide sequences represented by SEQ ID NOs: 54 to 69, 139 to 207, and 214, respectively. 
     In the present invention, whether or not a polypeptide encoded by a certain nucleic acid has 3-oxoadipyl-CoA reductase activity is determined as follows: transformant strains A and B described below are produced and grown in a culture test, and if the presence of 3-hydroxyadipic acid or α-hydromuconic acid in the resulting culture fluid is confirmed, it is judged that the nucleic acid encodes a polypeptide having 3-oxoadipyl-CoA reductase activity. The determination method will be described using the scheme 1 below which shows a biosynthesis pathway. 
     
       
         
         
             
             
         
       
     
     The above scheme 1 shows an exemplary reaction pathway required for the production of 3-hydroxyadipic acid, α-hydromuconic acid, and/or adipic acid. In this scheme, the reaction A represents a reaction that generates 3-oxoadipyl-CoA and coenzyme A from acetyl-CoA and succinyl-CoA. The reaction B represents a reaction that generates 3-hydroxyadipyl-CoA from 3-oxoadipyl-CoA. The reaction C represents a reaction that generates 2,3-dehydroadipyl-CoA from 3-hydroxyadipyl-CoA. The reaction D represents a reaction that generates adipyl-CoA from 2,3-dehydroadipyl-CoA. The reaction E generates 3-hydroxyadipic acid from 3-hydroxyadipyl-CoA. The reaction F represents a reaction that generates α-hydromuconic acid from 2,3-dehydroadipyl-CoA. The reaction G represents a reaction that generates adipic acid from adipyl-CoA. 
     The transformant strain A has enzymes that catalyze the reactions A, E, and F. The transformant strain B has enzymes that catalyze the reactions A, C, E, and F. 
     The transformant strain A is first produced. Plasmids for the expression of enzymes that catalyze the reactions A, E, and F, respectively, are produced. The reactions E and F can be catalyzed by an identical enzyme. The plasmids are introduced into  Escherichia coli  ( E. coli ) strain BL21 (DE3), which is a microorganism strain lacking abilities to produce all of 3-hydroxyadipic acid, α-hydromuconic acid, and adipic acid. An expression plasmid in which a nucleic acid encoding a polypeptide, which is a subject of analysis for the presence of the enzymatic activity of interest, is incorporated downstream of a suitable promoter is introduced to the obtained transformant strain, to obtain the transformant strain A. The transformant strain A is cultured, and the post-culture fluid is examined for the presence of 3-hydroxyadipic acid. Once the presence of 3-hydroxyadipic acid in the culture fluid is successfully confirmed, the transformant strain B is then produced. The transformant strain B is obtained by introducing a plasmid for the expression of an enzyme that catalyzes the reaction C into the transformant strain A. The transformant strain B is cultured, and the post-culture fluid is examined for the presence of α-hydromuconic acid. When the presence of α-hydromuconic acid in the post-culture fluid is confirmed, it indicates that 3-hydroxyadipic acid produced in the transformant strain A and α-hydromuconic acid produced in the transformant strain B are generated through production of 3-hydroxyadipyl-CoA and that the subject polypeptide has 3-oxoadipyl-CoA reductase activity. 
     As the gene encoding the enzyme that catalyzes the reaction A, pcaF from  Pseudomonas putida  strain KT2440 (NCBI Gene ID: 1041755; SEQ ID NO: 20) is used. 
     As the genes encoding the enzyme that catalyzes the reactions E and F, a continuous sequence including the full lengths of pcaI and pcaJ from  Pseudomonas putida  strain KT2440 (NCBI Gene IDs: 1046613 and 1046612; SEQ ID NOs: 23 and 24) is used. The polypeptides encoded by pcaI and pcaJ forms a complex and then catalyze the reactions E and F. 
     As the nucleic acid encoding the enzyme that catalyzes the reaction C, the paaF gene from  Pseudomonas putida  strain KT2440 (NCBI Gene ID: 1046932, SEQ ID NO: 47) is used. 
     The method of culturing the transformant strain A and the transformant strain B is as follows. Antibiotics for stable maintenance of the plasmids and/or a substance that induces the expression of the polypeptides encoded by the incorporated nucleic acids may be added as appropriate. A loopful of either the transformant strain A or B is inoculated into 5 mL of the culture medium I (10 g/L Bacto Tryptone (manufactured by Difco Laboratories), 5 g/L Bacto Yeast Extract (manufactured by Difco Laboratories), 5 g/L sodium chloride) adjusted at pH 7, and incubated at 30° C. with shaking at 120 min −1  for 18 hours to prepare a preculture fluid. Subsequently, 0.25 mL of the preculture fluid is added to 5 mL of the culture medium 11 (10 g/L succinic acid, 10 g/L glucose, 1 g/L ammonium sulfate, 50 mM potassium phosphate, 0.025 g/L magnesium sulfate, 0.0625 mg/L iron sulfate, 2.7 mg/L manganese sulfate, 0.33 mg/L calcium chloride, 1.25 g/L sodium chloride, 2.5 g/L Bacto Tryptone, 1.25 g/L Bacto Yeast Extract) adjusted to pH 6.5, and incubated at 30° C. with shaking at 120 min −1  for 24 hours. The obtained culture fluid is examined for the presence of 3-hydroxyadipic acid or α-hydromuconic acid. 
     The presence of 3-hydroxyadipic acid or α-hydromuconic acid in the culture fluid can be confirmed by centrifuging the culture fluid and analyzing the supernatant with LC-MS/MS. The analysis conditions are as described below:
         HPLC: 1290 Infinity (manufactured by Agilent Technologies, Inc.)
 
Column: Synergi hydro-RP (manufactured by Phenomenex Inc.), length: 100 mm, internal diameter: 3 mm, particle size: 2.5 μm
 
Mobile phase: 0.1% aqueous formic acid solution/methanol=70/30
 
Flow rate: 0.3 mL/min
 
Column temperature: 40° C.
 
LC detector: DA) (210 nm)
   MS/MS: Triple-Quad LC/MS (manufactured by Agilent Technologies, Inc.) Ionization method: ESI in negative mode.       

     The 3-oxoadipyl-CoA reductase activity value can be calculated by quantifying 3-hydroxyadipyl-CoA generated from 3-oxoadipyl-CoA used as a substrate by purified 3-oxoadipyl-CoA reductase, wherein the 3-oxoadipyl-CoA is prepared from 3-oxoadipic acid by an enzymatic reaction. The specific method is as follows. 
     3-Oxoadipic acid can be prepared by a known method (for example, a method described in Reference Example 1 of WO 2017/099209). 
     Preparation of 3-oxoadipyl-CoA solution: A PCR using the genomic DNA of  Pseudomonas putida  strain KT2440 as a template is performed in accordance with routine procedures, to amplify a nucleic acid encoding a CoA transferase (peal and pcaJ; NCBI-GeneIDs: 1046613 and 1046612) in the full-length form. The nucleotide sequences of primers used in this PCR are, for example, those represented by SEQ ID NOs: 25 and 26. The amplified fragment is inserted into the KpnI site of pRSF-1b (manufactured by Novagen), an expression vector for  E. coli , in-frame with the histidine-tag sequence. The plasmid is introduced into  E. coli  BL21 (DE3), and expression of the enzyme is induced with isopropyl-β-thiogalactopyranoside (IPTG) in accordance with routine procedures and the enzyme is purified using the histidine tag from the culture fluid to obtain a CoA transferase solution. The solution is used to prepare an enzymatic reaction solution for 3-oxoadipyl-CoA preparation with the following composition, which is allowed to react at 25° C. for 3 minutes and then filtered through a UF membrane (Amicon Ultra-0.5 mL 10K; manufactured by Merck Millipore) to remove the enzyme, and the obtained filtrate is designated as 3-oxoadipyl-CoA solution: 
     Enzymatic Reaction Solution for 3-Oxoadipyl-CoA Preparation: 
     100 mM Tris-HCl (pH 8.2) 
     10 mM MgCl 2    
     0.5 mM succinyl-CoA
 
5 mM 3-oxoadipic acid sodium salt
 
2 μM CoA transferase.
 
     Identification of 3-oxoadipyl-CoA reductase activity: A PCR using the genomic DNA of a subject microorganism strain as a template is performed in accordance with routine procedures, to amplify a nucleic acid encoding 3-oxoadipyl-CoA reductase in the full-length form. The nucleotide sequences of primers used in this PCR are, for example, those represented by SEQ ID NOs: 31 and 32. The amplified fragment is inserted into the BamHI site of pACYCDuet-1 (manufactured by Novagen), an expression vector for  E. coli , in-frame with the histidine-tag sequence. The plasmid is introduced into  E. coli  BL21 (DE3), and expression of the enzyme is induced with isopropyl-β-thiogalactopyranoside (IPTG) in accordance with routine procedures and the enzyme is purified using the histidine tag from the culture fluid to obtain a 3-oxoadipyl-CoA reductase solution. The 3-oxoadipyl-CoA reductase activity can be determined by using the enzyme solution to prepare an enzymatic reaction solution with the following composition and quantifying 3-hydroxyadipyl-CoA generated at 25° C. 
     100 mM Tris-HCl (pH 8.2) 
     10 mM MgCl 2    
     150 μL/mL 3-oxoadipyl-CoA solution 
     0.5 mM NADH 
     1 mM dithiothreitol
 
10 μM 3-oxoadipyl-CoA reductase.
 
     In the present invention, the genetically modified microorganism in which expression of any one of the polypeptides described in (a) to (c) is enhanced is a microorganism as a host which originally has the nucleic acids encoding any one of the polypeptides described in (a) to (c) and is genetically modified to increasingly express any one of the polypeptides described in (a) to (c) which are owned by the host microorganism. 
     Specific examples of the microorganisms which originally have a nucleic acid encoding any one of the polypeptides described in (a) to (c) include the following microorganisms of the genus  Serratia: Serratia marcescens  (a microorganism having the sequences represented by SEQ ID NOs: 1, 70 to 80, 82 to 85, and 87 to 118).  Serratia nematodiphila  (a microorganism having the sequences represented by SEQ ID NOs: 2, 81, and 119),  Serratia plymuthica  (a microorganism having the sequences represented by SEQ ID NOs: 3, 131 to 136, and 138).  Serratia proteamaculans  (a microorganism having the sequences represented by SEQ ID NOs: 4 and 137).  Serratia ureilytica  (a microorganism having the sequence represented by SEQ ID NO: 5),  Serratia  sp. BW106 (a microorganism having the sequence represented by SEQ ID NO: 6),  Serratia  sp. S19 (a microorganism having the sequence represented by SEQ ID NO: 7),  Serratia  sp. YD25 (a microorganism having the sequence represented by SEQ ID NO: 8),  Serratia  sp. FS14 (a microorganism having the sequence represented by SEQ ID NO: 9),  Serratia  sp. HMSC15F11 (a microorganism having the sequence represented by SEQ ID NO: 10).  Serratia  sp. JKS000199 (a microorganism having the sequence represented by SEQ ID NO: 11),  Serratia  sp. TEL (a microorganism having the sequence represented by SEQ ID NO: 12),  Serratia  sp. ISTD04 (a microorganism having the sequence represented by SEQ ID NO: 13),  Serratia  sp. SCB1 (a microorganism having the sequence represented by SEQ ID NO: 14),  Serratia  sp. S4 (a microorganism having the sequence represented by SEQ ID NO: 15),  Serratia  sp. C-1 (a microorganism having the sequence represented by SEQ ID NO: 16),  Serratia  sp. OMLW3 (a microorganism having the sequence represented by SEQ ID NO: 86),  Serratia  sp. OLEL1 (a microorganism having the sequence represented by SEQ ID NO: 120).  Serratia  sp. OLEL2 (a microorganism having the sequence represented by SEQ ID NO: 123),  Serratia liquefaciens  (a microorganism having the sequence represented by SEQ ID NO: 213), and the like. 
     Each of the polypeptides as described above in (a), (b), and (c) also has 3-hydroxybutyryl-CoA dehydrogenase activity, and the 3-hydroxybutyryl-CoA dehydrogenase is encoded by the 3-hydroxybutyryl-CoA dehydrogenase gene, which forms a gene cluster with the 5-aminolevulinic acid synthase gene in the microorganisms of the genus  Serratia.    
     As used herein, the term “gene cluster” in the phrase “the 3-hydroxybutyryl-CoA dehydrogenase gene, which forms a gene cluster with 5-aminolevulinic acid synthase gene in the microorganisms of the genus  Serratia ” refers to a region in which a set of nucleic acids encoding related functions are located in close proximity to each other. Specific components in a gene cluster include, for example, nucleic acids which are transcribed under control of a single transcription regulator, and those in an operon which are transcribed under control of a single transcription promoter. Whether or not a certain nucleic acid is a nucleic acid component of a gene cluster can also be investigated using an online gene cluster search program, such as antiSMASH. Additionally, whether or not a certain polypeptide is classified as a 3-hydroxybutyryl-CoA dehydrogenase or a 5-aminolevulinic acid synthase can be determined by performing a BLAST (Basic Local Alignment Search Tool) search on a website, such as that of NCBI (National Center for Biotechnology Information) or KEGG (Kyoto Encyclopedia of Genes and Genomes), to find any enzyme with high homology of the amino acid sequence to the polypeptide. For example, the amino acid sequence represented by SEQ ID NO: 4 is registered in an NCBI database under Protein ID: ABV40935.1, which is annotated as a putative protein with 3-hydroxybutyryl-CoA dehydrogenase activity, as judged from the amino acid sequence. A gene encoding the amino acid sequence represented by SEQ ID NO: 4 is registered in an NCBI database under Gene ID: CP000826.1, and can be identified through a database search as conserved on the genome of  Serratia proteamaculans  strain 568 or as conserved from 2015313 to 2016842 bp on the sequence of Gene ID: CP000826.1. Furthermore, the positional information of the gene can lead to identification of the sequences of flanking genes, from which the gene can be found to form a gene cluster with the 5-aminolevulinic acid synthase gene (Protein ID: ABV40933.1), as shown in  FIG. 1 . Similarly, for the amino acid sequences represented by SEQ ID NOs: 1 to 3, 6 to 16, 70 to 72, 74 to 82, 84 to 87, 89, 90, 92, 94 to 100, 103 to 108, 111 to 115, 117, 118, 120 to 125, 127 to 133, 135 to 137, and 213, the information can be checked on the NCBI site with Protein IDs and Gene IDs presented in Table 13. 
     
