# Patent

## Title
Compositions and methods for the modification of gene expression

## Abstract

Novel isolated plant polynucleotide promoter sequences are provided, together with genetic constructs comprising such polynucleotides. Methods for using such constructs in modulating the transcription of DNA sequences of interest are also disclosed, together with transgenic plants comprising such constructs.

## Background
CROSS REFERENCE TO RELATED APPLICATIONS
This application is a continuation of U.S. patent application Ser. No. 10/137,036, filed Apr. 30, 2002, now U.S. Pat. No. 7,211,711, the entire contents of which are incorporated herein by reference, which is a continuation-in-part of U.S. patent application Ser. No. 09/724,624, filed Nov. 28, 2000, now abandoned, which is a continuation-in-part of U.S. patent application Ser. No. 09/598,401, filed Jun. 20, 2000, now U.S. Pat. No. 6,596,925, which is a continuation-in-part of U.S. patent application Ser. No. 09/276,599, filed Mar. 25, 1999, now U.S. Pat. No. 6,380,459.


This application claims priority to International Patent Application No. PCT/NZ03/00076, filed Apr. 30, 2003; U.S. application Ser. No. 10/137,036, filed Apr. 30, 2002; International Patent Application No. PCT/NZ01/00115, filed Jun. 20, 2001; U.S. application Ser. No. 09/724,624 filed Nov. 28, 2000; U.S. patent application Ser. No. 09/598,401 filed Jun. 20, 2000; International Patent Application No. PCT/NZ00/00018, filed Feb. 24, 2000; U.S. Provisional Patent Application No. 60/146,591, filed Jul. 30, 1999; and U.S. patent application Ser. No. 09/276,599, filed Mar. 25, 1999.
TECHNICAL FIELD OF THE INVENTION
This invention relates to the regulation of polynucleotide transcription and/or expression. More specifically, this invention relates to polynucleotide regulatory sequences isolated from plants that are capable of initiating and driving the transcription of polynucleotides, and the use of such regulatory sequences in the modification of transcription of endogenous and/or heterologous polynucleotides and production of polypeptides. Polypeptide sequences are also disclosed.
BACKGROUND OF THE INVENTION
Gene expression is regulated, in part, by the cellular processes involved in transcription. During transcription, a single-stranded RNA complementary to the DNA sequence to be transcribed is formed by the action of RNA polymerases. Initiation of transcription in eukaryotic cells is regulated by complex interactions between cis-acting DNA motifs, located within the gene to be transcribed, and trans-acting protein factors. Among the cis-acting regulatory regions are sequences of DNA, termed promoters, to which RNA polymerase is first bound, either directly or indirectly. As used herein, the term “promoter” refers to the 5' untranslated region of a gene that is associated with transcription and which generally includes a transcription start site. Other cis-acting DNA motifs, such as enhancers, may be situated further up-and/or down-stream from the initiation site.
Both promoters and enhancers are generally composed of several discrete, often redundant elements, each of which may be recognized by one or more trans-acting regulatory proteins, known as transcription factors. Promoters generally comprise both proximal and more distant elements. For example, the so-called TATA box, which is important for the binding of regulatory proteins, is generally found about 25 basepairs upstream from the initiation site. The so-called CAAT box is generally found about 75 basepairs upstream of the initiation site. Promoters generally contain between about 100 and 1000 nucleotides, although longer promoter sequences are possible.
For the development of transgenic plants, constitutive promoters that drive strong transgene expression are preferred. Currently, the only available constitutive plant promoter that is widely used is derived from Cauliflower Mosaic Virus. Furthermore, there exists a need for plant-derived promoters for use in transgenic food plants due to public conceptions regarding the use of viral promoters. Few gymnosperm promoters have been cloned and those derived from angiosperms have been found to function poorly in gymnosperms. There thus remains a need in the art for polynucleotide promoter regions isolated from plants for use in modulating transcription and expression of polynucleotides in transgenic plants.
SUMMARY OF THE INVENTION
Briefly, isolated polynucleotide regulatory sequences from eucalyptus and pine that are involved in the regulation of gene expression are disclosed, together with methods for the use of such polynucleotide regulatory regions in the modification of expression of endogenous and/or heterologous polynucleotides in transgenic plants. The present invention provides polynucleotide promoter sequences from 5' untranslated, or non-coding, regions of plant genes that initiate and regulate transcription of polynucleotides placed under their control, together with isolated polynucleotides comprising such promoter sequences.
In a first aspect, the present invention provides isolated polynucleotide sequences comprising a polynucleotide selected from the group consisting of: (a) sequences recited in SEQ ID NO: 1-14, 20, 22-62, 81-86 and 88-127; (b) complements of the sequences recited in SEQ ID NO: 1-14, 20, 22-62, 81-86 and 88-127; (c) reverse complements of the sequences recited in SEQ ID NO: 1-14, 20, 22-62, 81-86 and 88-127; (d) reverse sequences of the sequences recited in SEQ ID NO: 1-14, 20, 22-62, 81-86 and 88-127; (e) sequences having either 40%, 60%, 75% or 90% identical nucleotides, as defined herein, to a sequence of (a)-(d); probes and primers corresponding to the sequences set out in SEQ ID NO: 1-14, 20, 22-62, 81-86 and 88-127; polynucleotides comprising at least a specified number of contiguous residues of any of the polynucleotides identified as SEQ ID NO: 1-14, 20, 22-62, 81-86 and 88-127; and extended sequences comprising portions of the sequences set out in SEQ ID NO: 1-14, 20, 22-62, 81-86 and 88-127; all of which are referred to herein as “polynucleotides of the present invention.” The present invention also provides isolated polypeptide sequences identified in the attached Sequence Listing as SEQ ID NO: 63-80, 87 and 130; polypeptide variants of those sequences; and polypeptides comprising the isolated polypeptide sequences and variants of those sequences.
In another aspect, the present invention provides genetic constructs comprising a polynucleotide of the present invention, either alone, or in combination with one or more additional polynucleotides of the present invention, or in combination with one or more known polynucleotides, together with cells and target organisms comprising such constructs.
In a related aspect, the present invention provides genetic constructs comprising, in the 5'-3' direction, a polynucleotide promoter sequence of the present invention, a polynucleotide to be transcribed, and a gene termination sequence. The polynucleotide to be transcribed may comprise an open reading frame of a polynucleotide that encodes a polypeptide of interest, or it may be a non-coding, or untranslated, region of a polynucleotide of interest. The open reading frame may be orientated in either a sense or antisense direction. Preferably, the gene termination sequence is functional in a host plant. Most preferably, the gene termination sequence is that of the gene of interest, but others generally used in the art, such as the Agrobacterium tumefaciens nopalin synthase terminator may be usefully employed in the present invention. The genetic construct may further include a marker for the identification of transformed cells.
In a further aspect, transgenic plant cells comprising the genetic constructs of the present invention are provided, together with organisms, such as plants, comprising such transgenic cells, and fruits, seeds and other products, derivatives, or progeny of such plants. Propagules of the inventive transgenic plants are included in the present invention. As used herein, the word “propagule” means any part of a plant that may be used in reproduction or propagation, sexual or asexual, including cuttings.
Plant varieties, particularly registerable plant varieties according to Plant Breeders' Rights, may be excluded from the present invention. A plant need not be considered a “plant variety” simply because it contains stably within its genome a transgene, introduced into a cell of the plant or an ancestor thereof.
In yet another aspect, methods for modifying gene expression in a target organism, such as a plant, are provided, such methods including stably incorporating into the genome of the organism a genetic construct of the present invention. In a preferred embodiment, the target organism is a plant, more preferably a woody plant, most preferably selected from the group consisting of eucalyptus and pine species, most preferably from the group consisting of Eucalyptus grandis and Pinus radiata. 
In another aspect, methods for producing a target organism, such as a plant, having modified polypeptide expression are provided, such methods comprising transforming a plant cell with a genetic construct of the present invention to provide a transgenic cell, and cultivating the transgenic cell under conditions conducive to regeneration and mature plant growth.
In other aspects, methods for identifying a gene responsible for a desired function or phenotype are provided, the methods comprising transforming a plant cell with a genetic construct comprising a polynucleotide promoter sequence of the present invention operably linked to a polynucleotide to be tested, cultivating the plant cell under conditions conducive to regeneration and mature plant growth to provide a transgenic plant; and comparing the phenotype of the transgenic plant with the phenotype of non-transformed, or wild-type, plants.
In yet a further aspect, the present invention provides isolated polynucleotides that encode ubiquitin. In specific embodiments, the isolated polynucleotides comprise a polynucleotide selected from the group consisting of: (a) sequences recited in SEQ ID NO: 1 and 34; (b) complements of the sequences recited in SEQ ID NO: 1 and 34; (c) reverse complements of the sequences recited in SEQ ID NO: 1 and 34; (d) reverse sequences of the sequence recited in SEQ ID NO: 1 and 34; and (e) sequences having either 40%, 60%, 75% or 90% identical nucleotides, as defined herein, to a sequence of (a)-(d). Polypeptides encoded by such polynucleotides are also provided, together with genetic constructs comprising such polynucleotides, and host cells and transgenic organisms, for example plants, transformed with such genetic constructs. In specific embodiments, such polypeptides comprise a sequence provided in SEQ ID NO: 80 or 67.
In yet further aspects, the present invention provides isolated polynucleotides comprising the DNA sequence of SEQ ID NO: 21, or a complement, reverse complement or variant of SEQ ID NO: 21, together with genetic constructs comprising such polynucleotides and cells transformed with such sequences. As discussed below, removal of the sequence of SEQ ID NO: 21 from a polynucleotide that comprises the sequence of SEQ ID NO: 21 may enhance expression of the polynucleotide. Conversely, the inclusion of the sequence of SEQ ID NO: 21 in a genetic construct comprising a polynucleotide of interest may decrease expression of the polynucleotide.
The above-mentioned and additional features of the present invention and the manner of obtaining them will become apparent, and the invention will be best understood by reference to the following more detailed description. All references disclosed herein are hereby incorporated by reference in their entirety as if each was incorporated individually.