       
         
           
               
               
               
             
               
                 TABLE 13 
               
               
                   
               
               
                 SEQ ID  
                   
                   
               
               
                 NO.  
                 Gene ID: Position (from . . . to)  
                 Protein ID 
               
               
                   
               
             
            
               
                   
               
            
           
           
               
               
               
            
               
                 1  
                 JMPQ01000047.1: 133194 . . . 134723  
                 KFD11732.1  
               
               
                 2  
                 JPUX00000000.1: 4202615 . . . 4204144  
                 WP_033633399.1  
               
               
                 3  
                 BCTU01000013.1: 85647 . . . 87176  
                 WP_063199278.1  
               
               
                 4  
                 CP000826.1: 2015313 . . . 2016842  
                 ABV40935.1  
               
               
                 6  
                 MCGS01000002.1: 43811 . . . 45340  
                 WP_099061672.1  
               
               
                 7  
                 MSFH01000022.1: 147976 . . . 149505  
                 ONK16968.1  
               
               
                 8  
                 CP016948.1: 1213474 . . . 1215003  
                 AOE98783.1  
               
               
                 9  
                 CP005927.1: 4244665 . . . 4246194  
                 WP_044031504.1  
               
               
                 10  
                 LWNG01000196.1: 83086 . . . 84615  
                 OFS85208.1  
               
               
                 11  
                 LT907843.1: 1172733 . . . 1174262  
                 SNY82966.1  
               
               
                 12  
                 LDEG01000005.1: 19627 . . . 21156  
                 KLE40298.1  
               
               
                 13  
                 MBDW01000089.1: 53478 . . . 55007  
                 ODJ15373.1  
               
               
                 14  
                 CP003424.1: 1869825 . . . 1871300  
                 AIM21329.1  
               
               
                 15  
                 APLA01000003.1: 1964823 . . . 1966352 
                 WP_017892361.1  
               
               
                 16  
                 CAQ001000118.1: 101692 . . . 103221  
                 WP_062792820.1  
               
               
                 70  
                 JVDI01000070.1: 19399 . . . 20928  
                 WP_049300487.1  
               
               
                 71  
                 FCGF01000001.1: 938090 . . . 939619  
                 WP_060444298.1  
               
               
                 72  
                 NC_020211.1: 1963542 . . . 1965071  
                 WP_015377392.1  
               
               
                 74  
                 JVNC01000043.1: 47711 . . . 49240  
                 WP_049187553.1  
               
               
                 75  
                 MCNK01000010.1: 591271 . . . 592800  
                 WP_076740355.1  
               
               
                 76  
                 JVZV01000138.1: 53080 . . . 54609  
                 WP_049277247.1  
               
               
                 77  
                 CP021984.1: 1963542 . . . 1965071  
                 WP_088381461.1  
               
               
                 78  
                 NERL01000025.1: 86571 . . . 88100  
                 WP_060559176.1  
               
               
                 79  
                 MTEH01000001.1: 215863 . . . 217392  
                 WP_085336366.1  
               
               
                 80  
                 JVCS01000001.1: 19397 . . . 20926  
                 WP_049239700.1  
               
               
                 81  
                 MTBJ01000002.1: 216232 . . . 217761  
                 WP_082996863.1  
               
               
                 82  
                 AORJ01000010.1: 70272 . . . 71801  
                 WP_033645451.1  
               
               
                 84  
                 LFJS01000012.1: 944087 . . . 945616  
                 WP_025302345.1  
               
               
                 85  
                 CP018930.1: 1161338 . . . 1162867  
                 WP_060447438.1  
               
               
                 86  
                 MSTK01000013.1: 54046 . . . 55575  
                 WP_099817374.1  
               
               
                 87  
                 CP018929.1: 1167577 . . . 1170106  
                 WP_089180755.1  
               
               
                 89  
                 FCGS01000006.1: 98915 . . . 100444  
                 WP_060438851.1  
               
               
                 90  
                 MQRI01000002.1: 585500 . . . 587029  
                 WP_060387554.1  
               
               
                 92  
                 FCFE01000001.1: 962839 . . . 964368  
                 WP_060435888.1  
               
               
                 94  
                 FCIO01000002.1: 145369146898 . . .  
                 WP_033637938.1  
               
               
                 95  
                 AP013063.1: 1329259 . . . 1330788  
                 WP_041034581.1  
               
               
                 96  
                 MQRJ01000004.1: 178926 . . . 180455  
                 WP_074026553.1  
               
               
                 97  
                 HG738868.1: 1928329 . . . 1929858  
                 WP_060437960.1  
               
               
                 98  
                 FCHQ01000006.1: 51377 . . . 52906  
                 WP_060420535.1  
               
               
                 99  
                 NPGG01000001.1: 301231 . . . 302760  
                 WP_047568134.1  
               
               
                 100  
                 FCME01000002.1: 205632 . . . 207161  
                 WP_060443161.1  
               
               
                 103  
                 FCIH01000014.1: 52403 . . . 53932  
                 WP_060429049.1  
               
               
                 104  
                 NBWV01000007.1: 110621 . . . 112150  
                 WP_039566649.1  
               
               
                 105  
                 FCKI01000001.1: 594106 . . . 595635  
                 WP_060429902.1  
               
               
                 106  
                 JPOB01000010.1: 81351 . . . 82880  
                 WP_033654196.1  
               
               
                 107  
                 FCFI01000001.1: 582222 . . . 583751  
                 WP_060443342.1  
               
               
                 108  
                 FCML01000001.1: 1005802 . . . 1007331  
                 WP_060456892.1  
               
               
                 111  
                 FCMR01000001.1: 1873566 . . . 1875095  
                 WP_060440240.1  
               
               
                 112  
                 LJEV02000002.1: 115432 . . . 116961  
                 WP_047727865.1  
               
               
                 113  
                 NPIX01000027.1: 38249 . . . 39778  
                 WP_094461128.1  
               
               
                 114  
                 NDXU01000091.1: 70343 . . . 71872  
                 WP_048233299.1  
               
               
                 115  
                 FNXW01000055.1: 13619 . . . 15148  
                 WP_080490898.1  
               
               
                 117  
                 AYMO01000023.1: 23978 . . . 25507  
                 WP_025160335.1  
               
               
                 118  
                 CP018926.1: 1215941 . . . 1217470  
                 WP_089191486.1  
               
               
                 120  
                 MORG01000026.1: 13723 . . . 15252  
                 WP_099782744.1  
               
               
                 121  
                 PEHC01000008.1: 57274 . . . 58803  
                 PHY81681.1  
               
               
                 122  
                 MEDA01000063.1: 13491 . . . 15020 
                 WP_072627918.1  
               
               
                 123  
                 MORH01000030.1: 13633 . . . 15162  
                 WP_099789708.1  
               
               
                 124  
                 KK214286.1: 392757 . . . 394286  
                 WP_033650708.1  
               
               
                 125  
                 KI929259.1: 1574567 . . . 1576096  
                 WP_033642621.1  
               
               
                 127  
                 CP012639.1: 230596 . . . 232125  
                 WP_060659686.1  
               
               
                 128  
                 LZOB01000011.1: 1613417 . . . 1614946  
                 WP_074054551.1  
               
               
                 129  
                 LCW101000024.1: 46336 . . . 47865  
                 WP_046899223.1  
               
               
                 130  
                 CP018924.1: 1213305 . . . 1214834  
                 WP_089194521.1  
               
               
                 131  
                 NC_015567.1: 1930552 . . . 1932081  
                 WP_013812379.1  
               
               
                 132  
                 MQML01000205.1: 9362 . . . 10891  
                 WP_073439751.1  
               
               
                 133  
                 AMSV01000032.1: 251478 . . . 253007  
                 WP_006324610.1  
               
               
                 135  
                 CP007439.1: 1991332 . . . 1992861  
                 AHY06789.1  
               
               
                 136  
                 CP012096.1: 319897 . . . 321426  
                 WP_037432641.1  
               
               
                 137  
                 FWWG01000018.1: 38528 . . . 40057  
                 WP_085116175.1  
               
               
                 213  
                 CP006252.1: 1825868 . . . 1827397  
                 AGQ30498.1 
               
               
                   
               
            
           
         
       
     
     A nucleic acid encoding a polypeptide encoded by the 3-hydroxybutyryl-CoA dehydrogenase gene of a microorganism of the genus  Serratia , which forms a gene cluster with the 5-aminolevulinic acid synthase gene, is hereinafter referred to as “the 3-hydroxybutyryl-CoA dehydrogenase gene used in the present invention,” and the polypeptide encoded by the 3-hydroxybutyryl-CoA dehydrogenase gene is referred as “the 3-hydroxybutyryl-CoA dehydrogenase used in the present invention.” 
     A gene cluster including the 3-hydroxybutyryl-CoA dehydrogenase gene used in the present invention may include other nucleic acids, provided that at least the 3-hydroxybutyryl-CoA dehydrogenase gene and the 5-aminolevulinic acid synthase gene are included in the gene cluster.  FIG. 1  shows a specific example of the gene cluster including the 3-hydroxybutyryl-CoA dehydrogenase gene used in the present invention. 
     Specific examples of the microorganisms of the genus  Serratia  that contain the above gene cluster include  S. marcescens, S. nematodiphila, S. plymuthica, S. proteamaculans, S. ureilytica, S. liquefaciens, Serratia  sp. BW106,  Serratia  sp. SI 19,  Serratia  sp. YD25 . Serratia  sp. FS14 , Serratia  sp. HMSC15F11,  Serratia  sp. JKS000199.  Serratia  sp. TEL,  Serratia  sp. ISTD04,  Serratia  sp. SCBHI,  Serratia  sp. S4,  Serratia  sp. C-1 , Serratia  sp. OMLW3,  Serratia  sp. OLEL1 , Serratia  sp. OLEL2, and  S. liquefaciens.    
     The 3-hydroxybutyryl-CoA dehydrogenase used in the present invention has an excellent 3-oxoadipyl-CoA reductase activity. Whether or not a 3-hydroxybutyryl-CoA dehydrogenase-encoding nucleic acid has a 3-oxoadipyl-CoA reductase activity can be determined by the same method as described above. 
     The polypeptide encoded by the 3-hydroxybutyryl-CoA dehydrogenase gene used in the present invention is characterized by containing the common sequence 1. Specific examples of amino acid sequences of such polypeptides include the amino acid sequences represented by SEQ ID NOs: 1 to 16, 70 to 138, and 213. 
     In the present invention, a nucleic acid encoding a polypeptide composed of the same amino acid sequence as that represented by any one of SEQ ID NOs: 7 to 16 or 70 to 138, except that one or several amino acids are substituted, deleted, inserted, and/or added, and having an enzymatic activity that catalyzes a reaction to reduce 3-oxoadipyl-CoA to 3-hydroxyadipyl-CoA, can be suitably used, provided that the common sequence 1 is contained in the polypeptide. In this respect, the range represented by the phrase “one or several” is preferably 10 or less, further preferably 5 or less, particularly preferably 4 or less, and most preferably one or two. In the case of amino acid substitution, the activity of the original polypeptide is more likely to be maintained when the amino acids are replaced by amino acids with similar properties (i.e., conservative substitution as described above). A nucleic acid encoding a polypeptide composed of an amino acid sequence with a sequence identity of not less than 70%, preferably not less than 80%, more preferably not less than 85%, further preferably not less than 90%, still further preferably not less than 95%, yet further preferably not less than 97%, even further preferably not less than 99%, to the sequence represented by any one of SEQ ID NOs: 7 to 16 or 70 to 138 and having an enzymatic activity that catalyzes a reaction to reduce 3-oxoadipyl-CoA to 3-hydroxyadipyl-CoA can also be suitably used. 
     On the other hand, examples of a polypeptide that is not the 3-hydroxybutyryl-CoA dehydrogenase used in the present invention but has 3-oxoadipyl-CoA reductase activity include PaaH from  Pseudomonas putida  strain KT2440 (SEQ ID NO: 208), PaaH from  Escherichia coli  str. K-12 substr. MG1655 (SEQ ID NO: 209). DcaH from  Acinetobacter baylyi  strain ADP1 (SEQ ID NO: 210), and PaaH from  Serratia plymuthica  strain NBRC102599 (SEQ ID NO: 211); these polypeptides are found not to contain the common sequence 1, as shown in Tables 4 and 5. It should be noted that those polypeptides are neither (b) polypeptides composed of the same amino acid sequence as that represented by any one of SEQ ID NOs: 1 to 6 and 213, except that one or several amino acids are substituted, deleted, inserted, and/or added, and having an enzymatic activity that catalyzes a reaction to reduce 3-oxoadipyl-CoA to 3-hydroxyadipyl-CoA, nor (c) polypeptides having an amino acid sequence with a sequence identity of not less than 70% to the sequence represented by any one of SEQ ID NOs: 1 to 6 and 213 and having an enzymatic activity that catalyzes a reaction to reduce 3-oxoadipyl-CoA to 3-hydroxyadipyl-CoA, polypeptide. 
     
       
         
           
               
             
               
                 TABLE 4 
               
               
                   
               
             
            
               
                 
                   
                     
                     
                         
                         
                     
                   
                 
               
               
                   
               
            
           
         
       
     
     
       
         
           
               
             
               
                 TABLE 5 
               
               
                   
               
             
            
               
                 
                   
                     
                     
                         
                         
                     
                   
                 
               
               
                   
               
            
           
         
       
     
     In the present invention, examples of the microorganisms that can be used as hosts to obtain the genetically modified microorganisms include microorganisms belonging to the genera  Escherichia, Serratia, Hafnia, Pseudomonas, Corynebacterium, Bacillus, Streptomyces, Cupriavidus, Acinetobacter, Alcaligenes, Brevibacterium, Delftia, Shimwellia, Aerobacter, Rhizobium, Thermobifida, Clostridium, Schizosaccharomyces, Kluyveromyces, Pichia , and  Candida . Among them, microorganisms belonging to the genera  Escherichia, Serratia, Hafnia , and  Pseudomonas  are preferable. 
     The method of producing 3-hydroxyadipic acid, α-hydromuconic acid, and/or adipic acid by using a genetically modified microorganisms according to the present invention will be described. 
     Any genetically modified microorganism according to the present invention can produce 3-hydroxyadipic acid, provided that the microorganism has an ability to generate 3-oxoadipyl-CoA and coenzyme A from acetyl-CoA and succinyl-CoA (the reaction A) and an ability to generate 3-hydroxyadipic acid from 3-hydroxyadipyl-CoA (the reaction E). By using a microorganism with these production abilities as the host microorganism, a genetically modified microorganism that can abundantly produce 3-hydroxyadipic acid can be obtained. Microorganisms that are speculated to originally have the above production abilities include the following microorganisms: microorganisms of the genus  Escherichia , such as  Escherichia fergusonii  and  Escherichia coli : the genus  Pseudomonas , such as  Pseudomonas chlororaphis, Pseudomonas putida, Pseudomonas azotoformans, and Pseudomonas chlororaphis  subsp.  aureofaciens : the genus  Hafnia , such as  Hafnia alvei ; the genus  Corynebacterium , such as  Corynebacterium acetoacidophilum, Corynebacterium acetoglutamicum, Corynebacterium ammoniagenes , and  Corynebacterium glutamicum ; the genus  Bacillus , such as  Bacillus badius, Bacillus magalerium , and  Bacillus roseus ; the genus  Streptomyces , such as  Streptomyces vinaceus, Streptomyces karnatakensis , and  Streptomyces olivaceus ; the genus  Cupriavidus , such as  Cupriavidus metallidurans, Cupriavidus necator , and  Cupriavidus oxalaticus ; the genus  Acinetobacter , such as  Acinetobacter baylyi  and  Acinetobacter radioresistens ; the genus  Alcaligenes , such as  Alcaligenes faecalis ; the genus  Nocardioides , such as  Nocardioides albus ; the genus  Brevibacterium , such as  Brevibacterium iodinum ; the genus  Delftia , such as  Delftia acidovorans ; the genus  Shimwellia , such as  Shimwellia blattae ; the genus  Aerobacter , such as  Aerobacter cloacae ; the genus  Rhizobium , such as  Rhizobium radiobacter ; the genus  Serratia , such as  Serratia grimesii, Serratia ficaria, Serratia fonticola, Serratia odorifera, Serratia plymuthica, Serratia entomophila , and  Serratia nematodiphila . Any of these microorganisms can be used as a host microorganism to obtain a genetically modified microorganism according to the present invention, which results in generation of a genetically modified microorganism that abundantly produces 3-hydroxyadipic acid. 
     Into a genetically modified microorganism according to the present invention which originally has no abilities to generate 3-oxoadipyl-CoA and coenzyme A from acetyl-CoA and succinyl-CoA (the reaction A) and/or to generate 3-hydroxyadipic acid from 3-hydroxyadipyl-CoA (the reaction E), an appropriate combination of nucleic acids encoding enzymes that catalyze the reactions A and E can be introduced to give the microorganisms these production abilities. 
     Any genetically modified microorganism according to the present invention can produce α-hydromuconic acid, provided that the microorganism has an ability to generate 3-oxoadipyl-CoA and coenzyme A from acetyl-CoA and succinyl-CoA (the reaction A), an ability to generate 2,3-dehydroadipyl-CoA by dehydrating 3-hydroxyadipyl-CoA (the reaction C), and an ability to generate α-hydromuconic acid from 2,3-dehydroadipyl-CoA (the reaction F). By using a microorganism with these production abilities as a host microorganism, a genetically modified microorganism that can abundantly produce α-hydromuconic acid can be obtained. Microorganisms that are speculated to originally have the above production abilities include the following microorganisms: microorganisms of the genus  Escherichia , such as  Escherichia fergusonii  and  Escherichia coli ; the genus  Pseudomonas , such as  Pseudomonas fluorescens, Pseudomonas putida, Pseudomonas azotoformans , and  Pseudomonas chlororaphis  subsp.  aureofaciens ; the genus  Hafnia , such as  Hafnia alvei ; the genus  Bacillus , such as  Bacillus badius ; the genus  Cupriavidus , such as  Cupriavidus metallidurans, Cupriavidus numazuensis , and  Cupriavidus oxalaticus ; the genus  Acinetobacter , such as  Acinetobacter baylyi  and  Acinetobacter radioresistens ; the genus  Alcaligenes , such as  Alcaligenes faecalis ; the genus  Delftia , such as  Delftia acidovorans ; the genus  Shimwellia , such as  Shimwellia blantae ; the genus  Serratia , such as  Serratia grimesii, Serratia ficaria, Serratia fonticola, Serratia odorifera, Serratia plymuthica, Serratia entomophila , and  Serratia nematodiphila.    
     Into a genetically modified microorganism according to the present invention which originally has no abilities to generate 3-oxoadipyl-CoA and coenzyme A from acetyl-CoA and succinyl-CoA (the reaction A), to generate 2,3-dehydroadipyl-CoA by dehydrating 3-hydroxyadipyl-CoA (the reaction C), and to generate α-hydromuconic acid from 2,3-dehydroadipyl-CoA (the reaction F), an appropriate combination of nucleic acids encoding enzymes that catalyze the reactions A, C, and F can be introduced to give the microorganism these production abilities. 
     Any genetically modified microorganism according to the present invention can produce adipic acid, provided that the microorganism has an ability to generate 3-oxoadipyl-CoA and coenzyme A from succinyl-CoA (the reaction A), an ability to generate 2,3-dehydroadipyl-CoA by dehydrating 3-hydroxyadipyl-CoA (the reaction C), an ability to generate adipyl-CoA by reducing 2,3-dehydroadipyl-CoA (the reaction D), and an ability to generate adipic acid from adipyl-CoA (the reaction G). By using a microorganism with these production abilities as a host microorganism, a genetically modified microorganism that can abundantly produce adipic acid can be obtained. Microorganisms that are speculated to originally have the above production abilities include microorganisms of the genus  Thermobifida , such as  Thermobifida fusca.    
     In cases where a genetically modified microorganism according to the present invention originally has no abilities to generate 3-oxoadipyl-CoA and coenzyme A from succinyl-CoA (the reaction A), to generate 2,3-dehydroadipyl-CoA by dehydrating 3-hydroxyadipyl-CoA (the reaction C), to generate adipyl-CoA by reducing 2,3-dehydroadipyl-CoA (the reaction D), and to generate adipic acid from adipyl-CoA (the reaction G), an appropriate combination of nucleic acids encoding enzymes that catalyze the reactions A, C, D, and G can be introduced into the microorganism to give the microorganism these production abilities. 
     Specific examples of the enzymes that catalyze the reactions A and C to G are presented below. 
     As an enzyme that catalyzes the reaction A to generate 3-oxoadipyl-CoA, for example, an acyl transferase (β-ketothiolase) can be used. The acyl transferase is not limited by a particular number in the EC classification, and is preferably an acyl transferase classified into EC 2.3.1.-, specifically including an enzyme classified as 3-oxoadipyl-CoA thiolase and classified into EC 2.3.1.174, an enzyme classified as acetyl-CoA C-acetyltransferase and classified into EC 2.3.1.9, and an enzyme classified as acetyl-CoA C-acyl transferase and classified into EC 2.3.1.16. Among them, PaaJ from  Escherichia coli  strain MG1655 (NCBI-ProteinID: NP_415915). PcaF from  Pseudomonas putida  strain KT2440 (NCBI-ProteinID: NP_743536), and the like can be suitably used. 
     Whether or not the above acyl transferases can generate 3-oxoadipyl-CoA from succinyl-CoA and acetyl-CoA used as substrates can be determined by measuring a decrease in NADH coupled with reduction of 3-oxoadipyl-CoA in a combination of the reaction to generate 3-oxoadipyl-CoA by purified acyl transferase and the reaction to reduce 3-oxoadipyl-CoA used as a substrate by purified 3-oxoadipyl-CoA reductase. The specific measurement method is, for example, as follows. 
     Identification of acyl transferase activity: A PCR using the genomic DNA of a subject microorganism strain as a template is performed in accordance with routine procedures, to amplify a nucleic acid encoding an acyl transferase in the full-length form. The amplified fragment is inserted into the SacI site of pACYCDuet-1 (manufactured by Novagen), an expression vector for  E. coli , in-frame with the histidine-tag sequence. The plasmid is introduced into  E. coli  BL21 (DE3), and expression of the enzyme is induced with isopropyl-β-thiogalactopyranoside (IPTG) in accordance with routine procedures and the enzyme is purified using the histidine tag from the culture fluid to obtain an acyl transferase solution. The acyl transferase activity can be determined by using the enzyme solution to prepare an enzymatic reaction solution with the following composition and measuring a decrease in absorbance at 340 nm coupled with oxidation of NADH at 30° C. 
     100 mM Tris-HCl (pH 8.0) 
     10 mM MgCl 2    
     0.1 mM succinyl-CoA
 
0.2 mM acetyl-CoA
 
     0.2 mM NADH 
     1 mM dithiothreitol
 
10 μg/mL 3-oxoadipyl-CoA reductase
 
5 μg/mL acyltransferase.
 
     Whether or not an enzyme originally expressed in a host microorganism used in the present invention has acyl transferase activity can be determined by performing the above-described measurement using cell homogenate (cell free extract: CFE) instead of purified acyl transferase. The specific measurement method targeted to  E. coli  is, for example, as follows. 
     Preparation of CFE: A loopful of  E. coli  strain MG1655 to be subjected to the measurement of the activity is inoculated into 5 mL of a culture medium (culture medium composition: 10 g/L tryptone, 5 g/L yeast extract, 5 g/L sodium chloride) adjusted to pH 7, and incubated at 30° C. with shaking for 18 hours. The obtained culture fluid is added to 5 mL of a culture medium (culture medium composition: 10 g/L tryptone, 5 g/L yeast extract, 5 g/L sodium chloride, 2.5 mM ferulic acid, 2.5 mM p-coumaric acid, 2.5 mM benzoic acid, 2.5 mM cis,cis-muconic acid, 2.5 mM protocatechuic acid, 2.5 mM catechol, 2.5 mM 3OA, 2.5 mM 3-hydroxyadipic acid, 2.5 mM α-hydromuconic acid, 2.5 mM adipic acid, 2.5 mM phenylethylamine) adjusted to pH 7, and incubated at 30° C. with shaking for 3 hours. 
     The obtained culture fluid is supplemented with 10 mL of 0.9% sodium chloride and then centrifuged to remove the supernatant from bacterial cells, and this operation is repeated three times in total to wash the bacterial cells. The washed bacterial cells are suspended in 1 mL of a Tris-HCl buffer composed of 100 mM Tris-HCl (pH 8.0) and 1 mM dithiothreitol, and glass beads (with a diameter of 0.1 mm) are added to the resulting suspension to disrupt the bacterial cells at 4° C. with an ultrasonic disruptor. The resulting bacterial homogenate is centrifuged to obtain the supernatant, and 0.5 mL of the supernatant is filtered through a UF membrane (Amicon Ultra-0.5 mL 10K; manufactured by Merck Millipore) to remove the resulting filtrate, followed by application of 0.4 mL of the Tris-HCl buffer to the UF membrane, and this operation is repeated three times in total to remove low-molecular-weight impurities, and the resulting supernatant is then resuspended in the Tris-HCl buffer to a final volume of 0.1 mL, which is designated as CFE. Instead of purified enzyme, 0.05 mL of the CFE is added to a total of 0.1 mL of the enzymatic reaction solution to determine the enzymatic activity. 
     As an enzyme that catalyzes the reaction C to generate 2,3-dehydroadipyl-CoA, for example, an enoyl-CoA hydratase can be used. The enoyl-CoA hydratase is not limited by a particular number in the EC classification, and is preferably an enoyl-CoA hydratase classified into EC 4.2.1.-, specifically including an enzyme classified as enoyl-CoA hydratase or 2,3-dehydroadipyl-CoA hydratase and classified into EC 4.2.1.17. Among them. PaaF from  Escherichia coli  strain MG1655 (NCBI-ProteinID: NP_415911), PaaF from  Pseudomonas putida  strain KT2440 (NCBI-ProteinID: NP_745427), and the like can be suitably used. 
     Since the reaction catalyzed by enoyl-CoA hydratase is generally reversible, whether or not an enoyl-CoA hydratase has an activity to catalyze a reaction that generates 2,3-dehydroadipyl-CoA from 3-hydroxyadipyl-CoA used as a substrate can be determined by detecting 3-hydroxyadipyl-CoA generated using purified enoyl-CoA hydratase with 2,3-dehydroadipyl-CoA used as a substrate thereof, which is prepared from α-hydromuconic acid through an enzymatic reaction. The specific measurement method is, for example, as follows. 
     The α-hydromuconic acid used in the above reaction can be prepared by a known method (for example, a method described in Reference Example 1 of WO 2016/199858 A1). 
     Preparation of 2,3-dehydroadipyl-CoA solution: A PCR using the genomic DNA of  Pseudomonas putida  strain KT2440 as a template is performed in accordance with routine procedures, to amplify a nucleic acid encoding a CoA transferase (including pcaI and pcaJ; NCBI-GeneIDs: 1046613 and 1046612) in the full-length form. The amplified fragment is inserted into the KpnI site of pRSF-1b (manufactured by Novagen), an expression vector for  E. coli , in-frame with the histidine-tag sequence. The plasmid is introduced into  E. coli  BL21 (DE3), and expression of the enzyme is induced with isopropyl-β-thiogalactopyranoside (IPTG) in accordance with routine procedures and the enzyme is purified using the histidine tag from the culture fluid to obtain a CoA transferase solution. The solution is used to prepare an enzymatic reaction solution for 2,3-dehydroadipyl-CoA preparation with the following composition, which is allowed to react at 30° C. for 10 minutes and then filtered through a UF membrane (Amicon Ultra-0.5 mL 10K; manufactured by Merck Millipore) to remove the enzyme, and the obtained filtrate is designated as 2,3-dehydroadipyl-CoA solution. 
     Enzymatic reaction solution for 2,3-dehydroadipyl-CoA preparation 
     100 mM Tris-HCl (pH 8.0) 
     10 mM MgCl 2    
     0.4 mM succinyl-CoA
 
2 mM α-hydromuconic acid sodium salt
 
20 μg/mL CoA transferase.
 
     Identification of enoyl-CoA hydratase activity: A PCR using the genomic DNA of a subject microorganism strain as a template is performed in accordance with routine procedures, to amplify a nucleic acid encoding an enoyl-CoA hydratase in the full-length form. The amplified fragment is inserted into the NdeI site of pET-16b (manufactured by Novagen), an expression vector for  E. coli , in-frame with the histidine-tag sequence. The plasmid is introduced into  E. coli  BL21 (DE3), and expression of the enzyme is induced with isopropyl-β-thiogalactopyranoside (IPTG) in accordance with routine procedures and the enzyme is purified using the histidine tag from the culture fluid to obtain an enoyl-CoA hydratase solution. The solution is used to prepare an enzymatic reaction solution with the following composition, which is allowed to react at 30° C. for 10 minutes and then filtered through a UF membrane (Amicon Ultra-0.5 mL 10K; manufactured by Merck Millipore) to remove the enzyme. The enoyl-CoA hydratase activity can be confirmed by detecting 3-hydroxyadipyl-CoA in the resulting filtrate on high-performance liquid chromatograph-tandem mass spectrometer (LC-MS/MS) (Agilent Technologies, Inc.). 
     100 mM Tris-HCl (pH 8.0) 
     10 mM MgCl 2    
     300 μL/mL 2,3-dehydroadipyl-CoA solution
 
1 mM dithiothreitol
 
20 μg/mL enoyl-CoA hydratase.
 
     Whether or not an enzyme originally expressed in a host microorganism used in the present invention has enoyl-CoA hydratase activity can be determined by adding 0.05 mL of the CFE, instead of purified enoyl-CoA hydratase, to a total of 0.1 mL of the enzymatic reaction solution and performing the above-described measurement. The specific CFE preparation method targeted to  E. coli  is as described for that used in determination of acyl transferase activity. 
     As an enzyme that catalyzes the reaction D to generate adipyl-CoA, for example, an enoyl-CoA reductase can be used. The enoyl-CoA reductase is not limited by a particular number in the EC classification, and is preferably an enoyl-CoA reductase classified into EC 1.3.-.-, specifically including an enzyme classified as trans-2-enoyl-CoA reductase and classified into EC 1.3.1.44, and an enzyme classified as acyl-CoA dehydrogenase and classified into EC 1.3.8.7. These specific examples are disclosed in, for example JP 2011-515111 A, J Appl Microbiol. 2015 October; 119 (4): 1057-63, and the like; among them, TER from  Euglena gracilis  strain Z (UniProtKB: Q5EU90), Tfu_1647 from  Thermobifida fusca  strain YX (NCBI-ProteinID: AAZ55682), DcaA from  Acinetobacter baylyi  strain ADP1 (NCBI-ProteinID: AAL09094.1), and the like can be suitably used. 
     Whether or not an enoyl-CoA reductase has an activity to generate adipyl-CoA from 2,3-dehydroadipyl-CoA used as a substrate can be determined by measuring a decrease in NADH coupled with reduction of 2,3-dehydroadipyl-CoA in a reaction using purified enoyl-CoA reductase with 2,3-dehydroadipyl-CoA used as a substrate thereof, which is prepared from α-hydromuconic acid through another enzymatic reaction. 
     Preparation of α-hydromuconic acid and a 2,3-dehydroadipyl-CoA solution can be performed in the same manner as described above. 
     Identification of enoyl-CoA reductase activity: A PCR using the genomic DNA of a subject microorganism strain as a template is performed in accordance with routine procedures, to amplify a nucleic acid encoding an enoyl-CoA reductase in the full-length form. The amplified fragment is inserted into the NdeI site of pET-16b (manufactured by Novagen), an expression vector for  E. coli , in-frame with the histidine-tag sequence. The plasmid is introduced into  E. coli  BL21 (DE3), and expression of the enzyme is induced with isopropyl-β-thiogalactopyranoside (IPTG) in accordance with routine procedures and the enzyme is purified using the histidine tag from the culture fluid to obtain an enoyl-CoA reductase solution. The enoyl-CoA reductase activity can be determined by using the enzyme solution to prepare an enzymatic reaction solution with the following composition and measuring a decrease in absorbance at 340 nm coupled with oxidation of NADH at 30° C. 
     100 mM Tris-HCl (pH 8.0) 
     10 mM MgCl 2    
     300 μL/mL 2,3-dehydroadipyl-CoA solution 
     0.2 mM NADH 
     1 mM dithiothreitol
 
20 μg/mL enoyl-CoA reductase.
 
     Whether or not an enzyme originally expressed in a host microorganism used in the present invention has enoyl-CoA reductase activity can be determined by adding 0.05 mL of the CFE, instead of purified enoyl-CoA reductase, to a total of 0.1 mL of the enzymatic reaction solution and performing the above-described measurement. The specific CFE preparation method targeted to  E. coli  is as described for that used in determination of acyl transferase activity. 
     As an enzyme that catalyzes the reaction E to generate 3-hydroxyadipic acid, the reaction F to generate α-hydromuconic acid, and the reaction G to generate adipic acid, for example, a CoA transferase or an acyl-CoA hydrolase, preferably a CoA transferase, can be used. 
     The CoA transferase is not limited by a particular number in the EC classification, and is preferably a CoA transferase classified into EC 2.8.3.-, specifically including an enzyme classified as CoA transferase or acyl-CoA transferase and classified into EC 2.8.3.6, and the like. 
     In the present invention, the term “CoA transferase” refers to an enzyme with activity (CoA transferase activity) to catalyze a reaction that generates carboxylic acid and succinyl-CoA from acyl-CoA and succinic acid used as substrates. 
     As an enzyme that catalyzes the reaction E to generate 3-hydroxyadipic acid and the reaction F to generate α-hydromuconic acid, PcaI and PcaJ from  Pseudomonas putida  strain KT2440 (NCBI-ProteinIDs: NP_746081 and NP_746082), and the like can be suitably used, among others. 
     As an enzyme that catalyzes the reaction G to generate adipic acid, DcaI and DcaJ from  Acinetobacter baylyi  strain ADP1 (NCBI-ProteinIDs: CAG68538 and CAG68539), and the like can be suitably used. 
     Since the above enzymatic reactions are reversible, the CoA transferase activity against 3-hydroxyadipyl-CoA, 2,3-dehydroadipyl-CoA, or adipyl-CoA used as a substrate can be determined by detecting 3-hydroxyadipyl-CoA, 2,3-dehydroadipyl-CoA, or adipyl-CoA generated respectively using purified CoA transferase with 3-hydroxyadipic acid and succinyl-CoA, α-hydromuconic acid and succinyl-CoA, or adipic acid and succinyl-CoA used as substrates thereof. The specific measurement method is, for example, as follows. 
     Preparation of 3-hydroxyadipic acid: Preparation of 3-hydroxyadipic acid is performed according to the method described in Reference Example 1 of WO 2016/199856 A1. 
     Identification of CoA transferase activity using 3-hydroxyadipic acid as a substrate: A PCR using the genomic DNA of a subject microorganism strain as a template is performed in accordance with routine procedures, to amplify a nucleic acid encoding a CoA transferase in the full-length form. The amplified fragment is inserted into the KpnI site of pRSF-1b (manufactured by Novagen), an expression vector for  E. coli , in-frame with the histidine-tag sequence. The plasmid is introduced into  E. coli  BL21 (DE3), and expression of the enzyme is induced with isopropyl-β-thiogalactopyranoside (IPTG) in accordance with routine procedures and the enzyme is purified using the histidine tag from the culture fluid to obtain a CoA transferase solution. The solution is used to prepare an enzymatic reaction solution with the following composition, which is allowed to react at 30° C. for 10 minutes and then filtered through a UF membrane (Amicon Ultra-0.5 mL 10K; manufactured by Merck Millipore) to remove the enzyme. The CoA transferase activity can be confirmed by detecting 3-hydroxyadipyl-CoA in the resulting filtrate on high-performance liquid chromatograph-tandem mass spectrometer (LC-MS/MS) (Agilent Technologies, Inc.). 
     100 mM Tris-HCl (pH 8.0) 
     10 mM MgCl 2    
     0.4 mM succinyl-CoA
 
2 mM 3-hydroxyadipic acid sodium salt
 
20 μg/ml, CoA transferase.
 