BRIEF DESCRIPTION OF THE DRAWINGS
FIG. 1 shows the expression in A. thaliana of the GUS gene in promoter reporter constructs containing either the superubiquitin promoter with introns, the superubiquitin promoter without introns, or the CaMV 35S promoter. The GUS expression was measured by fluorimetric determination of 4-methyl-umbelliferone (MU) in protein extracts from these plants.
FIG. 2 shows the expression of the GUS gene in tobacco plant protoplasts by deletion constructs containing the superubiquitin promoter with or without the intron. The constructs contained 1,103; 753; 573; 446; 368; and 195 bp upstream of the TATA sequence (bp numbers 1,104-1,110 of SEQ ID NO: 2). The GUS expression was measured by fluorimetric determination of 4-methyl-umbelliferone (MU) in protein extracts from these protoplasts.
FIG. 3 shows the expression of the GUS gene in tobacco plant protoplasts by constructs containing P. radiata either the constitutive promoters Elongation factor-1 alpha, 5-adenosylmethionine synthetase or the superubiquitin promoter without the intron. The GUS expression was measured by fluorimetric determination of 4-methyl-umbelliferone (MU) in protein extracts from these protoplasts.
FIG. 4 shows the expression in A. thaliana of the GUS gene in promoter reporter constructs containing the 3' UTR of the superubiquitin promoter in sense or antisense orientation together with either the superubiquitin promoter with intron, the superubiquitin promoter without intron, or the CaMV 35S promoter. The GUS expression was measured by fluorimetric determination of 4-methyl-umbelliferone (MU) in protein extracts from these plants.
FIG. 5 shows the expression of the GUS gene in tobacco plant protoplasts by a deletion construct containing a fragment of the E. grandis constitutive promoter Elongation factor-1 alpha.
FIGS. 6A and 6B show an annotated version of the full-length superubiquitin promoter, including the intron and the coding sequence (SEQ ID NO: 143). The intron is underlined and the coding sequence is in bold. Motifs are identified in boxes and described in the specification.
FIG. 7 shows an annotated superubiquitin construct without the intron identified and described as a 195 bp deletion (SEQ ID NO: 131).
FIG. 8 shows an annotated superubiquitin construct without the intron identified and described as a 368 bp deletion (SEQ ID NO: 132).
FIG. 9 shows an annotated superubiquitin construct without the intron identified and described as a 446 bp deletion (SEQ ID NO: 133).
FIG. 10 shows an annotated superubiquitin construct without the intron identified and described as a 573 bp deletion (SEQ ID NO: 134).
FIG. 11 shows an annotated superubiquitin construct without the intron identified and described as a 753 bp deletion (SEQ ID NO: 135).
FIG. 12 shows an annotated superubiquitin construct with the intron identified and described as a 195 bp deletion (SEQ ID NO: 136).
FIG. 13 shows an annotated superubiquitin construct with the intron identified and described as a 368 bp deletion (SEQ ID NO: 137).
FIG. 14 shows an annotated superubiquitin construct with the intron identified and described as a 446 bp deletion (SEQ ID NO: 138).
FIGS. 15A and B show an annotated superubiquitin construct with the intron identified and described as a 573 bp deletion (SEQ ID NO: 139).
FIGS. 16A and 16B show an annotated superubiquitin construct with the intron identified and described as a 753 bp deletion (SEQ ID NO: 140).



DETAILED DESCRIPTION OF THE INVENTION
The present invention provides isolated polynucleotide regulatory regions that may be employed in the manipulation of plant phenotypes, together with isolated polynucleotides comprising such regulatory regions. More specifically, polynucleotide promoter sequences isolated from pine and eucalyptus are disclosed. As discussed above, promoters are components of the cellular “transcription apparatus” and are involved in the regulation of gene expression. Both tissue- and temporal-specific gene expression patterns have been shown to be initiated and controlled by promoters during the natural development of a plant. The isolated polynucleotide promoter sequences of the present invention may thus be employed in the modification of growth and development of plants, and of cellular responses to external stimuli, such as environmental factors and disease pathogens.
Using the methods and materials of the present invention, the amount of a specific polypeptide of interest may be increased or reduced by incorporating additional copies of genes, or coding sequences, encoding the polypeptide, operably linked to an inventive promoter sequence, into the genome of a target organism, such as a plant. Similarly, an increase or decrease in the amount of the polypeptide may be obtained by transforming the target plant with antisense copies of such genes.
The polynucleotides of the present invention were isolated from forestry plant sources, namely from Eucalyptus grandis and Pinus radiata, but they may alternatively be synthesized using conventional synthesis techniques. Specifically, isolated polynucleotides of the present invention include polynucleotides comprising a sequence selected from the group consisting of sequences identified as SEQ ID NO: 1-14, 20, 22-62, 81-86, 88-127 and 131-143; complements of the sequences identified as SEQ ID NO: 1-14, 20, 22-62, 81-86, 88-127 and 131-143; reverse complements of the sequences identified as SEQ ID NO: 1-14, 20, 22-62, 81-86, 88-127 and 131-143; at least a specified number of contiguous residues (x-mers) of any of the above-mentioned polynucleotides; extended sequences corresponding to any of the above polynucleotides; antisense sequences corresponding to any of the above polynucleotides; and variants of any of the above polynucleotides, as that term is described in this specification.
In another embodiment, the present invention provides isolated polypeptides encoded by the polynucleotides of SEQ ID NO: 63-80, 87 and 130.
The polynucleotides and polypeptides of the present invention were identified by DNA and polypeptide similarity searches. In the attached Sequence Listing, SEQ ID NOS. 1-14, 20, 22-62, 81-86, 88-127 and 131-143 are polynucleotide sequences, and SEQ ID NOS. 63-80, 87 and 130 are polypeptide sequences. The polynucleotides and polypeptides of the present invention are involved in regulation of transcription and/or expression in plants. The identity of each of the inventive polynucleotides is shown below in Table 1, together with the 5' untranslated region (5' UTR) or promoter region (identified by residue number).