     Preparation of α-hydromuconic acid: Preparation of α-hydromuconic acid can be performed according to a method described in Reference Example 1 of WO 2016/199858 A1. 
     Identification of CoA transferase activity using α-hydromuconic acid as a substrate: A PCR using the genomic DNA of a subject microorganism strain as a template is performed in accordance with routine procedures, to amplify a nucleic acid encoding a CoA transferase in the full-length form. The amplified fragment is inserted into the KpnI site of pRSF-1b (manufactured by Novagen), an expression vector for  E. coli , in-frame with the histidine-tag sequence. The plasmid is introduced into  E. coli  BL21 (DE3), and expression of the enzyme is induced with isopropyl-β-thiogalactopyranoside (IPTG) in accordance with routine procedures and the enzyme is purified using the histidine tag from the culture fluid to obtain a CoA transferase solution. The solution is used to prepare an enzymatic reaction solution with the following composition, which is allowed to react at 30° C. for 10 minutes and then filtered through a UF membrane (Amicon Ultra-0.5 mL 10K; manufactured by Merck Millipore) to remove the enzyme. The CoA transferase activity can be confirmed by detecting 2,3-dehydroadipyl-CoA in the resulting filtrate on high-performance liquid chromatograph-tandem mass spectrometer (LC-MS/MS) (Agilent Technologies, Inc.). 
     100 mM Tris-HCl (pH 8.0) 
     10 mM MgCl 2    
     0.4 mM succinyl-CoA
 
2 mM α-hydromuconic acid sodium salt
 
20 μg/mL CoA transferase.
 
     Identification of CoA transferase activity using adipic acid as a substrate: A PCR using the genomic DNA of a subject microorganism strain as a template is performed in accordance with routine procedures, to amplify a nucleic acid encoding a CoA transferase in the full-length form. The amplified fragment is inserted into the KpnI site of pRSF-1b (manufactured by Novagen), an expression vector for  E. coli , in-frame with the histidine-tag sequence. The plasmid is introduced into  E. coli  BL21 (DE3), and expression of the enzyme is induced with isopropyl-β-thiogalactopyranoside (IPTG) in accordance with routine procedures and the enzyme is purified using the histidine tag from the culture fluid to obtain a CoA transferase solution. The solution is used to prepare an enzymatic reaction solution with the following composition, which is allowed to react at 30° C. for 10 minutes and then filtered through a UF membrane (Amicon Ultra-0.5 mL 10K; manufactured by Merck Millipore) to remove the enzyme. The CoA transferase activity can be confirmed by detecting adipyl-CoA in the resulting filtrate on high-performance liquid chromatograph-tandem mass spectrometer (LC-MS/MS) (Agilent Technologies, Inc.). 
     100 mM Tris-HCl (pH 8.0) 
     10 mM MgCl 2    
     0.4 mM succinyl-CoA
 
2 mM adipic acid sodium salt
 
20 μg/mL CoA-transferase.
 
     Whether or not an enzyme originally expressed in a host microorganism used in the present invention has CoA transferase activity can be determined by adding 0.05 mL of the CFE, instead of purified CoA transferase, to a total of 0.1 mL of the enzymatic reaction solution and performing the above-described measurement. The specific CFE preparation method targeted to  E. coli  is as described for that used in determination of acyl transferase activity. 
     Either the polypeptides described in (a) to (c) or the 3-hydroxybutyryl-CoA dehydrogenase in the present invention is characterized by having higher activity than 3-oxoadipyl-CoA reductases used in conventional techniques. In this respect, the phrase “higher activity” refers to production of 3-hydroxyadipic acid, α-hydromuconic acid, or adipic acid with a higher yield in a genetically modified microorganism expressing any one of the polypeptides than in a genetically modified microorganism expressing a conventional 3-oxoadipyl-CoA reductase when those microorganisms are derived from the same host microorganism species and are cultured under the same expression conditions in a culture medium containing a carbon source as a material for fermentation. In this respect, the yield of 3-hydroxyadipic acid is calculated according to the formula (3). The yield of α-hydromuconic acid or adipic acid is calculated according to the formula (3), where 3-hydroxyadipic acid is replaced by α-hydromuconic acid or adipic acid, respectively. 
       Yield (%)=amount of formed 3-hydroxyadipic acid (mol)/amount of consumed carbon source (mol)×100   (3)
 
     The specific method to confirm the higher activity of either the polypeptides described in (a) to (c) or the 3-hydroxybutyryl-CoA dehydrogenase in the present invention compared to the activity of 3-oxoadipyl-CoA reductases used in conventional techniques is as follows. The pBBR1MCS-2 vector, which is able to self-replicate in  E. coli  (ME Kovach, (1995), Gene 166: 175-176), is cleaved with XhoI to obtain pBBR1MCS-2/XhoI. To integrate a constitutive expression promoter into the vector, an upstream 200-b region of gapA (NCBI Gene ID: NC_000913.3) is amplified by PCR using the genomic DNA of  Escherichia coli  K-12 MG1655 as a template in accordance with routine procedures (for example, primers represented by SEQ ID NOs: 18 and 19 are used), and the resulting fragment and the pBBR1MCS-2/XhoI are ligated together using the In-Fusion HD Cloning Kit (manufactured by Clontech) to obtain the plasmid pBBR1MCS-2::Pgap. The pBBR1MCS-2::Pgap is cleaved with ScaI to obtain pBBR1MCS-2::Pgap/ScaI. A nucleic acid encoding an acyl transferase in the full length form is amplified by PCR in accordance with routine procedures (for example, primers represented by SEQ ID NOs: 21 and 22 are used), and the resulting fragment and the pBBR1MCS-2::Pgap/ScaI are ligated together using the In-Fusion HD Cloning Kit to obtain the plasmid pBBR1MCS-2::AT. The pBBR1MCS-2::AT is cleaved with HpaI to obtain pBBR1MCS-2::AT/HpaI. A nucleic acid encoding a CoA transferase in the full length form is amplified by PCR in accordance with routine procedures (for example, primers represented by SEQ ID NOs: 25 and 26 are used), and the resulting fragment and the pBBR1MCS-2::AT/HpaI are ligated together using the In-Fusion HD Cloning Kit to obtain the plasmid pBBR1MCS-2::ATCT. 
     On the other hand, the pACYCDuet-1 expression vector (manufactured by Novagen), which is able to self-replicate in  E. coli , is cleaved with BamHI to obtain pACYCDuet-1/BamHI. A nucleic acid encoding a polypeptide represented by any one of SEQ ID NOs: 1 to 16 or 70 to 138, or encoding a conventionally used 3-oxoadipyl-CoA reductase, is amplified by PCR in accordance with routine procedures (for example, primers represented by SEQ ID NOs: 31 and 32 are used), and the resulting fragment and the pACYCDuct-1/BamHI are ligated together using the In-Fusion HD Cloning Kit (manufactured by Clontech) to obtain a plasmid for expression of the polypeptide represented by any one of SEQ ID NOs: 1 to 16 or 70 to 138, or expression of the conventionally used 3-oxoadipyl-CoA reductase. 
     The obtained plasmid and the pBBR1MCS-2::ATCT are introduced into  E. coli  strain BL21 (DE3) by electroporation (N M Calvin, P C Hanawalt. J. Bacteriol, 170 (1988), pp. 2796-2801). A loopful of the strain after the introduction is inoculated into 5 mL of the culture medium I (10 g/L Bacto Tryptone (manufactured by Difco Laboratories), 5 g/L Bacto Yeast Extract (manufactured by Difco Laboratories), 5 g/L sodium chloride, 25 μg/mL, kanamycin, and 15 μg/mL chloramphenicol) adjusted to pH 7, and incubated at 30° C. with shaking at 120 min −1  for 18 hours. Subsequently, 0.25 mL of the culture fluid is added to 5 mL of the culture medium II (10 g/L succinic acid, 10 g/L glucose, 1 g/L ammonium sulfate, 50 mM potassium phosphate, 0.025 g/L magnesium sulfate, 0.0625 mg/L iron sulfate, 2.7 mg/L manganese sulfate, 0.33 mg/L calcium chloride, 1.25 g/L sodium chloride, 2.5 g/L Bacto Tryptone, 1.25 g/L Bacto Yeast Extract, 25 μg/mL kanamycin, 15 μg/mL chloramphenicol, and 0.01 mM IPTG) adjusted to pH 6.5, and incubated at 30° C. with shaking at 120 min −1  for 24 hours. The supernatant separated from bacterial cells by centrifugation of the culture fluid is processed by membrane treatment using Millex-GV (0.22 μm; PVDF; manufactured by Merck KGaA), and the resulting filtrate is analyzed to measure the 3-hydroxyadipic acid and carbon source concentrations in the culture supernatant. Quantitative analysis of 3-hydroxyadipic acid on LC-MS/MS is performed under the following conditions.
         HPLC: 1290 Infinity (manufactured by Agilent Technologies, Inc.)
 
Column: Synergi hydro-RP (manufactured by Phenomenex Inc.), length: 100 mm, internal diameter: 3 mm, particle size: 2.5 μm
 
Mobile phase: 0.1% aqueous formic acid solution/methanol=70/30
 
Flow rate: 0.3 mL/min
 
Column temperature: 40° C.
 
LC detector: DAD (210 nm)
   MS/MS: Triple-Quad LC/MS (manufactured by Agilent Technologies, Inc.) Ionization method: ESI in negative mode.       

     Quantitative analysis of carbon sources, such as sugars and succinic acid, on HPLC is performed under the following conditions.
         HPLC: Shimadzu Prominence (manufactured by Shimadzu Corporation)
 
Column: Shodex Sugar SH1011 (manufactured by Showa Denko K.K.), length: 300 mm, internal diameter: 8 mm, particle size: 6 μm
 
Mobile phase: 0.05M aqueous sulfuric acid solution
 
Flow rate: 0.6 mL/min
 
Column temperature: 65° C.
       

     Detector: RI. 
     When a nucleic acid encoding any one selected from the group of the acyl transferase, the CoA transferase, the enoyl-CoA hydratase, and the enoyl-CoA reductase is introduced into a host microorganism in the present invention, the nucleic acid may be artificially synthesized based on the amino acid sequence information of the enzyme in a database, or isolated from the natural environment. In cases where the nucleic acid is artificially synthesized, the usage frequency of codons corresponding to each amino acid in the nucleic acid sequence may be changed depending on the host microorganism into which the nucleic acid is introduced. 
     In the present invention, the method of introducing a nucleic acid encoding any one selected from the group of the acyl transferase, the CoA transferase, the enoyl-CoA hydratase, and the enoyl-CoA reductase into the host microorganism method is not limited to a particular method; for example, a method in which the nucleic acid is integrated into an expression vector capable of autonomous replication in the host microorganism and then introduced into the host microorganism, a method in which the nucleic acid is integrated into the genome of the host microorganism, and the like can be used. 
     In cases where nucleic acids encoding the enzymes are isolated from the natural environment, the organisms as sources of the genes are not limited to particular organisms, and examples of the organisms include those of the genus  Acinetobacter , such as  Acinetobacter baylyi  and  Acinetobacter radioresistens ; the genus  Aerobacter , such as  Aerobacter cloacae ; the genus  Alcaligenes , such as  Alcaligenes faecalis ; the genus  Bacillus , such as  Bacillus badius, Bacillus magaterium , and  Bacillus roseus ; the genus  Brevibacterium , such as  Brevibacterium iodinum ; the genus  Corynebacterium , such as  Corynebacterium acetoacidophilum, Corynebacterium acetoglutamicum, Corynebacterium ammoniagenes , and  Corynebacterium glutamicum ; the genus  Cupriavidus , such as  Cupriavidus metallidurans, Cupriavidus necator, Cupriavidus numazuensis , and  Cupriavidus oxalaticus ; the genus  Delftia , such as  Delftia acidovorans ; the genus  Escherichia , such as  Escherichia coli  and  Escherichia fergusonii ; the genus  Hafnia , such as  Hafnia alvei ; the genes  Microbacterium , such as  Microbacterium ammoniaphilum ; the genus  Nocardioides , such as  Nocardioides albus ; the genus  Planomicrobium , such as  Planomicrobium okeanokoites ; the genus  Pseudomonas , such as  Pseudomonas azotoformans. Pseudomonas chlororaphis, Pseudomonas fluorescens, Pseudomonas fragi, Pseudomonas putida , and  Pseudomonas reptilivora ; the genus  Rhizobium , such as  Rhizobium radiobacter ; the genus  Rhodosporidium , such as  Rhodosporidium toruloides ; the genus  Saccharomyces , such as  Saccharomyces cerevisiae ; the genus  Serratia , such as  Serratia entomophila, Serratia ficaria, Serratia fonticola, Serratia grimesii, Serratia nematodiphila, Serratia odorifera , and  Serratia plymuthica ; the genus  Shimwellia , such as  Shimwellia blattae ; the genus  Streptomyces , such as  Streptomyces vinaceus, Streptomyces karnatakensis, Streptomyces olivaceus , and  Streptomyces vinaceus ; the genus  Yarrowia , such as  Yarrowia lipolytica ; the genus  Yersinia , such as  Yersinia ruckeri ; the genus  Euglena , such as  Euglena gracilis ; and the genus  Thermobifida , such as  Thermobifida fusca ; preferably those of the genera  Acinetobacter, Corynebacterium, Escherichia, Pseudomonas, Serratia, Euglena , and  Thermobifida.    
     When a nucleic acid encoding a polypeptide expressed in the present invention is integrated into an expression vector or the genome of a host microorganism, the nucleic acid being integrated into the expression vector or the genome is preferably composed of a promoter, a ribosome-binding sequence, a nucleic acid encoding the polypeptide to be expressed, and a transcription termination sequence, and may additionally contain a gene that controls the activity of the promoter. 
     The promoter used in the present invention is not limited to a particular promoter, provided that the promoter drives expression of the enzyme in the host microorganism; examples of the promoter include gap promoter, trp promoter, lac promoter, tac promoter, and T7 promoter. 
     In cases where an expression vector is used in the present invention to introduce the nucleic acid or to enhance the expression of the polypeptide, the expression vector is not limited to a particular vector, provided that the vector is capable of autonomous replication in the microorganism; examples of the vector include pBBR1MCS vector, pBR322 vector, pMW vector, pET vector, pRSF vector, pCDF vector, pACYC vector, and derivatives of the above vectors. 
     In cases where a nucleic acid for genome integration is used in the present invention to introduce the nucleic acid or to enhance the expression of the polypeptide, the nucleic acid for genome integration is introduced by site-specific homologous recombination. The method for site-specific homologous recombination is not limited to a particular method, and examples of the method include a method in which λ Red recombinase and FLP recombinase are used (Proc Natl Acad Sci U.S.A. 2000 Jun. 6; 97 (12): 6640-6645.), and a method in which. Red recombinase and the sacB gene are used (Biosci Biotechnol Biochem. 2007 December; 71 (12):2905-11.). 
     The method of introducing the expression vector or the nucleic acid for genome integration is not limited to a particular method, provided that the method is for introduction of a nucleic acid into a microorganism; examples of the method include the calcium ion method (Journal of Molecular Biology, 53, 159 (1970)), and electroporation (N M Calvin, P C Hanawalt. J. Bacteriol, 170 (1988), pp. 2796-2801). 
     In the present invention, a genetically modified microorganism in which a nucleic acid encoding a 3-oxoadipyl-CoA reductase is introduced or expression of the corresponding polypeptide is enhanced is cultured in a culture medium, preferably a liquid culture medium, containing a carbon source as a material for fermentation which can be used by ordinary microorganisms. The culture medium used contains, in addition to the carbon source that can be used by the genetically modified microorganism, appropriate amounts of a nitrogen source, inorganic salts, and, if necessary, organic trace nutrients such as amino acids and vitamins. Any of natural and synthetic culture media can be used as long as the medium contains the above-described nutrients. 
     The material for fermentation is a material that can be metabolized by the genetically modified microorganism. The term “metabolize” refers to conversion of a chemical substance, which a microorganism has taken up from the extracellular environment or intracellularly generated from a different chemical substance, to another chemical substance through an enzymatic reaction. Sugars can be suitably used as the carbon source. Specific examples of the sugars include monosaccharides, such as glucose, sucrose, fructose, galactose, mannose, xylose, and arabinose; disaccharides and polysaccharides formed by linking these monosaccharides; and saccharified starch solution, molasses, and saccharified solution from cellulose-containing biomass, each containing any of those saccharides. 
     Other than the above sugars, succinic acid, a substrate of the CoA transferase, can also be added to the culture medium for efficient production of 3-hydroxyadipic acid, α-hydromuconic acid, and/or adipic acid. 
     The above-listed carbon sources may be used individually or in combination. When a carbon source is added, the concentration of the carbon source in the culture medium is not particularly limited, and can be appropriately selected depending on the type of the carbon source: in the case of sugars, the concentration is preferably from 5 g/L to 300 g/L; in the case of succinic acid, the concentration is preferably from 0.1 g/L to 100 g/L. 
     As the nitrogen source used for culturing the genetically modified microorganism, for example, ammonia gas, aqueous ammonia, ammonium salts, urea, nitric acid salts, other supportively used organic nitrogen sources, such as oil cakes, soybean hydrolysate, casein degradation products, other amino acids; vitamins, corn steep liquor, yeast or yeast extract, meat extract, peptides such as peptone, and bacterial cells and hydrolysate of various fermentative bacteria can be used. The concentration of the nitrogen source in the culture medium is not particularly limited, and is preferably from 0.1 g/L to 50 g/L. 
     As the inorganic salts used for culturing the genetically modified microorganism, for example, phosphoric acid salts, magnesium salts, calcium salts, iron salts, and manganese salts can be appropriately added to the culture medium and used. 
     The culture conditions for the genetically modified microorganism to produce 3-hydroxyadipic acid, α-hydromuconic acid, and/or adipic acid are set by appropriately adjusting or selecting, for example, the culture medium with the above composition, culture temperature, stirring speed, pH, aeration rate, and inoculation amount, depending on, for example, the species of the genetically modified microorganism and external conditions. In cases where foam is formed in a liquid culture, an antifoaming agent such as a mineral oil, silicone oil, or surfactant may be appropriately added to the culture medium. 
     After a recoverable amount of 3-hydroxyadipic acid, α-hydromuconic acid, and/or adipic acid is produced during culturing of the microorganism, the produced products can be recovered. The produced products can be recovered, for example isolated, according to a commonly used method, in which the culturing is stopped once a product of interest is accumulated to an appropriate level, and the fermentation product is collected from the culture. Specifically, the products can be isolated from the culture by separation of bacterial cells through, for example, centrifugation or filtration prior to, for example, column chromatography, ion exchange chromatography, activated charcoal treatment, crystallization, membrane separation, or distillation. More specifically, examples include, but are not limited to, a method in which an acidic component is added to salts of the products, and the resulting precipitate is collected; a method in which water is removed from the culture by concentration using, for example, a reverse osmosis membrane or an evaporator to increase the concentrations of the products and the products and/or salts of the products are then crystallized and precipitated by cooling or adiabatic crystallization to recover the crystals of the products and/or salts of the products by, for example, centrifugation or filtration; and a method in which an alcohol is added to the culture to produce esters of the products and the resulting esters of the products are subsequently collected by distillation and then hydrolyzed to recover the products. These recovery methods can be appropriately selected and optimized depending on, for example, physical properties of the products. 
     EXAMPLES 
     The present invention will now be specifically described by way of Examples. 
     Reference Example 1 
     Production of a Plasmid for Expression of an Enzyme Catalyzing a Reaction to Generate 3-Oxoadipyl-CoA and Coenzyme a from Acetyl-CoA and Succinyl-CoA (the Reaction A) and an Enzyme Catalyzing a Reaction to Generate 3-Hydroxyadipic Acid from 3-Hydroxyadipyl-CoA (the Reaction E) and a Reaction to Generate α-Hydromuconic Acid from 2,3-Dehydroadipyl-CoA (the Reaction F) 
     The pBBR1MCS-2 vector, which is capable of autonomous replication in  E. coli  (ME Kovach, (1995), Gene 166: 175-176), was cleaved with XhoI to obtain pBBR1MCS-2/XhoI. To integrate a constitutive expression promoter into the vector, primers (SEQ ID NOs: 18 and 19) were designed for use in amplification of an upstream 200-b region (SEQ ID NO: 17) of gapA (NCBI Gene ID: NC_000913.3) by PCR using the genomic DNA of  Escherichia coli  K-12 MG1655 as a template, and a PCR reaction was performed in accordance with routine procedures. The resulting fragment and the pBBR1MCS-2/XhoI were ligated together using the In-Fusion HI) Cloning Kit (manufactured by Clontech), and the resulting plasmid was introduced into  E. coli  strain DH5a. The nucleotide sequence on the plasmid extracted from the obtained recombinant  E. coli  strain was confirmed in accordance with routine procedures, and the plasmid was designated as pBBR1MCS-2::Pgap. Then, the pBBR1MCS-2::Pgap was cleaved with ScaI to obtain pBBR1MCS-2::Pgap/ScaI. To amplify a gene encoding an enzyme catalyzing the reaction A, primers (SEQ ID NOs: 21 and 22) were designed for use in amplification of the full length of the acyl transferase gene pcaF (NCBI Gene ID: 1041755; SEQ ID NO: 20) by PCR using the genomic DNA of  Pseudomonas putida  strain KT2440 as a template, and a PCR reaction was performed in accordance with routine procedures. The resulting fragment and the pBBR1MCS-2::Pgap/ScaI were ligated together using the In-Fusion HD Cloning Kit, and the resulting plasmid was introduced into  E. coli  strain DH5a. The nucleotide sequence on the plasmid isolated from the obtained recombinant strain was confirmed in accordance with routine procedures, and the plasmid was designated as pBBR1MCS-2::AT. Then, the pBBR1MCS-2::AT was cleaved with HpaI to obtain pBBR1MCS-2::AT/HpaI. To amplify a gene encoding an enzyme catalyzing the reactions E and F, primers (SEQ ID NOs: 25 and 26) were designed for use in amplification of a continuous sequence including the full lengths of genes together encoding a CoA transferase, pcaI and pcaJ (NCBI Gene IDs: 1046613 and 1046612, SEQ ID NOs: 23, 24), by PCR using the genomic DNA of  Pseudomonas putida  strain KT2440 as a template, and a PCR reaction was performed in accordance with routine procedures. The resulting fragment and the pBBR1MCS-2::AT/HpaI were ligated together using the In-Fusion HD Cloning Kit. and the resulting plasmid was introduced into  E. coli  strain DH5α. The nucleotide sequence on the plasmid isolated from the obtained recombinant strain was confirmed in accordance with routine procedures, and the plasmid was designated as pBBR1MCS-2::ATCT. 
     Reference Example 2 
     Production of Plasmids for Expression of Polypeptides Represented by SEQ ID NOs: 1, 2, 3, 4, 5, 6, and 213 
     The pACYCDuet-1 expression vector (manufactured by Novagen), which is capable of autonomous replication in  E. coli , was cleaved with BamHI to obtain pACYCDuet-1/BamHI. To amplify a nucleic acid encoding a polypeptide represented by SEQ ID NO: 1, primers (SEQ ID NOs: 31 and 32) were designed for use in amplification of a nucleic acid represented by SEQ ID NO: 54 using the genomic DNA of  Serratia marcescens  strain ATCC 13880 as a template, and a PCR reaction was performed in accordance with routine procedures. To amplify a nucleic acid encoding a polypeptide represented by SEQ ID NO: 2, primers (SEQ ID NOs: 33 and 34) were designed for use in amplification of a nucleic acid represented by SEQ ID NO: 55 using the genomic DNA of  Serratia nematodiphila  strain DSM21420 as a template, and a PCR reaction was performed in accordance with routine procedures. To amplify a nucleic acid encoding a polypeptide represented by SEQ ID NO: 3, primers (SEQ ID NOs: 35 and 36) were designed for use in amplification of a nucleic acid represented by SEQ ID NO: 56 using the genomic DNA of  Serratia plymuthica  strain NBRC102599 as a template, and a PCR reaction was performed in accordance with routine procedures. To amplify a nucleic acid encoding a polypeptide represented by SEQ ID NO: 4, primers (SEQ ID NOs: 37 and 38) were designed for use in amplification of a nucleic acid represented by SEQ ID NO: 57 using the genomic DNA of  Serratia proteamaculans  strain 568 as a template, and a PCR reaction was performed in accordance with routine procedures. To amplify a nucleic acid encoding a polypeptide represented by SEQ ID NO: 5, primers (SEQ ID NOs: 215 and 216) were designed for use in amplification of a nucleic acid represented by SEQ ID NO: 58 using the genomic DNA of  Serratia ureilytica  strain Lr5/4 as a template, and a PCR reaction was performed in accordance with routine procedures. To amplify a nucleic acid encoding a polypeptide represented by SEQ ID NO: 6, primers (SEQ ID NOs: 217 and 218) were designed for use in amplification of a nucleic acid represented by SEQ ID NO: 59 using the genomic DNA of  Serratia  sp. strain BW106 as a template, and a PCR reaction was performed in accordance with routine procedures. To amplify a nucleic acid encoding a polypeptide represented by SEQ ID NO: 213, primers (SEQ ID NOs: 219 and 220) were designed for use in amplification of a nucleic acid represented by SEQ ID NO: 214 using the genomic DNA of  Serratia liquefaciens  strain FK01 as a template, and a PCR reaction was performed in accordance with routine procedures. Each of the obtained fragments and the pACYCDuet-1/BamHI were ligated together using the In-Fusion HD Cloning Kit (manufactured by Clontech), and each of the resulting plasmids was introduced into  E. coli  strain DH5α. The nucleotide sequences on the plasmids isolated from the obtained recombinant strains were confirmed in accordance with routine procedures. The expression of the 3-oxoadipyl-CoA reductase gene integrated into each of the plasmids is induced by IPTG, which resulted in addition of 14 extra amino acids including a histidine tag to the N terminus of the expressed polypeptide. 
     The plasmid for expression of the polypeptide represented by SEQ ID NO: 1 is designated as “pACYCDuet-1::Smr1”; the plasmid for expression of the polypeptide represented by SEQ ID NO: 2 is designated as “pACYCDuet-1::Snm1”; the plasmid for expression of the polypeptide represented by SEQ ID NO: 3 is designated as “pACYCDuet-1::Spl1”; the plasmid for expression of the polypeptide represented by SEQ ID NO: 4 is designated as “pACYCDuet-1::Spe1”; the plasmid for expression of the polypeptide represented by SEQ ID NO: 5 is designated as “pACYCDuet-1:Sur1”: the plasmid for expression of the polypeptide represented by SEQ ID NO: 6 is designated as “pACYCDuet-1::Ssp1”; and the plasmid for expression of the polypeptide represented by SEQ ID NO: 213 is designated as “pACYCDuet-1::Slq1”. The information about these plasmids is presented in Table 6. 
     Reference Example 3 
     Production of Plasmids for Expression of 3-Oxoadipyl-CoA Reductase 
     Other than plasmids for expression of the polypeptides described in (a) to (c) according to the present invention, plasmids for expression of four different enzymes, each of which catalyzes a reduction reaction to generate 3-hydroxyacyl-CoA from 3-oxoacyl-CoA used as a substrate, were produced. Four genes, namely paaH from  Pseudomonas putida  strain KT2440 (SEQ ID NO: 27), paaH from  Escherichia coli  str. K-12 substr. MG1655 (SEQ ID NO: 28), dcaH from  Acinetobacter baylyi  strain ADP1 (SEQ ID NO: 29), and paaH from  Serratia plymuthica  strain NBRC102599 (SEQ ID NO: 30), were used. The plasmids were produced in the same manner as in Reference Example 2, except that primers (SEQ ID NOs: 39 and 40) for amplification of a nucleic acid represented by SEQ ID NO: 27, primers (SEQ ID NOs: 41 and 42) for amplification of a nucleic acid represented by SEQ ID NO: 28, primers (SEQ ID NOs: 43 and 44) for amplification of a nucleic acid represented by SEQ ID NO: 29, and primers (SEQ ID NOs: 45 and 46) for amplification of a nucleic acid represented by SEQ ID NO: 30 were used. 
     The plasmid for expression of the polypeptide encoded by the nucleic acid represented by SEQ ID NO: 27 is designated as “pACYCDuet-1::Ppu1”; the plasmid for expression of the polypeptide encoded by the nucleic acid represented by SEQ ID NO: 28 is designated as “pACYCDuet-1::Eco1”; the plasmid for expression of the polypeptide encoded by the nucleic acid represented by SEQ ID NO: 29 is designated as “pACYCDuct-1::Aci1”; and the plasmid for expression of the polypeptide encoded by the nucleic acid represented by SEQ ID NO: 30 is designated as “pACYCDuet-1::Spl2”. The information about these plasmids is presented in Table 6. 
     
       
         
           
               
               
               
               
             
               
                 TABLE 6 
               
               
                   
               
               
                   
                   
                   
                 SEQ  
               
               
                   
                   
                   
                 ID  
               
               
                 Plasmid  
                 Source organism  
                 Gene ID  
                 NO 
               
               
                   
               
             
            
               
                   
               
            
           
           
               
               
               
               
            
               
                 pACYCDuct-1::Smr1  
                 
                   Serratia marcescens  
                 
                 JMPQ01000047.1  
                 54  
               
               
                   
                 ATCC 13880  
                   
                   
               
               
                 pACYCDuet-1::Snm1  
                 
                   Serratia 
                   nematodiphila  
                 
                 JPUX00000000.1  
                 55  
               
               
                   
                 DSM21420  
                   
                   
               
               
                 pACYCDuet-1::Spl1  
                 
                   Serratia 
                   plymuthica 
                 
                 BCTU01000013.1  
                 56  
               
               
                   
                 NBRC102599  
                   
                   
               
               
                 pACYCDuet-1::Spe1  
                 
                   Serratia  
                 
                 CP000826.1  
                 57  
               
               
                   
                   proteamaculans  568  
                   
                   
               
               
                 pACYCDuct-1::Ppu1  
                 
                   Pseudomonas 
                   putida  
                 
                 NC_002947.4  
                 27  
               
               
                   
                 KT2440  
                   
                   
               
               
                 pACYCDuet-1::Eco1  
                   Escherichia   coli  str.  
                 NC_000913.3  
                 28  
               
               
                   
                 K-12 substr. MG1655  
                   
                   
               
               
                 pACYCDuet-1::Aci1  
                 
                   Acinetobacter baylyi  
                 
                 CR543861.1  
                 29  
               
               
                   
                 ADP1  
                   
                   
               
               
                 pACYCDuet-1::Spl2  
                 
                   Serratia 
                   plymuthica  
                 
                 NZ_  
                 30  
               
               
                   
                 NBRC102599  
                 BCTU01000001.1  
                   
               
               
                 pACYCDuet-1::Sur1  
                 
                   Serratia 
                   ureilytica  
                 
                 JSFB01000001  
                 58  
               
               
                   
                 Lr5/4  
                   
                   
               
               
                 pACYCDuet-1::Ssp1  
                   Serratia  sp. BW106  
                 MCGS01000002.1  
                 59  
               
               
                 pACYCDuet-1::Slq1  
                 
                   Serratia 
                   liquefaciens  
                 
                 CP006252.1  
                 214  
               
               
                   
                 FK01 
               
               
                   
               
            
           
         
       
     