TABLE 1





Polynucleotide
Polypeptide




SEQ ID NO:
SEQ ID NO:
5′ UTR
IDENTITY


















1
80
1-2064
Super Ubiquitin coding





region and UTRs


2
—
1-2064
Super Ubiquitin promoter





with intron


3
—
1-1226
Super Ubiquitin promoter





without intron


4
—
1-431
Cell division control


5
—
1-167
Xylogenesis - specific


6
—
1-600
4-Coumarate-CoA Ligase





(4CL)


7
—
1-591
Cellulose synthase


8
—
1-480
3′ end, Cellulose





synthase


20
—
1-363
5′ end, Cellulose





synthase


9
—
1-259
Leaf specific


10
—
1-251
Leaf specific


11
—
1-248
Leaf specific


12
—
1-654
O-methyl transferase


13
—
1-396
Root specific


14
—
1-763
Root specific


22
63
1-406
Pollen coat protein


23
—
1-350
Pollen allergen


24
—
1-49
Pollen allergen


25
64
1-284
Pollen allergen


26
65
1-77
Auxin-induced protein


27
—
1-74
Auxin-induced protein


28
66
1-99
Auxin-induced protein


29
—
1-927
Flower specific


30
—
1-411
Flower specific


31
—
1-178
Flower specific


32
—
1-178
Flower specific


33
—
1-178
Flower specific


34
67
1-805
Ubiquitin


35
68
1-81
Glyceraldehyde-3-





phosphate dehydrogenase


36
69
1-694
Carbonic anhydrase


37
—
1-648
Isoflavone reductase


38
—
1-288
Isoflavone reductase


39
—
1-382
Glyceraldehyde-3-





phosphate dehydrogenase


40
70
1-343
Bud specific


41
—
1-313
Xylem-specific


42
—
1-713
Xylem-specific


43
—
1-28
Xylem-specific


44
—
1-35
Xylem-specific


45
71
1-180
Meristem-specific


46
72
1-238
Senescence-like protein


47
—
1-91
Senescence-like protein


48
—
1-91
Senescence-like protein


49
—
1-809
Pollen-specific


50
—
1-428
Pollen-specific


51
73
1-55
Pollen-specific


52
74
1-575
Pollen-specific


53
75
1-35
Pollen-specific


54
—
1-335
Nodulin homolog pollen





specific


55
—
1-336
Nodulin homolog pollen





specific


56
76
1-157
Sucrose synthase


57
77
1-446
Sucrose synthase


58
—
1-326
Sucrose synthase


59
—
1-311
Flower specific


60
78
1-694
O-methyl transferase


61
79
1-112
Elongation factor A


62
—
1-420
Elongation factor A


81
—
—
MIF homologue


82
—
—
MIF homologue


83
—
—
MIF homologue


84
—
—
MIF homologue


85
—
—
MIF homologue


86
87
1-87
MIF homologue


88
—
1-1156
Chalcone synthase


89
—
1-2590
Unknown flower specific


90
—
1-1172
Unknown flower specific


91
—
1-446
Sucrose synthase


92
—
1-2119
Unknown xylem specific


93
—
1-2571
Glyceraldehyde-3-





Phosphate dehydrogenase


94
—
1-1406
Unknown pollen specific


95
—
1-2546
Pinus radiata male-





specific protein





(PrMALE1)


96
—
1-4726
Pinus radiata male-





specific protein





(PrMALE1)


97
—
1-635
UDP glucose glycosyl-





transferase


98
—
1-468
Elongation Factor A1


99
—
1-222
Elongation Factor A1


100
—
1-410
S-adenosylmethionine





synthetase


101
—
1-482
S-adenosylmethionine





synthetase


102
—
1-230
S-adenosylmethionine





synthetase


103
—
1-596
UDP glucose 6 dehydro-





genase


104
—
1-653
Hypothetical protein


105
—
1-342
Laccase 1


106
—
1-342
Laccase 1


107
—
1-948
Arabinogalactan-like 1


108
—
1-362
Arabinogalactan-like 2


109
—
1-326
Arabinogalactan like-2


110
—
1-296
Root Receptor-like





kinase


111
—
1-723
Root Receptor-like





kinase


112
—
1-1301
Pinus radiata Lipid





Transfer Protein 2





(PrLTP2)


113
—
1-1668
Caffeic acid O-methyl-





transferase


114
—
1-850
UDP glucose glycosyl-





transferase


115
—
1-986
UDP glucose 6 dehydro-





genase


116
—
1-947
Laccase 1


117
—
1-1766
Arabinogalactan like-1


118
—
1-1614
Constans


119
—
1-602
Flowering Promoting





Factor 1 (FPF1)


120
—
1-901
Agamous


121
—
1-1,245
Dreb 1A Transcription





factor


122
—
1-959
Drought Induced





Protein 19


123
—
1-1,140
Salt Tolerance protein


124
130
1-887
Low Temperature Induced





LTI-16


125
—
1-1,243
Xylem specific receptor-





like kinase


126
—
1-1,047
Root specific


127
—
1-3,552
Elongation Factor 1-





alpha


131

1-
Superubiquitin deletion





sequence without intron





including 195 bp





upstream of TATA box


132

1-
Superubiquitin deletion





sequence without intron





including 368 bp





upstream of TATA box


133

1-
Superubiquitin deletion





sequence without intron





including 446 bp





upstream of TATA box


134

1-
Superubiquitin deletion





sequence without intron





including 573 bp





upstream of TATA box


135

1-
Superubiquitin deletion





sequence without intron





including 753 bp





upstream of TATA box


136

1-1156
Superubiquitin deletion





sequence with intron





including 195 bp





upstream of TATA box


137

1-1329
Superubiquitin deletion





sequence with intron





including 368 bp





upstream of TATA box


138

1-1407
Superubiquitin deletion





sequence with intron





including 446 bp





upstream of TATA box


139

1-1534
Superubiquitin deletion





sequence with intron





including 573 bp





upstream of TATA box


140

1-1714
Superubiquitin deletion





sequence with intron





including 753 bp





upstream of TATA box


141

1-1193
Full length superubi-





quitin promoter


142

1-
Full length superubi-





quitin promoter with





intron


143

1-
Full length superubi-





quitin promoter with





intron and coding





sequence and 3′ UTR









In one embodiment, the present invention provides polynucleotide sequences isolated from Pinus radiata and Eucalyptus grandis that have promoter activity and, in Pinus radiata and Eucalyptus grandis are associated with the coding region for a ubiquitin polypeptide. The ubiquitin promoter isolated from Pinus radiata and disclosed herein is referred to herein as “superubiquitin” as a consequence of its high level of promoter activity. Full-length sequences for the ubiquitin polynucleotide isolated from Pinus radiata, including the full-length superubiquitin promoter, an intron, the ubiquitin coding sequence and the 3' UTR are provided in SEQ ID NOS: 1 and 143, with sequence for the promoter region including an intron being provided in SEQ ID NOS: 2 and 142, and sequences for the promoter region excluding the intron being provided in SEQ ID NOS: 3 and 141. The sequences vary slightly in length and composition as a consequence of using different sequencing techniques and criteria.
An annotated version of the full-length ubiquitin polynucleotide of SEQ ID NO: 143, including the full-length superubiquitin promoter, an intron, the ubiquitin coding sequence and the 3' UTR, is shown in FIGS. 6A and 6B. In the figures, an intron is shown, underlined, at residues 1196-2035; the coding region for the ubiquitin protein is shown, in bold, at residues 2066-2755; the 3'UTR is shown at residues 2756-3084; and the full-length promoter is shown at residues 1-1193.
Polynucleotide motifs identified in the full-length ubiquitin polynucleotide of SEQ ID NO: 143 are shown in the annotations of FIGS. 6A and 6B.
Numerous forms and variations of the superubiquitin promoter have demonstrated promoter activity in experimental studies. Preliminary studies, performed by introducing constructs containing the GFP reporter gene operably linked to either the superubituitin promoter of SEQ ID NO: 2 (promoter with intron) or SEQ ID NO: 3 (promoter without intron) into Arabidopsis, are described below in Example 1. These preliminary studies showed that the superubiquitin promoter, both with and without the intron, demonstrated promoter activity, with the intron-less sequence showing higher levels of expression than the promoter sequence with the intron.
Subsequent studies are described in Examples 16, 17, 20 and 21. Experimental studies described in Example 16, done in Arabidopsis plants and quantitating GUS activity, demonstrated that a construct containing the superubiquitin promoter without the intron showed seven (7) times more GUS activity than the commercial CaMV 35S promoter, and the construct containing the superubiquitin promoter with the intron showed sixty-two (62) times more GUS activity than the CaMV 35S promoter. These follow-up studies thus confirmed that both the superubiquitin promoter sequence, with and without the intron, show high levels of promoter activity, with the superubiquitin sequence including the intron showing exceptionally high levels of promoter activity. Studies described in Example 17, done in tobacco protoplasts, demonstrated promoter activity of deletion constructs of the superubiquitin promoter, both with and without the intron. These studies confirmed that both the superubiquitin promoter sequence, with and without the intron, show high levels of promoter activity, with the superubiquitin sequence including the intron showing exceptionally high levels of promoter activity. Some of the deletion constructs demonstrated promoter activity, with greater activity in the longer constructs and no activity in the shortest constructs.
Experimental studies using superubiquitin deletion constructs, both with and without the intron, were repeated in Arabidopsis and tobacco plants, as described in Example 21. These experiments demonstrated that the partial superubiquitin promoter sequences of SEQ ID NOS: 132, 133, 134, 135, 137, 138, 139 and 140 showed constitutive promoter activity by GUS staining, in both Arabidopsis and tobacco plants. Only the shortest deletion constructs, SEQ ID NOS: 131 and 136, did not show constitutive promoter activity by GUS staining in the experimental studies described in Example 21.
Example 20 describes experimental work done to determine the effect of the 3'UTR superubiquitin sequences on gene expression in Arabidopsis. These studies showed that a construct containing the superubiquitin 3'UTR in the sense orientation and the intron-less superubiquitin promoter demonstrated high GUS expression levels, and enhanced the expression of the superubiquitin intron-less promoter to nearly the level of the superubiquitin promoter with the intron. This demonstrates that the combination of the superubiquitin promoter without the intron and the ubiquitin 3'UTR shows high levels of promoter activity.
The present invention thus contemplates a polynucleotide having promoter activity comprising a sequence of one of SEQ ID NOS: 2, 3, 132-135 and 137-142, as well as fragments and variants of such sequences having promoter activity. The present invention furthermore contemplates a polynucleotide having promoter activity comprising a sequence of one of SEQ ID NOS: 2, 3, 132-135 and 137-142, as well as fragments and variants of such sequences having promoter activity, in combination with a fragment of the 3'UTR ubiquitin sequence in the sense orientation. The 3'UTR ubiquitin sequence includes residues 2,755-3,073 of SEQ ID NO: 1 and is shown, in FIGS. 6A and 6B, as residues 2756-3084. A 250 bp fragment of the 3'UTR ubiquitin sequence, including residues 2,755-3,073 of SEQ ID NO: 1 is suitable and one of skill in the art would anticipate that smaller fragments and fragments from elsewhere within the ubiquitin 3'UTR would, in combination with a sequence of one of SEQ ID NOS: 2, 3, 132-135 and 137-142, as well as fragments and variants of such sequences, provide a sequence having promoter activity.
Numerous motifs have been identified in superubiquitin sequences, and in deletion constructs used to test the promoter activity of fragments of the superubiquitin promoter. Various of the motifs are described below in Table 2, and are identified in the sequences shown in FIGS. 6-16.









TABLE 2





REF-
POLY-



ERENCE
NUCLEOTIDE


NUMBER
MOTIF
DESCRIPTION

















1
TATAAT
−10 Mustard plastid box, also a




Pribnow box, first TA and last T




highly conserved


2
TATAAAA
(TATTAAA in SU promoter); a −35




Mustard plastid gene TATA box


3
TATTTWAT
(TATTTAAT in SU promoter); Nodule




specific nuclear factor (NAT2,




soybean). This sequence is important




for protein recognition (Forde et al.,




Plant Cell 2:925-939, 1990)


4
CACGTG
G-box-binding factor (GBF) commonly




found in many plant promoters which




binds a subclass of bZIP DNA binding




proteins. These elements are targets




for nuclear DNA-binding factors, e.g.




chlorophyll a/b binding proteins and




chalcone synthase. ACGT is the core




sequence and is also known as R-motif.




Found in light-responsive genes, e.g.,




rbcS and chalcone synthase (chs),




but also in other unrelated genes such as




adh, Bz-2, Em, and chs. Binds with




GBF (G box of rbcS), with GT-1 or




with cG-1 (chs); ABA; UV; visible




light; Factors groups 1, 2 and 3 have




affinity for C-box; G-box is not




essential for the elicitor responsiveness




of the Str1 gene. GBF4 has similarities




to Fos oncoprotein (Menkens and




Cashmore, Proc. Natl. Acad. Sci. USA




91:2522-2526, 1994). The G-box is a




cis-acting DNA sequence present




in several plant promoters that are




regulated by diverse signals such as




UV irradiation, anaerobiosis, abscissic




acid and light. Several basic/leucine




zipper (bZIP) proteins from




different plant species have been




identified as high affinity G-box binding




proteins. Although their capability to




enhance transcription has been




demonstrated, their precise function




in transcriptional activation is still




unknown (Meier and Gruissem, Nucleic




Acids Res. 22:470-478, 1994).


5
TCTTTTC (C/T
Pyrimidine box sequence, amylase



CTTTT C/T)
gene, is implied but not required




for GA3 inducibility.


6
ACCTTTCC
If G is substituted for T, this motif is an




8 bp motif adjacent to wound




inducible nuclear protein binding site.


7
TCTCCAC
Origin of genes and nuclear extract -




Parsley PAL and 4CL genes


8
GATAAG
Origin of genes and nuclear extract -




Lemna and Arabidopsis rbcS




gene, tobacco cabE gene I-box, binding




factor LRF-1


9
AACCCA
Soybean embryo factor 3 (SEF3)




binding site. Soybean B-conglycinin




gene alpha subunit (embryo-specific)




SEF-3, SEF-1 binding factors. Soybean




(Glycine max) consensus sequence




found in the 5′ upstream region of




beta-conglycinin (7S globulin) gene;




AACCCA(-27 bp-)AACCCA.


10
TGACG
ASF-1 binding site in CaMV 35S pro-




moter. ASF-1 binds to two TGACG




motifs. The same motif is also found




in HBP-1 binding site of wheat histone




H3 gene. TGACG motifs are found in




many promoters and are involved in




transcriptional activation of several




genes by auxin and/or salicylic acid




and play a role in light regulation.




It is also the binding site of tobacco




TGA1a (TGA1a-sequence specific




binding protein). Activating sequence




factor 1 (ASF-1) is a nuclear DNA-




binding activity that is found in




monocots and dicots. It interacts with




several TGACG-containing elements




that have been characterized from viral




and T-DNA genes, the prototypes of




which are the as-1 element of the




CaMV 35S promoter and the ocs




element from the octopine synthase




promoter. This class of cis-acting




elements can respond to auxin and




salicylic acid treatments (Lam and




Lam, Nucleic Acids Res. 23:3778-3785,




1005).


11
GATA
Binding site, designated as-2 (activating




sequence-2) at the −100 region of the




cauliflower mosaic virus 35S promoter.




These motifs are related to the I-boxes




which bind nuclear factors. Similar




to the GATA motif in CaMV 35S pro-




moter. Binding with ASF-2; three




GATA box repeats were found in the




promoter of Petunia (P.h.) chlorophyll




a/b binding protein, Cab22 gene;




required for high level, light




regulated, and tissue specific expres-




sion; Conserved in the promoter of all




LHCII type I Cab genes.


12
GTGG
Maize Adh1 B1 G-box cis-acting DNA




sequence elements are present in the




promoter region of a number of signal-




inducible plant genes and are essential




for gene expression.


13
CCCC
Arabidopsis AdH interacts with GBF


14
CCAGCGG
The AT-1 binding site in cabE gene,




tobacco, if C were a T.


15
GAGAAG
I-box binding GA-1 for tobacco cabE




gene >IBOX “I box”; “I-box”; Con-




served sequence upstream of light-




regulated genes; Sequence found in the




promoter region of rbcS of tomato and




Arabidopsis; I box (Giuliano et al.




1988); Binding site of LeMYB1, which




is a member of a novel class of myb-




like proteins; LeMYBI act as a




transcriptional activator GAGAA =




>IBOXCORE “I box”; “I-box”;




Conserved sequence upstream of light-




regulated genes; Conserved sequence




upstream of light-regulated genes of




both monocots and dicots; See IBOX




(S000124)


16
GGATA
MYBST1 core motif >MYBST1 Core




motif of MybSt1 (a potato MYB




homolog) binding site; core motif of




MybSt1 (a potato MYB homolog)




binding site; MybSt1 cDNA clone was




isolated by using CaMV 35S promoter




domain A as a probe (Baranowskij et al.




1994); The Myb motif of the MybSt1




protein is distinct from the plant Myb




DNA binding domain described




thus far.