     Example 1 
     Generation of  E. coli  Strains Having an Ability to Produce 3-Hydroxyadipic Acid by Introduction of Each of the Nucleic Acids Encoding the Polypeptides Represented by SEQ ID NOs: 1, 2, 3, 4, 5, 6, and 213 
     The plasmid pBBR1MCS-2::ATCT produced in Reference Example 1 was introduced into  E. coli  strain BL21 (DE3) by electroporation (N M Calvin, P C Hanawalt. J. Bacteriol, 170 (1988), pp. 2796-2801). The strain after the introduction was cultured on LB agar medium containing 25 μg/mL of kanamycin at 37° C. The obtained recombinant strain was designated as BL2 I (DE3)/pBBR1MCS-2::ATCT. 
     Next, each of the seven plasmids produced in Reference Example 2 was individually introduced into the BL21 (DE3)/pBBR1MCS-2::ATCT by electroporation. Each of the strains after the introduction was cultured on LB agar medium containing 25 μg/mL kanamycin and 15 μg/mL chloramphenicol at 37° C. The recombinant strain in which “pACYCDuet-1::Smr1” is introduced is designated as “Ec/Smr1_3HA”; the recombinant strain in which “pACYCDuet-1::Snm1” is introduced is designated as “Ec/Snm1_3HA”; the recombinant strain in which “pACYCDuet-1::Spl1” is introduced is designated as “Ec/Spl1_3HA”; the recombinant strain in which “pACYCDuet-1::Spe1” is introduced is designated as “Ec/Spe1_3HA”; the recombinant strain in which “pACYCDuct-1::Sur1” is introduced is designated as “Ec/Sur1_3HA”; the recombinant strain in which “pACYCDuet-1::Ssp1” is introduced is designated as “Ec/Ssp1_3HA”; and the recombinant strain in which “pACYCDuet-1::Slq1” is introduced is designated as “Ec/Slq1_3HA”. The information about the recombinant strains obtained in this example is presented in Table 7. 
     Comparative Example 1 
     Generation of  E. coli  Strains Having an Ability to Produce 3-Hydroxyadipic Acid by Introduction of Each of the Nucleic Acids Encoding 3-Oxoadipyl-CoA Reductases 
     The plasmid pBBR1MCS-2::ATCT produced in Reference Example 1 was introduced into  E. coli  strain BL21 (DE3) by electroporation (N M Calvin, P C Hanawalt. J. Bacteriol, 170 (1988), pp. 2796-2801). The strain after the introduction was cultured on LB agar medium containing 25 μg/mL kanamycin at 37° C. The obtained recombinant strain was designated as BL21 (DE3)/pBBR1MCS-2::ATCT. 
     Next, each of the four plasmids produced in Reference Example 3 was individually introduced into the BL21 (DE3)/pBBR1MCS-2::ATCT by electroporation. Each of the strains after the introduction was cultured on LB agar medium containing 25 μg/mL kanamycin and 15 μg/mL chloramphenicol at 37° C. 
     The recombinant strain in which “pACYCDuet-1::Ppu1” is introduced is designated as “Ec/Ppu1_3HA”; the recombinant strain in which “pACYCDuct-1::Eco1” is introduced is designated as “Ec/Eco1_3HA”; the recombinant strain in which “pACYCDuet-1::Aci1” is introduced is designated as “Ec/Aci1_3HA”; and the recombinant strain in which “pACYCDuet-1::Spl2” is introduced is designated as “Ec/Spl2_3HA”. The information about the recombinant strains obtained in this comparative example is presented in Table 7. 
     Example 2 
     Test for 3-Hydroxyadipic Acid Production Using the  E. coli  Strains Having an Ability to Produce 3-Hydroxyadipic Acid by Introduction of Each of the Nucleic Acids Encoding the Polypeptides Represented by SEQ ID NOs: 1, 2, 3, 4, 5, 6, and 213 
     The recombinant  E. coli  strains produced in Example 1 were used to perform a test for 3-hydroxyadipic acid production. 
     A loopful of each recombinant strain produced in Example 1 was inoculated into 5 mL of the culture medium 1 (10 g/L Bacto Tryptone (manufactured by Difco Laboratories), 5 g/l, Bacto Yeast Extract (manufactured by Difco Laboratories), 5 g/L sodium chloride, 25 μg/mL kanamycin, and 15 μg/mL chloramphenicol) adjusted to pH 7, and incubated at 30° C. with shaking at 120 min −1  for 18 hours. Subsequently, 0.25 mL of the culture fluid was added to 5 mL of the culture medium II (10 g/L succinic acid, 10 g/L glucose, 1 g/L ammonium sulfate, 50 mM potassium phosphate, 0.025 g/L magnesium sulfate, 0.0625 mg/L iron sulfate, 2.7 mg/L manganese sulfate, 0.33 mg/L calcium chloride, 1.25 g/L sodium chloride, 2.5 g/L Bacto Tryptone, 1.25 g/L Bacto Yeast Extract, 25 μg/mL kanamycin, 15 μg/mL chloramphenicol, and 0.01 mM IPTG) adjusted to pH 6.5, and incubated at 30° C. with shaking at 120 min −1  for 24 hours. 
     Quantitative Analyses of 3-Hydroxyadipic Acid and Carbon Sources 
     The supernatant separated from bacterial cells by centrifugation of the culture fluid was processed by membrane treatment using Millex-GV (0.22 μm; PVDF; manufactured by Merck KGaA), and the resulting filtrate was analyzed according to the following method to measure the accumulated 3-hydroxyadipic acid and carbon source concentrations in the culture supernatant. The results are presented in Table 7. Additionally, the yield of 3-hydroxyadipic acid calculated according to the formula (3) is presented in Table 7. 
     Quantitative analysis of 3-hydroxyadipic acid by LC-MS/MS
         HPLC: 1290 Infinity (manufactured by Agilent Technologies, Inc.)
 
Column: Synergi hydro-RP (manufactured by Phenomenex Inc.), length: 100 mm, internal diameter: 3 mm, particle size: 2.5 μm
 
Mobile phase: 0.1% aqueous formic acid solution/methanol=70/30
 
Flow rate: 0.3 mL/min
 
Column temperature: 40° C.
 
LC detector: DAD (210 nm)
   MS/MS: Triple-Quad LC/MS (manufactured by Agilent Technologies, Inc.) Ionization method: ESI in negative mode.       

     Quantitative Analysis of Sugars and Succinic Acid by HPLC 
     
         
         
           
             HPLC: Shimadzu Prominence (manufactured by Shimadzu Corporation)
 
Column: Shodex Sugar SH1011 (manufactured by Showa Denko K.K.), length: 300 mm, internal diameter: 8 mm, particle size: 6 μm
 
Mobile phase: 0.05M aqueous sulfuric acid solution
 
Flow rate: 0.6 mL/min
 
Column temperature: 65° C.
 
           
         
       
    
     Detector: RI 
     
         
         
           
             HPLC: 1290 Infinity (manufactured by Agilent Technologies, Inc.)
 
Column: Synergi hydro-RP (manufactured by Phenomenex Inc.), length: 100 mm, internal diameter: 3 mm, particle size: 2.5 μm
 
Mobile phase: 0.1% aqueous formic acid solution/methanol=70/30
 
Flow rate: 0.3 mL/min
 
Column temperature: 40° C.
 
LC detector: DAD (210 nm)
 
             MS/MS: Triple-Quad LC/MS (manufactured by Agilent Technologies, Inc.) Ionization method: ESI in negative mode. 
           
         
       
    
     Comparative Example 2 
     Test for 3-Hydroxyadipic Acid Production Using the  E. coli  Strains Having an Ability to Produce 3-Hydroxyadipic Acid by Introduction of Each of the Nucleic Acids Encoding 3-Oxoadipyl-CoA Reductases 
     The results of a test for 3-hydroxyadipic acid production performed in the same manner as in Example 2 by using the  E. coli  strains produced in Comparative Example 1 are presented in Table 7. 
     The results presented in Table 7 indicate that the yield of 3-hydroxyadipic acid was increased in the recombinant strains used in Example 2 compared to that in the recombinant strains used in Comparative Example 2. That is, it was demonstrated that the production of 3-hydroxyadipic acid was much increased by introduction of any of the nucleic acids encoding the polypeptides represented by SEQ ID NOs: 1, 2, 3, 4, 5, 6, and 213 into microorganisms. 
     
       
         
           
               
               
               
               
             
               
                 TABLE 7 
               
               
                   
               
               
                   
                   
                 3HA  
                 3HA  
               
               
                   
                   
                 Concentration  
                 Yield  
               
               
                   
                 Strain  
                 (g/L)  
                 (%) 
               
               
                   
               
             
            
               
                   
               
            
           
           
               
               
               
               
            
               
                 Example 2  
                 Ec/Smr1_3HA  
                 1.65  
                 12.6  
               
               
                   
                 Ec/Snm1_3HA  
                 2.69  
                 18.9  
               
               
                   
                 Ec/Spl1_3HA  
                 2.18  
                 17.0  
               
               
                   
                 Ec/Spe1_3HA  
                 2.72  
                 19.3  
               
               
                   
                 Ec/Sur1_3HA  
                 3.42  
                 25.8  
               
               
                   
                 Ec/Ssp1_3HA  
                 1.94  
                 18.0  
               
               
                   
                 Ec/Slq1_3HA  
                 2.67  
                 21.8  
               
               
                 Comparative  
                 Ec/Ppu1_3HA  
                 0.67  
                 5.7  
               
               
                 Example 2  
                 Ec/Eco1_3HA  
                 0.88  
                 7.2  
               
               
                   
                 Ec/Aci1_3HA  
                 0.82  
                 6.8  
               
               
                   
                 Ec/Spl2_3HA  
                 0.91  
                 7.4 
               
               
                   
               
            
           
         
       
     
     Reference Example 4 
     Production of a plasmid for expression of an enzyme catalyzing a reaction to generate 2,3-dehydroadipyl-CoA from 3-hydroxyadipyl-CoA (the reaction C) 
     The pCDF-1b expression vector (manufactured by Novagen), which is capable of autonomous replication in  E. coli , was cleaved with KpnI to obtain pCDF-1b/KpnI. To amplify a gene encoding an enzyme catalyzing the reaction C, primers (SEQ ID NOs: 48 and 49) were designed for use in amplification of the full length of the enoyl-CoA hydratase gene paaF (NCBI Gene ID: 1046932, SEQ ID NO: 47) by PCR using the genomic DNA of  Pseudomonas putida  strain KT2440 as a template, and a PCR reaction was performed in accordance with routine procedures. The resulting fragment and the pCDF-1b/KpnI were ligated together using the In-Fusion HD Cloning Kit (manufactured by Clontech), and the resulting plasmid was introduced into  E. coli  strain DH5α. The nucleotide sequence on the plasmid extracted from the obtained recombinant strain was confirmed in accordance with routine procedures. The expression of the enoyl-CoA hydratase gene integrated into the plasmid is induced by IPTG, which resulted in addition of 11 extra amino acids including a histidine tag to the N terminus of the expressed polypeptide. The obtained plasmid was designated as “pCDF-1b::EHa.” 
     Example 3 
     Generation of  E. coli  Strains Having an Ability to Produce α-Hydromuconic Acid by Introduction of the Nucleic Acids Encoding the Polypeptides Represented by SEQ ID NOs: 1, 2, 3, 4, 5, 6, and 213 
     The plasmid pCDF-1b::EHa produced in Reference Example 4 was introduced by electroporation into the  E. coli  strain BL21 (DE3)/pBBR1MCS-2::ATCT produced in Example 1. The strain after the introduction was cultured on LB agar medium containing 25 μg/mL kanamycin and 50 μg/mL streptomycin at 37° C. The resulting recombinant strain was designated as BL21 (DE3)/pBBR1MCS-2::ATCT/pCDF-1b::EHa. 
     Next, each of the plasmids produced in Reference Example 2, namely “pACYCDuet-1::Smr1,” “pACYCDuet-1::Snm1”, “pACYCDuet-1::Spl1”, “pACYCDuet-1::Spe1”, “pACYCDuet-1::Sur1”, and “pACYCDuet-1::Ssp1,” “pACYCDuet-1::Slq1,” was individually introduced into the BL21 (DE3)/pBBR1MCS-2::ATCT/pCDF-1b::EHa by electroporation. Each of the strains after the introduction was cultured on LB agar medium containing 25 μg/mL kanamycin, 50 μg/mL streptomycin, and 15 μg/mL chloramphenicol at 37° C. The recombinant strain in which “pACYCDuet-1::Smr1” is introduced is designated as “Ec/Smr1_HMA”: the recombinant strain in which “pACYCDuet-1::Snm1” is introduced is designated as “Ec/Snm1_HMA”; the recombinant strain in which “pACYCDuct-1::Spl1” is introduced is designated as “Ec/Spl1_HMA”: the recombinant strain in which “pACYCDuet-1::Spe1” is introduced is designated as “Ec/Spe1_HMA”; the recombinant strain in which “pACYCDuet-::Sur1” is introduced is designated as “Ec/Sur1_HMA”; the recombinant strain in which “pACYDuet-1::Ssp1” is introduced is designated as “Ec/Ssp1_HMA”; and the recombinant strain in which “pACYCDuet-1::Slq1” is introduced is designated as “Ec/Slq1_HMA”. The information about the recombinant strains obtained in this example is presented in Table 8. 
     Comparative Example 3 
     Generation of  E. coli  Strains Having an Ability to Produce α-Hydromuconic Acid by Introduction of Each of the Nucleic Acids Encoding 3-Oxoadipyl-CoA Reductases 
     The plasmid pCDF-1b::EHa produced in Reference Example 4 was introduced by electroporation into the  E. coli  strain BL21 (DE3)/pBBR1MCS-2::ATCT produced in Reference Example 2. The strain after the introduction was cultured on LB agar medium containing 25 μg/mL kanamycin and 50 μg/mL streptomycin at 37° C. The obtained recombinant strain was designated as BL21 (DE3)/pBBR1MCS-2::ATCT/pCDF-1b::EHa. 
     Next, each of the plasmids produced in Reference Example 3, namely “pACYCDuet-1::Ppu1,” “pACYCDuet-1::Eco1,” “pACYCDuet-1::Aci1,” and “pACYDuet-1::Spl2,” was individually introduced into the BL21 (DE3)/pBBR1MCS-2::ATCT/pCDF-1b::EHa by electroporation. Each of the strains after the introduction was cultured on LB agar medium containing 25 μg/mL kanamycin, 50 μg/mL streptomycin, and 15 μg/mL chloramphenicol at 37° C. 
     The recombinant strain in which “pACYCDuet-1::Ppu1” is introduced is designated as “Ec/Ppu1_HMA”; the recombinant strain in which “pACYCDuet-1::Eco1” is introduced is designated as “Ec/Eco1_HMA”: the recombinant strain in which “pACYCDuet-1::Aci1” is introduced is designated as “Ec/Aci1_HMA”; and the recombinant strain in which “pACYCDuet-1::Spl2” is introduced is designated as “Ec/Spl2_HMA”. The information about the recombinant strains obtained in this comparative example is presented in Table 8. 
     Example 4 
     Test for α-Hydromuconic Acid Production Using the  E. coli  Strains Having an Ability to Produce α-Hydromuconic Acid by Introduction of the Nucleic Acids Encoding the Polypeptides Represented by SEQ ID NOs: 1, 2, 3, 4, 5, 6, and 213 
     The  E. coli  strains produced in Example 3 were used to perform a test for α-hydromuconic acid production. A loopful of each recombinant  E. coli  strain produced in Example 3 was inoculated into 5 mL of the culture medium I (10 g/L Bacto Tryptone (manufactured by Difco Laboratories), 5 g/L Bacto Yeast Extract (manufactured by Difco Laboratories), 5 g/L sodium chloride, 25 μg/mL kanamycin, 50 μg/mL streptomycin, and 15 μg/mL chloramphenicol) adjusted to pH 7, and incubated at 30° C. with shaking at 120 min −1  for 18 hours. Subsequently, 0.25 mL of the culture fluid was added to 5 mL of the culture medium II (10 g/L succinic acid, 10 g/L glucose, 1 g/L ammonium sulfate, 50 mM potassium phosphate, 0.025 g/L magnesium sulfate, 0.0625 mg/L iron sulfate, 2.7 mg/L manganese sulfate, 0.33 mg/L calcium chloride, 1.25 g/L sodium chloride, 2.5 g/L Bacto Tryptone, 1.25 g/L Bacto Yeast Extract, 25 μg/mL kanamycin, 50 μg/mL streptomycin, 15 g/mL chloramphenicol and 0.01 mM IPTG) adjusted to pH 6.5, and incubated at 30° C. with shaking at 120 min −1  for 24 hours. 
     Quantitative Analyses of α-Hydromuconic Acid and Carbon Sources 
     The supernatant separated from bacterial cells by centrifugation of the culture fluid was processed by membrane treatment using Millex-GV (0.22 μm; PVDF; manufactured by Merck KGaA), and the resulting filtrate was analyzed by LC-MS/MS in the same manner as in Example 2. The results of the quantitative analysis of α-hydromuconic acid accumulated in the culture supernatant, and the yield of α-hydromuconic acid calculated according to the formula (3) are presented in Table 8. 
     Comparative Example 4 
     Test for α-Hydromuconic Acid Production Using the  E. coli  Strains Having an Ability to Produce α-Hydromuconic Acid by Introduction of Each of the Nucleic Acids Encoding 3-Oxoadipyl-CoA Reductases 
     The results of a test for α-hydromuconic acid production performed in the same manner as in Example 4 using the  E. coli  strains produced in Comparative Example 3 are presented in Table 8. 
     The results presented in Table 8 indicate that the yield of α-hydromuconic acid was increased in the recombinant strains used in Example 4 compared to that in the recombinant strains used in Comparative Example 4. That is, it was demonstrated that the production of α-hydromuconic acid was much increased by introduction of any of the nucleic acids encoding the polypeptides represented by SEQ ID NOs: 1, 2, 3, 4, 5, 6, and 213 into microorganisms. 
     