17
TGTAAAG
Prolamin box or P Box is a highly con-




served 7-bp sequence element found in




the promoters of many cereal seed




storage protein genes. Nuclear factors




from maize endosperm specifically




interact with the P-box present in maize




prolamin genes (zeins). A prolamin-box




binding factor (PBF) has been identified




that encodes a member of the recently




described Dof class of plant




Cys2-Cys2 zinc-finger DNA binding




proteins. PBF interacts in vitro with the




basic leucine zipper protein Opaque2, a




known transcriptional activator of zein




gene expression. (Vicente-Carbajosa




et al., Proc. Natl. Acad. Sci.




USA 94:7685-7690, 1997).


18
TGTCTC
Occurs 3 times in intron: auxin response




factor (ARF) binding site found in the




promoters of primary/early auxin




response genes of Arabidopsis thaliana.




More than 10 ARFs have been identi-




fied in A. thaliana. This conserved




sequence is the binding site of




Arabidopsis ARF1 (Auxin response




factor 1) in auxin response elements




(Ulmasov et al., Science




276:1865-1868, 1997). The sequence is




also found in the NDE element in




soybean (Li et al., Plant Physiol.




106:37-43, 1994) 15A gene promoter.




The NDE element is involved in




auxin responsiveness in SAUR (Small




Auxin-Up RNA) by conferring auxin




inducibility to the SAUR promoters.


19
AGCGGG
BS1 (binding site 1) found in




Eucalyptus gunnii Cinnamoyl-CoA




reductase (CCR) gene promoter.




Cinnamoyl-CoA reductase (CCR)




catalyzes the first specific step in the




biosynthesis of monolignols, the




monomeric units of lignins. BS1 is a




nuclear protein binding site that




is required for vascular expression.


20
CAAT
CAAT promoter consensus sequence is




found in legA gene of pea


21
TGCAGG
This motif is commonly found at the




3′ of intron-exon splice junctions of




plant introns and exons.


22
ACCGACA
Low temperature responsive element




(LTRE) found in Arabidopsis thaliana




low-temperature-induced (lti) genes.




This element is repeated four times in




lti78 or cor78 and rd29A (Baker et




al., Plant Mol. Biol. 24:701, 1994). The




element is also found in the barley low




temperature responsive genes blt4.2,




blt4.6, blt4.9 (lipid transfer genes)




and is cold inducible (Nordin et al.,




Plant Mol. Biol. 21:641-653, 1993).




The core motif is CCGAC and is a




portion of repeat-C (C-repeat),




TGGCCGAC, which is repeated twice




in con15a promoter. This element




plays a role in cold-regulated gene




expression of the cor15a gene and is




also involved in drought and abscisic




acid (ABA) responsiveness (Baker




et al., Plant Mol. Biol. 24:701-713




1994).


23
CTAACCA
Binding site for MYB (ATMYB2) in




the dehydration-responsive gene rd22,




that is induced by ABA-induction




(Iwasaki et al., Mol. Gen. Genet.




247:391-398, 1995).


24
TAACAAA
Central element of gibberellin (GA)




response complex (GARC) in high-pI




alpha-amylase gene in barley and




similar to c-myb and v-myb consensus




binding site. GAmyb binds




specifically to the TAACAAA box




in vitro and is the sole GA-regulated




transcriptional factor required for




transcriptional activation of the




high-pI alpha-amylase (Rogers and




Rogers, Plant Cell 4:1443-1451, 1992).


25
CCWACC
Core of consensus maize P (myb




homolog) binding site where W could




be A or T. Maize P gene specifies red




pigmentation of kernel pericarp,




cob, and other floral organs. (Grotewold




et al., Cell 76:543-553 1994).


26
CACATG
Identified in SU intron. Binding site




for MYC (rd22BP1) in Arabidopsis




dehydration-resposive gene, rd22 rd22,




that is induced by ABA-induction




(Iwasaki et al., Mol. Gen. Genet.




247:391-398, 1995).


27
CATCCAACG
Nonamer motif found in promoter of




wheat histone genes H3 and H4 (Shen




and Gigot, Plant Mol. Biol. 33:367-379,




1997).


28
ACTTTA
Identified in SU intron - BBF1 (Dof




protein from tobacco) binding site in




Agrobacterium rhizogenes rolB




oncogene and is required for tissue-




specific expression and auxin induction




of rolB (Baumann et al., Plant Cell




11:323-334, 1999).


29
AGAAA
AGAAA and TCCACCATA (S000246)




are required for pollen specific




expression in SU; TCCACCATA:




one of two co-dependent regulatory




elements responsible for pollen




specific activation of tomato (L.e.) lat52




gene; Found at −72 to −68 region;




See S000246 (POLLEN2LELAT52).


30
CCTTTT
In intron; pyrimidine box found in rice




(O.s.) alpha-amylase (RAmy1A) gene;




Gibberellin-response cis-element of




GARE and pyrimidine box are




partially involved in sugar repression.


31
CAACA
Binding consensus sequence of




Arabidopsis (A.t.) transcription




factor, RAV1; RAV1 specifically binds




to DNA with bipartite sequence motifs




of RAV1-A (CAACA) and RAV1-B




(CACCTG); RAV1 protein contain




AP2-like and B3-like domains; The




AP2-like and B3-like domains




recognize the CAACA and CACCTG




motifs, respectively; The expression




level of RAV1 were relatively high in




rosette leaves and roots; See




S000315(CACCTG).


32
AATCCAA
“rbcS general consensus sequence”;




AATCCAA or AATCCAAC


33
AACCAA
2 motifs present; “REalpha” found in




Lemna gibba Lhcb21 gene promoter;




Located at −134 to −129; Binding




site of proteins of whole-cell




extracts; The DNA binding activity is




high in etiolated plants but much




lower in green plants; Required for




phytochrome regulation; See S000363


34
TACTATT
In intron; one of SPBF binding site




(SP8b); Found at −330, −220, and −200




of gSPO-B1 (sporamin) gene, and also




at −80 of gB-Amy (beta-amylase) gene;




SP8BF recognizes both SP8a and SP8b




sequences; See also SP8BFIBSP8AIB




(S000183); SP8BF activity is also




found in tobacco; “SP8b” found




in the 5′ upstream region of three




different genes coding for sporamin and




beta-amylase; Binding site of




SPF1; SPF1 also binds to the SP8b; See




S000184.


35
TATCCAY
(TATCCAC in SU promoter);




“TATCCAY motif” found in rice




(O.s) RAmy3D alpha-amylase gene pro-




moter; Y = T/C; a GATA motif




as its antisense sequence; TATCCAY




motif and G motif (see S000130) are




responsible for sugar




repression (Toyofuku et al. 1998).


36
ATAAAAAAAATT
The AT-1 binding site in cabE gene,




tobacco, if A were a T.









SEQ ID NO: 132 is the shortest fragment of the superubiquitin promoter for which promoter activity has been demonstrated experimentally. SEQ ID NO: 32 includes motifs 12, 14, 4, 15, 10, 9, 22, 4, 13, 19, 15, 27, 2, 5, 1 and 11, as described above in Table 2. It is expected that a sequence comprising at least ten (10), more preferably twelve (12), and most preferably fifteen (15) of the sixteen (16) motifs, selected from the group consisting of: motifs 12, 14, 4, 15, 10, 9, 22, 4, 13, 19, 15, 27, 2, 5, 1 and 11, as described above in Table 2, would exhibit promoter activity, and such sequences are contemplated by the present invention. Such sequences may also be combined with a 3'UTR fragment of the ubiquitin sequence comprising at least 50 consecutive bp, more preferably at least 100 or 150 consecutive bp, and most preferably at least 250 consecutive bp from the ubiquitin 3'UTR sequence identified as residues 2,755-3,073 of SEQ ID NO: 1. Additionally or alternatively, such sequences may also be combined with an intron, such as the intron identified as residues 1196-2034 of SEQ ID NO: 143 or 142. Fragments of the 3'UTR and intron sequences may also be combined with the sequences of SEQ ID NOS: 132-135 and 137-140 to provide promoters of the present invention. All of these sequences have features in common, in that they share ten or more common motifs, as described above, and more likely share sequence similarities over a substantial portion of the sequence.
The sequence for the ubiquitin polynucleotide isolated from Eucalyptus grandis is provided in SEQ ID NO: 34. In a related embodiment, the present invention provides isolated polypeptides encoded by the isolated polynucleotides of SEQ ID NO: 1 and 34, including polypeptides comprising the sequences of SEQ ID NO: 80 and 67.
The term “polynucleotide(s),” as used herein, means a single or double-stranded polymer of deoxyribonucleotide or ribonucleotide bases and includes DNA and corresponding RNA molecules, including HnRNA and mRNA molecules, both sense and anti-sense strands, and comprehends cDNA, genomic DNA and recombinant DNA, as well as wholly or partially synthesized polynucleotides. An HnRNA molecule contains introns and corresponds to a DNA molecule in a generally one-to-one manner. An mRNA molecule corresponds to an HnRNA and DNA molecule from which the introns have been excised. A polynucleotide may consist of an entire gene, or any portion thereof. Operable anti-sense polynucleotides may comprise a fragment of the corresponding polynucleotide, and the definition of “polynucleotide” therefore includes all such operable anti-sense fragments. Anti-sense polynucleotides and techniques involving anti-sense polynucleotides are well known in the art and are described, for example, in Robinson-Benion et al. “Antisense techniques,” Methods in Enzymol. 254(23):363-375, 1995; and Kawasaki et al., in Artific. Organs 20(8):836-848, 1996.
All of the polynucleotides and polypeptides described herein are isolated and purified, as those terms are commonly used in the art. Preferably, the polypeptides and polynucleotides are at least about 80% pure, more preferably at least about 90% pure, and most preferably at least about 99% pure.
The definition of the terms “complement”, “reverse complement” and “reverse sequence”, as used herein, is best illustrated by the following example. For the sequence 5' AGGACC 3', the complement, reverse complement and reverse sequence are as follows:











Complement
3′ TCCTGG 5′




 



Reverse complement
3′ GGTCCT 5′



 



Reverse sequence
5′ CCAGGA 3′






Some of the polynucleotides of the present invention are “partial” sequences, in that they do not represent a full-length gene encoding a full-length polypeptide. Such partial sequences may be extended by analyzing and sequencing various DNA libraries using primers and/or probes and well known hybridization and/or PCR techniques. Partial sequences may be extended until an open reading frame encoding a polypeptide, a full-length polynucleotide and/or gene capable of expressing a polypeptide, or another useful portion of the genome is identified. Such extended sequences, including full-length polynucleotides and genes, are described as “corresponding to” a sequence identified as one of the sequences of SEQ ID NO: 1-14, 20, 22-62, 81-86 and 88-127, or a variant thereof, or a portion of one of the sequences of SEQ ID NO: 1-14, 20, 22-62, 81-86 and 88-127, or a variant thereof, when the extended polynucleotide comprises an identified sequence or its variant, or an identified contiguous portion (x-mer) of one of the sequences of SEQ ID NO: 1-14, 20, 22-62, 81-86 and 88-127, or a variant thereof. Such extended polynucleotides may have a length of from about 50 to about 4,000 nucleic acids or base pairs, and preferably have a length of less than about 4,000 nucleic acids or base pairs, more preferably yet a length of less than about 3,000 nucleic acids or base pairs, more preferably yet a length of less than about 2,000 nucleic acids or base pairs. Under some circumstances, extended polynucleotides of the present invention may have a length of less than about 1,800 nucleic acids or base pairs, preferably less than about 1,600 nucleic acids or base pairs, more preferably less than about 1,400 nucleic acids or base pairs, more preferably yet less than about 1,200 nucleic acids or base pairs, and most preferably less than about 1,000 nucleic acids or base pairs.
Similarly, RNA sequences, reverse sequences, complementary sequences, antisense sequences, and the like, corresponding to the polynucleotides of the present invention, may be routinely ascertained and obtained using the cDNA sequences identified as SEQ ID NO: 1-14, 20, 22-62, 81-86 and 88-127.
The polynucleotides identified as SEQ ID NO: 1-14, 20, 22-62, 81-86 and 88-127, and their extensions, may contain open reading frames (“ORFs”) or partial open reading frames encoding polypeptides. Additionally, open reading frames encoding polypeptides may be identified in extended or full length sequences corresponding to the sequences set out as SEQ ID NO: 1-14, 20, 22-62, 81-86 and 88-127. Open reading frames may be identified using techniques that are well known in the art. These techniques include, for example, analysis for the location of known start and stop codons, most likely reading frame identification based on codon frequencies, etc. Suitable tools and software for ORF analysis include, for example, “GeneWise”, available from The Sanger Center, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, United Kingdom; “Diogenes”, available from Computational Biology Centers, University of Minnesota, Academic Health Center, UMHG Box 43, Minneapolis Minn. 55455 and “GRAIL”, available from the Informatics Group, Oak Ridge National Laboratories, Oak Ridge, Tenn. Open reading frames and portions of open reading frames may be identified in the polynucleotides of the present invention. Once a partial open reading frame is identified, the polynucleotide may be extended in the area of the partial open reading frame using techniques that are well known in the art until the polynucleotide for the full open reading frame is identified. Thus, open reading frames encoding polypeptides may be identified using the polynucleotides of the present invention.
Once open reading frames are identified in the polynucleotides of the present invention, the open reading frames may be isolated and/or synthesized. Expressible genetic constructs comprising the open reading frames and suitable promoters, initiators, terminators, etc., which are well known in the art, may then be constructed. Such genetic constructs may be introduced into a host cell to express the polypeptide encoded by the open reading frame. Suitable host cells may include various prokaryotic and eukaryotic cells, including plant cells, mammalian cells, bacterial cells, algae and the like.
Polypeptides encoded by the polynucleotides of the present invention may be expressed and used in various assays to determine their biological activity. Such polypeptides may be used to raise antibodies, to isolate corresponding interacting proteins or other compounds, and to quantitatively determine levels of interacting proteins or other compounds.
The term “polypeptide”, as used herein, encompasses amino acid chains of any length including full length proteins, wherein amino acid residues are linked by covalent peptide bonds. Polypeptides of the present invention may be isolated and purified natural products, or may be produced partially or wholly using recombinant techniques. The term “polypeptide encoded by a polynucleotide” as used herein, includes polypeptides encoded by a nucleotide sequence which includes the partial isolated DNA sequences of the present invention.
In a related aspect, polypeptides are provided that comprise at least a functional portion of a polypeptide having a sequence selected from the group consisting of sequences provided in SEQ ID NO: 63-80, 87 and 130, and variants thereof. As used herein, the “functional portion” of a polypeptide is that portion which contains the active site essential for affecting the function of the polypeptide, for example, the portion of the molecule that is capable of binding one or more reactants. The active site may be made up of separate portions present on one or more polypeptide chains and will generally exhibit high binding affinity.
Functional portions of a polypeptide may be identified by first preparing fragments of the polypeptide by either chemical or enzymatic digestion of the polypeptide, or by mutation analysis of the polynucleotide that encodes the polypeptide and subsequent expression of the resulting mutant polypeptides. The polypeptide fragments or mutant polypeptides are then tested to determine which portions retain biological activity, using, for example, the representative assays provided below. A functional portion comprising an active site may be made up of separate portions present on one or more polypeptide chains and generally exhibits high substrate specificity.
Portions and other variants of the inventive polypeptides may be generated by synthetic or recombinant means. Synthetic polypeptides having fewer than about 100 amino acids, and generally fewer than about 50 amino acids, may be generated using techniques well known to those of ordinary skill in the art. For example, such polypeptides may be synthesized using any of the commercially available solid-phase techniques, such as the Merrifield solid-phase synthesis method, wherein amino acids are sequentially added to a growing amino acid chain. (Merrifield, J. Am. Chem. Soc. 85: 2149-2154, 1963). Equipment for automated synthesis of polypeptides is commercially available from suppliers such as Perkin Elmer/Applied Biosystems, Inc. (Foster City, Calif.), and may be operated according to the manufacturer's instructions. Variants of a native polypeptide may be prepared using standard mutagenesis techniques, such as oligonucleotide-directed site-specific mutagenesis (Kunkel, Proc. Natl. Acad. Sci. USA 82: 488-492, 1985). Sections of DNA sequences may also be removed using standard techniques to permit preparation of truncated polypeptides.
As used herein, the term “variant” comprehends nucleotide or amino acid sequences different from the specifically identified sequences, wherein one or more nucleotides or amino acid residues is deleted, substituted, or added. Variants may be naturally occurring allelic variants, or non-naturally occurring variants. Variant sequences (polynucleotide or polypeptide) preferably exhibit at least 50%, more preferably at least 75%, and most preferably at least 90% identity to a sequence of the present invention. The percentage identity is determined by aligning the two sequences to be compared as described below, determining the number of identical residues in the aligned portion, dividing that number by the total number of residues in the inventive (queried) sequence, and multiplying the result by 100.