       
         
           
               
               
               
               
             
               
                 TABLE 8 
               
               
                   
               
               
                   
                   
                 HMA  
                 HMA  
               
               
                   
                   
                 Concentration  
                 Yield  
               
               
                   
                 Strain  
                 (mg/L)  
                 (%) 
               
               
                   
               
             
            
               
                   
               
            
           
           
               
               
               
               
            
               
                 Example 4  
                 Ec/Smr1_HMA  
                 42.9  
                 0.660  
               
               
                   
                 Ec/Snm1_HMA  
                 50.6  
                 0.755  
               
               
                   
                 Ec/Spl1_HMA  
                 39.1  
                 0.629  
               
               
                   
                 Ec/Spe1_HMA  
                 47.7  
                 0.731  
               
               
                   
                 Ec/Sur1_HMA  
                 62.4  
                 0.801  
               
               
                   
                 Ec/Ssp1_HMA  
                 35.6  
                 0.626  
               
               
                   
                 Ec/Slq1_HMA  
                 48.5  
                 0.719  
               
               
                 Comparative  
                 Ec/Ppu1_HMA  
                 0.7  
                 0.012  
               
               
                 Example 4  
                 Ec/Eco1_HMA  
                 1.4  
                 0.023  
               
               
                   
                 Ec/Aci1_HMA  
                 2.1  
                 0.035  
               
               
                   
                 Ec/Spl2_HMA  
                 2.1  
                 0.034 
               
               
                   
               
            
           
         
       
     
     Reference Example 5 
     Production of Plasmids to Enhance Expression of the Polypeptides Represented by SEQ ID NOs: 2 and 3 
     Different plasmids were produced for constitutive expression of the polypeptides represented by SEQ ID NOs: 2 and 3. 
     To amplify a nucleic acid encoding the polypeptide represented by SEQ ID NO: 2, primers (SEQ ID NOs: 50 and 51) were designed for use in amplification of the nucleic acid represented by SEQ ID NO: 55 using the genomic DNA of  Serratia nematodiphila  strain DSM21420 as a template, and a PCR reaction was performed in accordance with routine procedures. To amplify a nucleic acid encoding the polypeptide represented by SEQ ID NO: 3, primers (SEQ ID NOs: 52 and 53) were also designed for use in amplification of the nucleic acid represented by SEQ ID NO: 56 using the genomic DNA of  Serratia plymuthica  strain NBRC102599 as a template, and a PCR reaction was performed in accordance with routine procedures. Each of the resulting fragments and the pBBR1MCS-2::Pgap/ScaI produced in Reference Example 1 were ligated together using the In-Fusion HD Cloning Kit, and the resulting plasmids were individually introduced into  E. coli  strain DH5α. The nucleotide sequences on the plasmids isolated from the obtained recombinant strains were confirmed in accordance with routine procedures, and the plasmids were designated as “pBBR1MCS-2::Snm1” and “pBBR1MCS-2::Spl1”, respectively. 
     Example 5 
     Generation of Microorganisms of the Genus  Serratia  Modified to Enhance Expression of the Polypeptides Represented by SEQ ID NOs: 2 and 3 
       Serratia nematodiphila  strain DSM21420, which is a microorganism originally having the nucleic acid encoding the polypeptide represented by SEQ ID NO: 2, and  Serratia plymuthica  strain NBRC102599, which is a microorganism originally having the nucleic acid encoding the polypeptide represented by SEQ ID NO: 3, were used as host microorganisms to produce recombinant strains with enhanced expression of the polypeptides. The pBBR1MCS-2::Snm1 or pBBR1MCS-2::Spl1 produced in Reference Example 5 was introduced into each of the above described microorganism strains of the genes  Serratia  by electroporation (NM Calvin. PC Hanawalt. J. Bacteriol. 170 (1988), pp. 2796-2801). The strains after the introduction were cultured on LB agar medium containing 25 g/mL kanamycin at 30° C. The recombinant strains obtained in this example were designated as Sn/Snm1 and Sp/Spl1. 
     Example 6 
     Test for 3-Hydroxyadipic Acid and α-Hydromuconic Acid Production Using the Microorganisms of the Genus  Serratia  Modified to Enhance Expression of the Polypeptides Represented by SEQ ID NOs: 2 and 3 
     To evaluate the effects of enhanced expression of the polypeptides represented by SEQ ID NOs: 2 and 3, the recombinant microorganism strains of the genus  Serratia  produced in Example 5 were used to perform a test for 3-hydroxyadipic acid and α-hydromuconic acid production. 
     A loopful of each recombinant strain produced in Example 5 was inoculated into 5 mL of the culture medium I (10 g/L Bacto Tryptone (manufactured by Difco Laboratories), 5 g/L Bacto Yeast Extract (manufactured by Difco Laboratories), 5 g/L, sodium chloride, 25 μg/mL kanamycin) adjusted to pH 7, and incubated at 30° C. with shaking at 120 min −1  for 18 hours. Subsequently, 0.25 mL of the culture fluid was added to 5 mL of the culture medium 11 (10 g/L succinic acid, 10 g/L glucose, I g/L ammonium sulfate, 50 mM potassium phosphate, 0.025 g/L magnesium sulfate, 0.0625 mg/L iron sulfate, 2.7 mg/L manganese sulfate, 0.33 mg/L calcium chloride, 1.25 g/L sodium chloride, 2.5 g/L Bacto Tryptone, 1.25 g/L Bacto Yeast Extract, 25 μg/mL kanamycin) adjusted to pH 6.5, and incubated at 30° C. with shaking at 120 min −1  for 24 hours. 
     Quantitative Analyses of 3-Hydroxyadipic Acid, α-Hydromuconic Acid, and Carbon Sources 
     The supernatant separated from bacterial cells by centrifugation of the culture fluid was processed by membrane treatment using Millex-GV (0.22 μm; PVDF; manufactured by Merck KGaA), and the resulting filtrate was analyzed by LC-MS/MS in the same manner as in Example 2. The results of the quantitative analyses of 3-hydroxyadipic acid and α-hydromuconic acid accumulated in the culture supernatant, and the yields of those products are presented in Table 9. 
     Comparative Example 5 
     Generation of Microorganisms of the Genus  Serratia  not Modified to Enhance Expression of the Polypeptides Represented by SEQ ID NOs: 2 and 3 
     The pBBR1MCS-2::gap was introduced into each of  Serratia nematodiphila  strain DSM21420 and  Serratia plymuthica  strain NBRC102599 in the same manner as in Example 5. The resulting recombinant strains were designated as Sn/NC and Sp/NC. 
     Comparative Example 6 
     Test for 3-Hydroxyadipic Acid and α-Hydromuconic Acid Production Using the Microorganisms of the Genus  Serratia  not Modified to Enhance Expression of the Polypeptides Represented by SEQ ID NOs: 2 and 3 
     The microorganisms of the genus  Serratia  produced in Comparative Example 5 were used to perform a test for 3-hydroxyadipic acid and α-hydromuconic acid production in the same manner as in Example 6. The results are presented in Table 9. 
     The results presented in Table 9 indicate that the yields of 3-hydroxyadipic acid and α-hydromuconic acid were increased in the recombinant strains used in Example 6 with enhanced expression of the polypeptides represented by SEQ ID NOs: 2 and 3 compared to those in the recombinant strains used in Comparative Example 6 without enhanced expression of the polypeptides represented by SEQ ID NOs: 2 and 3. That is, it was demonstrated that the production of 3-hydroxyadipic acid and α-hydromuconic acid was much increased by enhancing the expression of the polypeptides represented by SEQ ID NOs: 2 and 3. 
     
       
         
           
               
               
               
               
               
               
             
               
                 TABLE 9 
               
               
                   
               
               
                   
                   
                 3HA  
                 3HA  
                 HMA  
                 HMA  
               
               
                   
                   
                 Concentraiton  
                 Yield  
                 Concentration  
                 Yield  
               
               
                   
                 Strain  
                 (mg/L)  
                 (%)  
                 (mg/L)  
                 (%) 
               
               
                   
               
             
            
               
                   
               
            
           
           
               
               
               
               
               
               
            
               
                 Example 6  
                 Sn/Snm1  
                 37.4  
                 0.193  
                 13.7  
                 0.077  
               
               
                   
                 Sp/Spl1  
                 64.1  
                 0.331  
                 14.2  
                 0.080  
               
               
                 Comparative  
                 Sn/NC  
                 2.5  
                 0.013  
                 1.7  
                 0.010  
               
               
                 Example 6  
                 Sp/NC  
                 4.6  
                 0.024  
                 4.1  
                 0.023 
               
               
                   
               
            
           
         
       
     
     Comparative Example 7 
     Control Test for Confirming the Activity of Each of the Polypeptides Represented by SEQ ID NOs: 1, 2, 3, 4, 5, 6, and 213 to Reduce 3-Oxoadipyl-CoA to 3-Hydroxyadipyl-CoA 
     An  E. coli  recombinant expressing the enzymes catalyzing the reactions A, E, and F was produced. The pACYCDuet-1 was introduced into the BL21 DE3)/pBBR1MCS-2::ATCT in the same manner as in Example 1. The resulting recombinant strain was designated as Ec/NC_3HA. 
     An  E. coli  recombinant expressing the enzymes catalyzing the reactions A, E, F, and C was produced. The pACYCDuct-1 was introduced into the BL21 (DE3)/pBBR1MCS-2::ATCT/pCDF-1b::EHa in the same manner as in Example 3. The resulting recombinant strain was designated as Ec/NC_HMA. 
     Ec/NC_3HA, Ec/NC_HMA, the seven recombinant  E. coli  strains produced in Example 1 (Ec/Smr1_3HA, Ec/Snm1_3HA, Ec/Spl1_3HA, Ec/Spe1_3HA, Ec/Sur1_3HA, Ec/Ssp1_3HA, Ec/Slq1_3HA), and the seven recombinant  E. coli  strains produced in Example 3 (Ec/Smr1_HMA, Ec/Snm1_HMA, Ec/Spl1_HMA, Ec/Spe1_HMA, Ec/Sur1_HMA, Ec/Ssp1_HMA, Ec/Slq1_HMA) were used and cultured under the same conditions as in either Example 2 or Example 4 to quantify 3-hydroxyadipic acid or α-hydromuconic acid in culture fluid. The results are presented in Table 10. 
     The results presented in Table 10 indicate that neither 3-hydroxyadipic acid nor α-hydromuconic acid was detected in Ec/NC_3HA and Ec/NC_HMA, and confirmed that the successful production of 3-hydroxyadipic acid and α-hydromuconic acid in Example 2 and 4 was caused by expression of each of the polypeptides represented by SEQ ID NOs: 1, 2, 3, 4, 5, 6, and 213. Additionally, the results indicate that α-hydromuconic acid was not detected in Ec/Smr1_3HA, Ec/Snm1_3HA, Ec/Spl1_3HA, Ec/Spe1_3HA, Ec/Sur1_3HA, Ec/Ssp1_3HA, and Ec/Slq1_3HA, and confirmed that expression of the enzyme catalyzing the reaction C in Ec/Smr1_HMA, Ec/Snm1_HMA, Ec/Spl1 HMA, Ec/Spe1_HMA, Ec/Sur1_HMA, Ec/Ssp1_HMA, and Ec/Slq1_HMA resulted in production of α-hydromuconic acid. This indicates that 3-hydroxyadipic acid produced in Ec/Smr1_3HA, Ec/Snm1_3HA, Ec/Spl1_3HA, Ec/Spe1_3HA, Ec/Sur1_3HA, Ec/Ssp1_3HA, and Ec/Slq1_3HA, and α-hydromuconic acid produced in Ec/Smr1_HMA, Ec/Snm1_HMA, Ec/Spl1_HMA, Ec/Spe1_HMA, Ec/Sur1_HMA, Ec/Ssp1_HMA, and Ec/Slq1_HMA were both produced through production of 3-hydroxyadipyl-CoA. Thus, it was found that the polypeptides represented by SEQ ID NOs: 1, 2, 3, 4, 5, 6, and 213 have an activity to reduce 3-oxoadipyl-CoA to 3-hydroxyadipyl-CoA. 
     
       
         
           
               
               
               
               
             
               
                 TABLE 10 
               
               
                   
               
               
                   
                   
                 3HA  
                 HMA  
               
               
                   
                   
                 Concentration  
                 Concentration  
               
               
                   
                 Strain  
                 (g/L)  
                 (mg/L) 
               
               
                   
               
             
            
               
                 Example 2  
                 Ec/Smr1_3HA  
                 1.65  
                 N.D.  
               
               
                   
                 Ec/Snm1_3HA  
                 2.69  
                 N.D.  
               
               
                   
                 Ec/Spl1_3HA  
                 2.18  
                 N.D.  
               
               
                   
                 Ec/Spe1_3HA  
                 2.72  
                 N.D.  
               
               
                   
                 Ec/Sur1_3HA  
                 3.42  
                 N.D.  
               
               
                   
                 Ec/Ssp1_3HA  
                 1.94  
                 N.D.  
               
               
                   
                 Ec/Slq1_3HA  
                 2.67  
                 N.D.  
               
               
                 Example 4  
                 Ec/Smr1_HMA  
                 0.85  
                 42.9  
               
               
                   
                 Ec/Snm1_HMA  
                 0.98  
                 50.6  
               
               
                   
                 Ec/Spl1_HMA  
                 0.67  
                 39.1  
               
               
                   
                 Ec/Spe1_HMA  
                 0.96  
                 47.7  
               
               
                   
                 Ec/Sur1_HMA  
                 1.37  
                 62.4  
               
               
                   
                 Ec/Ssp1_HMA  
                 0.84  
                 35.6  
               
               
                   
                 Ec/Slq1_HMA  
                 0.93  
                 48.5  
               
               
                 Comparative  
                 Ec/NC_3HA  
                 N.D.  
                 N.D.  
               
               
                 Example 7  
                 Ec/NC_HMA  
                 N.D.  
                 N.D. 
               