Polynucleotide and polypeptide sequences may be aligned, and percentage of identical residues in a specified region may be determined against other polynucleotide and polypeptide sequences, using computer algorithms that are publicly available. Two exemplary algorithms for aligning and identifying the similarity of polynucleotide sequences are the BLASTN and FASTA algorithms. Polynucleotides may also be analyzed using the BLASTX algorithm, which compares the six-frame conceptual translation products of a nucleotide query sequence (both strands) against a protein sequence database. The similarity of polypeptide sequences may be examined using the BLASTP algorithm. The BLASTN algorithm Version 2.0.4 [Feb.-24-1998], Version 2.0.6 [Sep.-16-1998] and Version 2.0.11 [Jan.-20-2000], set to the default parameters described in the documentation and distributed with the algorithm, are preferred for use in the determination of polynucleotide variants according to the present invention. The BLASTP algorithm, is preferred for use in the determination of polypeptide variants according to the present invention. The use of the BLAST family of algorithms, including BLASTN, BLASTP, and BLASTX, is described in the publication of Altschul, et al., “Gapped BLAST and PSI-BLAST: a new generation of protein database search programs,” Nucleic Acids Res. 25: 3389-3402, 1997. The BLASTN software is available on the NCBI anonymous FTP server (ftp://ncbi.nlm.nih.gov) under /blast/executables/ and is available from the National Center for Biotechnology Information (NCBI), National Library of Medicine, Building 38A, Room 8N805, Bethesda, Md. 20894 USA.
The FASTA software package is available from the University of Virginia (University of Virginia, PO Box 9025, Charlottesville, Va. 22906-9025). Version 2.0u4, February, 1996, set to the default parameters described in the documentation and distributed with the algorithm, may be used in the determination of variants according to the present invention. The use of the FASTA algorithm is described in Pearson and Lipman, “Improved Tools for Biological Sequence Analysis,” Proc. Natl. Acad. Sci. USA 85: 2444-2448, 1988; and Pearson, “Rapid and Sensitive Sequence Comparison with FASTP and FASTA,” Methods in Enzymol. 183: 63-98, 1990.
The following running parameters are preferred for determination of alignments and similarities using BLASTN that contribute to the E values and percentage identity for polynucleotide sequences: Unix running command: blastall -p blastn -d embldb -e 10-G0 -E0 -r 1-v 30-b 30 -i queryseq -o results; the parameters are: -p Program Name [String]; -d Database [String]; -e Expectation value (E) [Real]; -G Cost to open a gap (zero invokes default behavior) [Integer]; -E Cost to extend a gap (zero invokes default behavior) [Integer]; -r Reward for a nucleotide match (BLASTN only) [Integer]; -v Number of one-line descriptions (V) [Integer]; -b Number of alignments to show (B) [Integer]; -i Query File [File In]; and -o BLAST report Output File [File Out] Optional.
The following running parameters are preferred for determination of alignments and similarities using BLASTP that contribute to the E values and percentage identity of polypeptide sequences: blastall -p blastp -d swissprotdb -e 10 -G 0-E 0 -v 30 -b 30 -i queryseq -o results; the parameters are: -p Program Name [String]; -d Database [String]; -e Expectation value (E) [Real]; -G Cost to open a gap (zero invokes default behavior) [Integer]; -E Cost to extend a gap (zero invokes default behavior) [Integer]; -v Number of one-line descriptions (v) [Integer]; -b Number of alignments to show (b) [Integer]; -I Query File [File In]; -o BLAST report Output File [File Out] Optional.
The “hits” to one or more database sequences by a queried sequence produced by BLASTN, FASTA, BLASTP or a similar algorithm, align and identify similar portions of sequences. The hits are arranged in order of the degree of similarity and the length of sequence overlap. Hits to a database sequence generally represent an overlap over only a fraction of the sequence length of the queried sequence.
The BLASTN, FASTA and BLASTP algorithms also produce “Expect” values for alignments. The Expect value (E) indicates the number of hits one can “expect” to see over a certain number of contiguous sequences by chance when searching a database of a certain size. The Expect value is used as a significance threshold for determining whether the hit to a database, such as the preferred EMBL database, indicates true similarity. For example, an E value of 0.1 assigned to a polynucleotide hit is interpreted as meaning that in a database of the size of the EMBL database, one might expect to see 0.1 matches over the aligned portion of the sequence with a similar score simply by chance. By this criterion, the aligned and matched portions of the polynucleotide sequences then have a probability of 90% of being the same. For sequences having an E value of 0.01 or less over aligned and matched portions, the probability of finding a match by chance in the EMBL database is 1% or less using the BLASTN or FASTA algorithm.
According to one embodiment, “variant” polynucleotides and polypeptides, with reference to each of the polynucleotides and polypeptides of the present invention, preferably comprise sequences having the same number or fewer nucleic or amino acids than each of the polynucleotides or polypeptides of the present invention and producing an E value of 0.01 or less when compared to the polynucleotide or polypeptide of the present invention. That is, a variant polynucleotide or polypeptide is any sequence that has at least a 99% probability of being the same as the polynucleotide or polypeptide of the present invention, measured as having an E value of 0.01 or less using the BLASTN, FASTA, or BLASTP algorithms set at parameters described above. According to a preferred embodiment, a variant polynucleotide is a sequence having the same number or fewer nucleic acids than a polynucleotide of the present invention that has at least a 99% probability of being the same as the polynucleotide of the present invention, measured as having an E value of 0.01 or less using the BLASTN or FASTA algorithms set at parameters described above. Similarly, according to a preferred embodiment, a variant polypeptide is a sequence having the same number or fewer amino acids than a polypeptide of the present invention that has at least a 99% probability of being the same as a polypeptide of the present invention, measured as having an E value of 0.01 or less using the BLASTP algorithm set at the parameters described above.
Alternatively, variant polynucleotides of the present invention hybridize to the polynucleotide sequences recited in SEQ ID NO: 1-14, 20, 22-62, 81-86 and 88-127, or complements, reverse sequences, or reverse complements of those sequences under stringent conditions. As used herein, “stringent conditions” refers to prewashing in a solution of 6X SSC, 0.2% SDS; hybridizing at 65° C., 6X SSC, 0.2% SDS overnight; followed by two washes of 30 minutes each in 1X SSC, 0.1% SDS at 65° C. and two washes of 30 minutes each in 0.2X SSC, 0.1% SDS at 65° C.
The present invention also encompasses polynucleotides that differ from the disclosed sequences but that, as a consequence of the discrepancy of the genetic code, encode a polypeptide having similar activity to a polypeptide encoded by a polynucleotide of the present invention. Thus, polynucleotides comprising sequences that differ from the polynucleotide sequences recited in SEQ ID NO: 1-14, 20, 22-62, 81-86 and 88-127, or complements, reverse sequences, or reverse complements thereof, as a result of conservative substitutions are contemplated by and encompassed within the present invention. Additionally, polynucleotides comprising sequences that differ from the polynucleotide sequences recited in SEQ ID NO: 1-14, 20, 22-62, 81-86 and 88-127, or complements, reverse complements or reverse sequences thereof, as a result of deletions and/or insertions totaling less than 10% of the total sequence length are also contemplated by and encompassed within the present invention. Similarly, polypeptides comprising sequences that differ from the polypeptide sequences recited in SEQ ID NO: 63-80, 87 and 130, as a result of amino acid substitutions, insertions, and/or deletions totaling less than 10% of the total sequence length are contemplated by an encompassed within the present invention. In certain embodiments, variants of the inventive polypeptides and polynucleotides possess biological activities that are the same or similar to those of the inventive polypeptides or polynucleotides. Such variant polynucleotides function as promoter sequences and are thus capable of modifying gene expression in a plant.
The polynucleotides of the present invention may be isolated from various libraries, or may be synthesized using techniques that are well known in the art. The polynucleotides may be synthesized, for example, using automated oligonucleotide synthesizers (e.g., Beckman Oligo 1000M DNA Synthesizer) to obtain polynucleotide segments of up to 50 or more nucleic acids. A plurality of such polynucleotide segments may then be ligated using standard DNA manipulation techniques that are well known in the art of molecular biology. One conventional and exemplary polynucleotide synthesis technique involves synthesis of a single stranded polynucleotide segment having, for example, 80 nucleic acids, and hybridizing that segment to a synthesized complementary 85 nucleic acid segment to produce a 5-nucleotide overhang. The next segment may then be synthesized in a similar fashion, with a 5-nucleotide overhang on the opposite strand. The “sticky” ends ensure proper ligation when the two portions are hybridized. In this way, a complete polynucleotide of the present invention may be synthesized entirely in vitro.