               
                   
               
            
           
         
       
     
     Reference Example 6 
     Production of a Plasmid for Expression of the Enzyme Catalyzing a Reaction to Generate 3-Oxoadipyl-CoA and Coenzyme a from Acetyl-CoA and Succinyl-CoA (the Reaction A) and an Enzyme Catalyzing a Reaction to Generate Adipic Acid from Adipyl-CoA (the Reaction G) 
     A 6.6-kb fragment obtained by cleaving the pBBR1MCS-2::AT produced in Reference Example 1 with HpaI was designated as pBBR1MCS-2::AT/HpaI. To amplify a gene encoding an enzyme catalyzing the reaction G, primers (SEQ ID NOs: 223 and 224) were designed for use in amplification of a continuous sequence including the full-length CoA transferase genes dcaI and dcaJ (NCBI Gene ID: CR543861.1, SEQ ID NOs: 221 and 222) by PCR using the genomic DNA of  Acinetobacter baylyi  strain ADP1 as a template, and a PCR reaction was performed in accordance with routine procedures. The resulting fragment and the pBBR1MCS-2::AT/HpaI were ligated together using the In-Fusion HD Cloning Kit, and the resulting plasmid was introduced into  E. coli  strain DH5α. The nucleotide sequence on the plasmid isolated from the obtained recombinant strain was confirmed in accordance with routine procedures, and the plasmid was designated as pBBR1MCS-2::ATCT2. 
     Reference Example 7 
     Production of a Plasmid for Expression of an Enzyme Catalyzing a Reaction to Generate Adipyl-CoA from 2,3-Dehydroadipyl-CoA (the Reaction D) 
     The pMW19 expression vector (manufactured by Nippon Gene Co., Ltd.), which is capable of autonomous replication in  E. coli , was cleaved with SacI to obtain pMW119/SacI. To integrate a constitutive expression promoter into the vector, primers (SEQ ID NOs: 225 and 226) were designed for use in amplification of an upstream 200-b region (SEQ ID NO: 17) of gapA (NCBI Gene ID: NC_000913.3) by PCR using the genomic DNA of  Escherichia coli  K-12 MG1655 as a template, and a PCR reaction was performed in accordance with routine procedures. The resulting fragment and the pMW119/SacI were ligated together using the In-Fusion HD Cloning Kit (manufactured by Clontech), and the resulting plasmid was introduced into  E. coli  strain DH5α. The nucleotide sequence on the plasmid isolated from the obtained recombinant  E. coli  strain was confirmed in accordance with routine procedures, and the plasmid was designated as pMW119::Pgap. Then, the pMW119::Pgap was cleaved with SphI to obtain pMW119::Pgap/SphI. To amplify a gene encoding an enzyme catalyzing the reaction I), primers (SEQ ID NOs: 228 and 229) were designed for use in amplification of the full length of dcaA from  Acinetobacter baylyi  strain ADP1 (NCBI-ProteinID: AAL09094.1, SEQ ID NO: 227) by PCR, and a PCR reaction was performed in accordance with routine procedures. The resulting fragment and the pMW119::Pgap/SphI were ligated together using the In-Fusion HID Cloning Kit (manufactured by Clontech), and the resulting plasmid was introduced into  E. coli  strain DH5α. The nucleotide sequence on the plasmid isolated from the obtained recombinant strain was confirmed in accordance with routine procedures, and the plasmid was designated as pMW119::ER. 
     Example 7 
     Generation of  E. coli  Strains Having an Ability to Produce Adipic Acid by Introduction of the Nucleic Acids Encoding the Polypeptides Represented by SEQ ID NOs: 1, 2, 3, 4, 5, 6, and 213 
     The plasmid pBBR1MCS-2::ATCT2 produced in Reference Example 6 was introduced into  E. coli  strain BL21 (DE3) by electroporation (N M Calvin, P C Hanawalt. J. Bacteriol, 170 (1988), pp. 2796-2801). The strain after the introduction was cultured on LB agar medium containing 25 μg/mL kanamycin at 37° C. The resulting recombinant strain was designated as BL21 (DE3)/pBBR1MCS-2::ATCT2. 
     The plasmid pCDF-1b::EHa produced in Reference Example 4 was introduced into the BL21 (DE3)/pBBR1MCS-2::ATCT2 by electroporation. The strain after the introduction was cultured on LB agar medium containing 25 μg/mL kanamycin and 50 g/mL streptomycin at 37° C. The resulting recombinant strain was designated as BL21 (DE3)/pBBR1MCS-2::ATCT2/pCDF-1b::EHa. 
     The plasmid pMW119::ER produced in Reference Example 7 was introduced into the BL21 (DE3)/pBHR1MCS-2::ATCT2/pCDF-1b::EHa by electroporation. The strain after the introduction was cultured on LB agar medium containing 25 μg/mL kanamycin, 50 μg/mL streptomycin, and 100 μg/mL ampicillin at 37° C. The resulting recombinant strain was designated as BL21 (DE3)/pBBR1MCS-2::ATCT2/pCDF-1b::EHa/pMW119::ER. 
     Each of the seven plasmids produced in Reference Example 2 was individually introduced into the BL21 (DE3)/pBBR1MCS-2::ATCT2/pCDF-1b::EHa/pMW119::ER by electroporation. The strains after the introduction were cultured on LB agar medium containing 25 μg/mL kanamycin, 50 μg/mL streptomycin, 100 μg/mL ampicillin, and 15 μg/ml, chloramphenicol at 37° C. The recombinant strain in which “pACYCDuet-1::Smr1” is introduced is designated as “Ec/Smr1_ADA”; the recombinant strain in which “pACYCDuet-1::Snm1” is introduced is designated as “Ec/Snm1_ADA”; the recombinant strain in which “pACYCDuet-1::Spl1” is introduced is designated as “Ec/Spl1_ADA”; the recombinant strain in which “pACYCDuet-1::Spe1” is introduced is designated as “Ec/Spe1_ADA”; the recombinant strain in which “pACYCDuet-1::Sur1” is introduced is designated as “Ec/Sur1_ADA”; the recombinant strain in which “pACYCDuet-1::Ssp1” is introduced is designated as “Ec/Ssp1_ADA”; and the recombinant strain in which “pACYCDuet-1::Slq1” is introduced is designated as “Ec/Slq1_ADA”. The information about the recombinant strains obtained in this example is presented in Table 11. 
     Comparative Example 8 
     Generation of  E. coli  Strains Having an Ability to Produce Adipic Acid by Introduction of Each of the Nucleic Acids Encoding 3-Oxoadipyl-CoA Reductases 
     Each of the plasmids produced in Reference Example 3, namely “pACYCDuet-1::Ppu1”, “pACYCDuet-1::Eco1”, “pACYCDuet-1::Aci1” and “pACYCDuet-1::Spl2” was individually introduced into the BL21 (DE3)/pBBR1MCS-2::ATCT2/pCDF-1b::EHa/pMW119::ER by electroporation. The strains after the introduction were cultured on LB agar medium containing 25 μg/mL kanamycin, 50 μg/mL streptomycin, 100 μg/mL ampicillin, and 15 μg/mL chloramphenicol at 37° C. 
     The recombinant strain in which “pACYCDuet-1::Ppu1” is introduced is designated as “Ec/Ppu1_ADA”; the recombinant strain in which “pACYCDuet-1::Eco1” is introduced is designated as “Ec/Eco1_ADA”; the recombinant strain in which “pACYCDuet-1::Aci1” is introduced is designated as “Ec/Aci1_ADA”; and the recombinant strain in which “pACYCDuet-1::Spl2” is introduced is designated as “Ec/Spl2_ADA”. The information about the recombinant strains obtained in this comparative example is presented in Table 1. 
     Example 8 
     Test for Adipic Acid Production Using the  E. coli  Strains Having an Ability to Produce Adipic Acid by Introduction of the Nucleic Acids Encoding the Polypeptides Represented by SEQ ID NOs: 1, 2, 3, 4, 5, 6, and 213 
     The  E. coli  strains produced in Example 7 were used to perform a test for adipic acid production. A loopful of each recombinant  E. coli  strain produced in Example 3 was inoculated into 5 mL of the culture medium 1 (10 g/L Bacto Tryptone (manufactured by Difco Laboratories), 5 g/L Bacto Yeast Extract (manufactured by Difco Laboratories), 5 g/L sodium chloride, 25 μg/mL kanamycin, 50 μg/mL streptomycin, 100 μg/mL ampicillin, and 15 μg/mL chloramphenicol) adjusted to pH 7, and incubated at 30° C. with shaking at 120 min −1  for 18 hours. Subsequently, 0.25 mL of the culture fluid was added to 5 mL of the culture medium II (10 g/L succinic acid, 10 g/L glucose, 1 g/L ammonium sulfate, 50 mM potassium phosphate, 0.025 g/L, magnesium sulfate, 0.0625 mg/L iron sulfate, 2.7 mg/L manganese sulfate, 0.33 mg/L calcium chloride, 1.25 g/L sodium chloride, 2.5 g/L Bacto Tryptone, 1.25 g/L Bacto Yeast Extract, 25 μg/mL kanamycin, 50 μg/mL streptomycin, 100 g/ml, ampicillin, and 15 μg/mL chloramphenicol, and 0.01 mM IPTG) adjusted to pH 6.5, and incubated at 30° C. with shaking at 120 min −1  for 24 hours. 
     Quantitative Analyses of Adipic Acid and Carbon Sources 
     The supernatant separated from bacterial cells by centrifugation of the culture fluid was processed by membrane treatment using Millex-GV (0.22 μm; PVDF: manufactured by Merck KGaA), and the resulting filtrate was analyzed by LC-MS/MS in the same manner as in Example 2. The results of the quantitative analysis of adipic acid accumulated in the culture supernatant, and the yield of adipic acid calculated according to the formula (3) are presented in Table 11. 
     Comparative Example 9 
     Test for Adipic Acid Production Using the  E. coli  Strains Having an Ability to Produce Adipic Acid by Introduction of Each of the Nucleic Acids Encoding 3-Oxoadipyl-CoA Reductases 
     The results of a test for adipic acid production performed in the same manner as in Example 8 by using the  E. coli  strains produced Comparative Example 8 are presented in Table 11. 
     The results presented in Table 11 indicate that the yield of adipic acid was increased in the recombinant strains used in Example 8 compared to that in the recombinant strains used in Comparative Example 9. That is, it was demonstrated that the production of adipic acid was significantly increased by introduction of any of the nucleic acids encoding the polypeptides represented by SEQ ID NOs: 1, 2, 3, 4. 5, 6, and 213 into microorganisms. 
     
       
         
           
               
               
               
               
             
               
                 TABLE 11 
               
               
                   
               
               
                   
                   
                 ADA  
                 ADA  
               
               
                   
                   
                 Concentration  
                 Yield  
               
               
                   
                 Strain  
                 (mg/L)  
                 (%) 
               
               
                   
               
             
            
               
                 Example 8  
                 Ec/Smr1_ADA  
                 5.18  
                 0.076  
               
               
                   
                 Ec/Snm1_ADA  
                 6.94  
                 0.084  
               
               
                   
                 Ec/Spl1_ADA  
                 5.38  
                 0.075  
               
               
                   
                 Ec/Spe1_ADA  
                 6.01  
                 0.093  
               
               
                   
                 Ec/Sur1_ADA  
                 7.93  
                 0.101  
               
               
                   
                 Ec/Ssp1_ADA  
                 4.76  
                 0.072  
               
               
                   
                 Ec/Slq1_ADA  
                 6.82  
                 0.082  
               
               
                 Comparative  
                 Ec/Ppu1_ADA  
                 N.D.  
                 N.D.  
               
               
                 Example 9  
                 Ec/Eco1_ADA  
                 N.D.  
                 N.D.  
               
               
                   
                 Ec/Aci1_ADA  
                 N.D.  
                 N.D.  
               
               
                   
                 Ec/Spl2_ADA  
                 N.D.  
                 N.D. 
               
               
                   
               
            
           
         
       
     
     Example 9 
     Confirmation of 3-Oxoadipyl-CoA Reductase Activity of the Polypeptides Represented by SEQ ID NOs: 2 and 4 
     Each of the plasmids produced in Reference Example 2, namely pACYCDuet-1::Snm1 and pACYCDuet-1::Spe1, was introduced into  E. coli  strain BL21 (DE3) by electroporation. The strains after the introduction were cultured on LB agar medium containing 15 μg/mL chloramphenicol at 37° C. The resulting recombinant strains were designated as BL21 (DE3)/pACYCDuet-1::Snm1 and BL21 (DE3)/pACYCDuet-1::Spe1. 
     A loopful of either the BL21 (DE3)/pACYCDuet-1::Snm1 or the BL21 (DE3)/pACYCDuet-1::Spe1 was inoculated into 20 mL of the culture medium I (10 g/l, Bacto Tryptone (manufactured by Difco Laboratories), 5 g/L Bacto Yeast Extract (manufactured by Difco Laboratories), 5 g/L sodium chloride, and 15 μg/mL chloramphenicol) adjusted to pH 7, and incubated at 37° C. with rotation at 120 rpm for 17 hours. Subsequently, 10 mL of the culture fluid was added to 2 L of the culture medium 1, and incubated at 37° C. with shaking at 100 min −1  for 2 hours. The culture fluid was supplemented with IPTG to a concentration of 500 μM, and incubated at 16° C. with shaking at 100 min −1  for 18 hours. The culture fluid was then centrifuged at 6000 rpm at 4° C. for 15 minutes to remove the supernatant, and the resulting cell pellet was suspended in the Binding Buffer provided in the His-Bind Buffer Kit (manufactured by Merck KGaA). The obtained cell suspension was subjected to sonication with Digital Sonifier (manufactured by Branson Ultrasonics Co.), while being cooled on ice. The sonicated solution was centrifuged at 13,000 rpm at 4° C. for 30 minutes, and the obtained supernatant was designated as cell homogenate. 
     A suitable volume of the His-Bind Resin solution was added to 30 mL of the cell homogenate, and the resulting solution was incubated at 4° C. for 1 hour. The solution was centrifuged at 4000 rpm at 4° C. for 5 minutes to remove 20 mL of the supernatant, and the remaining His-Bind Resin solution was then loaded onto a column, which was washed with 10 mL of the Binding Buffer twice, and subsequently with 10 mL of the Wash Buffer 1 (with 25 mM imidazole) twice, and then 10 mL of the Wash Buffer 2 (with 60 mM imidazole) twice. Finally, elution was performed with 2 mL of the Elution Buffer (with 1 mM imidazole) four times, and the resulting fractions were collected. 
     A fraction showing a band corresponding to a polypeptide of around 55 kDa, which is equal to the molecular weight of each of the target enzymes, was centrifuged at 8000 rpm at 4° C. for 15 minutes to remove the supernatant, and 5 mL of the Strage Buffer was then added to the remains for washing. The resulting suspension was further centrifuged at 8000 rpm at 4° C. for 15 minutes to remove the supernatant, and 3 mL of the Strage Buffer was then added to the remains, and this operation was repeated twice in total. The obtained solutions were designated as enzyme solutions Snm1 and Spe1. 
     Preparation of 3-oxoadipic acid: Preparation of 3-oxoadipic acid was performed according to the method described in Reference Example 1 of WO 2017/099209. 
     Preparation of 3-oxoadipyl-CoA solution: The pRSF-1b expression vector (manufactured by Novagen), which is capable of autonomous replication in  E. coli , was cleaved with KpnI to obtain pRSF-1b/KpnI. To amplify a gene encoding an enzyme catalyzing the reaction E, primers (SEQ ID NOs: 230 and 231) were designed for use in amplification of the full-length CoA transferase genes pcaI and pcaJ (NCBI-GeneIDs: 1046613 and 1046612, SEQ ID NOs: 23 and 24) by PCR using the genomic DNA of  Pseudomonas putida  strain KT2440 as a template, and a PCR reaction was performed in accordance with routine procedures. The resulting fragment and the pRSF-1b/KpnI were ligated together using the In-Fusion HD Cloning Kit (manufactured by Clontech), and the resulting plasmid was introduced into  E. coli  strain DH5α. The nucleotide sequence on the plasmid extracted from the obtained recombinant strain was confirmed in accordance with routine procedures. The obtained plasmid was designated as “pRSF-1b::CT”. 
     The pRSF-1b::CT was introduced into  E. coli  BL21 (DE3), and expression of the enzyme was induced with isopropyl-β-thiogalactopyranoside (IPTG) in accordance with routine procedures and the enzyme was purified using the histidine tag from the culture fluid to obtain a CoA transferase solution. The solution was used to prepare an enzymatic reaction solution for 3-oxoadipyl-CoA preparation with the following composition, which was allowed to react at 25° C. for 3 minutes and then filtered through a UF membrane (Amicon Ultra-0.5 mL 10K; manufactured by Merck Millipore) to remove the enzyme, and the obtained filtrate was designated as 3-oxoadipyl-CoA solution. 
     Enzymatic reaction solution for 3-oxoadipyl-CoA preparation: 
     100 mM Tris-HCl (pH 8.2) 
     10 mM MgCl 2    
     0.5 mM succinyl-CoA
 
5 mM 3-oxoadipic acid sodium salt
 
2 μM CoA transferase.
 
     Identification of 3-oxoadipyl-CoA reductase activity: The 3-oxoadipyl-CoA reductase activity was determined by measuring 3-hydroxyadipyl-CoA production. Each of the enzyme solutions Snm1 and Spe1 was used to prepare an enzymatic reaction solution with the following composition, which was allowed to react at 25° C. for 1 hour and then processed by membrane treatment using Millex-GV (0.22 μm; PVDF; manufactured by Merck KGaA), and the resulting filtrate was analyzed by LC-MS/MS in the same manner as in Example 2. In this respect, the concentration of 3-oxoadipyl-CoA was measured according to a method of Kaschabek et al. (J Bacteriol. 2002 January: 184 (1): 207-215), and adjusted to 15 μM in the enzymatic reaction solution. The result is presented in Table 12, along with the result from a similar reaction as a control in which Tris-HCl is added instead of the enzyme solution. 
     100 mM Tris-HCl (pH 8.2) 
     10 mM MgCl 2    
     150 μL/mL 3-oxoadipyl-CoA solution 
     0.5 mM NADH 
     1 mM dithiothreitol
 
10 μM 3-oxoadipyl-CoA reductase.
 
     The results presented in Table 12 confirmed production of 3-hydroxyadipyl-CoA in the reactions using the enzyme solutions Snm1 and Spe1. In contrast, 3-hydroxyadipyl-CoA was not detected in the control. Thus, it was demonstrated that the enzyme solutions Snm1 and Spe1 had 3-oxoadipyl-CoA reductase activity. 
     
       
         
           
               
               
               
             
               
                 TABLE 12 
               
               
                   
               
               
                   
                   
                 3-hydroxyadipyl-CoA  
               
               
                   
                 Enzyme Solution  
                 concentration (μM) 
               
               
                   
               
             
            
               
                 Example 9  
                 Snm1  
                 13.9  
               
               
                   
                 Spe1  
                 13.8  
               
               
                   
                 control  
                 N.D.