Polynucleotides of the present invention also comprehend polynucleotides comprising at least a specified number of contiguous residues (x-mers) of any of the polynucleotides identified as SEQ ID NO: 1-14, 20, 22-62, 81-86 and 88-127, complements, reverse sequences, and reverse complements of such sequences, and their variants. Similarly, polypeptides of the present invention comprehend polypeptides comprising at least a specified number of contiguous residues (x-mers) of any of the polypeptides identified as SEQ ID NO: 63-80, 87 and 130, and their variants. As used herein, the term “x-mer,” with reference to a specific value of “x,” refers to a sequence comprising at least a specified number (“x”) of contiguous residues of any of the polynucleotides identified as SEQ ID NO: 1-14, 20, 22-62, 81-86 and 88-127, or the polypeptides identified as SEQ ID NO: 63-80, 87 and 130. According to preferred embodiments, the value of x is preferably at least 20, more preferably at least 40, more preferably yet at least 60, and most preferably at least 80. Thus, polynucleotides and polypeptides of the present invention comprise a 20-mer, a 40-mer, a 60-mer, an 80-mer, a 100-mer, a 120-mer, a 150-mer, a 180-mer, a 220-mer, a 250-mer, a 300-mer, 400-mer, 500-mer or 600-mer of a polynucleotide or polypeptide identified as SEQ ID NO: 1-14, 20, 22-62, 81-86 and 88-127, and variants thereof.
As noted above, the inventive polynucleotide promoter sequences may be employed in genetic constructs to drive transcription and/or expression of a polynucleotide of interest. The polynucleotide of interest may be either endogenous or heterologous to an organism, for example a plant, to be transformed. The inventive genetic constructs may thus be employed to modulate levels of transcription and/or expression of a polynucleotide, for example gene, that is present in the wild-type plant, or may be employed to provide transcription and/or expression of a DNA sequence that is not found in the wild-type plant.
In certain embodiments, the polynucleotide of interest comprises an open reading frame that encodes a target polypeptide. The open reading frame is inserted in the genetic construct in either a sense or antisense orientation, such that transformation of a target plant with the genetic construct will lead to a change in the amount of polypeptide compared to the wild-type plant. Transformation with a genetic construct comprising an open reading frame in a sense orientation will generally result in over-expression of the selected polypeptide, while transformation with a genetic construct comprising an open reading frame in an antisense orientation will generally result in reduced expression of the selected polypeptide. A population of plants transformed with a genetic construct comprising an open reading frame in either a sense or antisense orientation may be screened for increased or reduced expression of the polypeptide in question using techniques well known to those of skill in the art, and plants having the desired phenotypes may thus be isolated.
Alternatively, expression of a target polypeptide may be inhibited by inserting a portion of the open reading frame, in either sense or antisense orientation, in the genetic construct. Such portions need not be full-length but preferably comprise at least 25 and more preferably at least 50 residues of the open reading frame. A much longer portion or even the full length DNA corresponding to the complete open reading frame may be employed. The portion of the open reading frame does not need to be precisely the same as the endogenous sequence, provided that there is sufficient sequence similarity to achieve inhibition of the target gene. Thus a sequence derived from one species may be used to inhibit expression of a gene in a different species.
In further embodiments, the inventive genetic constructs comprise a polynucleotide including an untranslated, or non-coding, region of a gene coding for a target polypeptide, or a polynucleotide complementary to such an untranslated region. Examples of untranslated regions which may be usefully employed in such constructs include introns and 5'-untranslated leader sequences. Transformation of a target plant with such a genetic construct may lead to a reduction in the amount of the polypeptide expressed in the plant by the process of cosuppression, in a manner similar to that discussed, for example, by Napoli et al., Plant Cell 2:279-290, 1990 and de Carvalho Niebel et al., Plant Cell 7:347-358, 1995.
Alternatively, regulation of polypeptide expression can be achieved by inserting appropriate sequences or subsequences (e.g. DNA or RNA) in ribozyme constructs (McIntyre and Manners, Transgenic Res. 5(4):257-262, 1996). Ribozymes are synthetic RNA molecules that comprise a hybridizing region complementary to two regions, each of which comprises at least 5 contiguous nucleotides in a mRNA molecule encoded by one of the inventive polynucleotides. Ribozymes possess highly specific endonuclease activity, which autocatalytically cleaves the mRNA.
The polynucleotide of interest, such as a coding sequence, is operably linked to a polynucleotide promoter sequence of the present invention such that a host cell is able to transcribe an RNA from the promoter sequence linked to the polynucleotide of interest. The polynucleotide promoter sequence is generally positioned at the 5' end of the polynucleotide to be transcribed. Use of a constitutive promoter, such as the Pinus radiata ubiquitin polynucleotide promoter sequence of SEQ ID NO: 2 and 3 or the Eucalyptus grandis ubiquitin polynucleotide promoter sequence contained within SEQ ID NO: 34, will affect transcription of the polynucleotide of interest in all parts of the transformed plant. Use of a tissue specific promoter, such as the leaf-specific promoters of SEQ ID NO: 9-11, the root-specific promoters of SEQ ID NO: 13 and 14, the flower-specific promoters of SEQ ID NO: 29-33, 59 and 89-90, the pollen-specific promoters of SEQ ID NO: 49-55 and 94, the bud-specific promoter of SEQ ID NO: 40 or the meristem-specific promoter of SEQ ID NO: 45, will result in production of the desired sense or antisense RNA only in the tissue of interest. Temporally regulated promoters, such as the xylogenesis-specific promoters of SEQ ID NO: 5, 41-44 and 92, can be employed to effect modulation of the rate of DNA transcription at a specific time during development of a transformed plant. With genetic constructs employing inducible gene promoter sequences, the rate of DNA transcription can be modulated by external stimuli, such as light, heat, anaerobic stress, alteration in nutrient conditions and the like.
The inventive genetic constructs further comprise a gene termination sequence which is located 3' to the polynucleotide of interest. A variety of gene termination sequences which may be usefully employed in the genetic constructs of the present invention are well known in the art. One example of such a gene termination sequence is the 3' end of the Agrobacterium tumefaciens nopaline synthase gene. The gene termination sequence may be endogenous to the target plant or may be exogenous, provided the promoter is functional in the target plant. For example, the termination sequence may be from other plant species, plant viruses, bacterial plasmids and the like.
The genetic constructs of the present invention may also contain a selection marker that is effective in cells of the target organism, such as a plant, to allow for the detection of transformed cells containing the inventive construct. Such markers, which are well known in the art, typically confer resistance to one or more toxins. One example of such a marker is the NPTII gene whose expression results in resistance to kanamycin or hygromycin, antibiotics which are usually toxic to plant cells at a moderate concentration (Rogers et al., in Weissbach A and H, eds. Methods for Plant Molecular Biology, Academic Press Inc.: San Diego, Calif., 1988). Transformed cells can thus be identified by their ability to grow in media containing the antibiotic in question. Alternatively, the presence of the desired construct in transformed cells can be determined by means of other techniques well known in the art, such as Southern and Western blots.
Techniques for operatively linking the components of the inventive genetic constructs are well known in the art and include the use of synthetic linkers containing one or more restriction endonuclease sites as described, for example, by Sambrook et al., (Molecular cloning: a laboratory manual, CSHL Press: Cold Spring Harbor, N.Y., 1989). The genetic construct of the present invention may be linked to a vector having at least one replication system, for example E. coli, whereby after each manipulation, the resulting construct can be cloned and sequenced and the correctness of the manipulation determined.
The genetic constructs of the present invention may be used to transform a variety of target organisms including, but not limited to, plants. Plants which may be transformed using the inventive constructs include both monocotyledonous angiosperms (e.g., grasses, corn, grains, oat, wheat and barley) and dicotyledonous angiosperms (e.g., Arabidopsis, tobacco, legumes, alfalfa, oaks, eucalyptus, maple), and Gymnosperms (e.g., Scots pine; see Aronen, Finnish Forest Res. Papers, Vol. 595, 1996), white spruce (Ellis et al., Biotechnology 11:84-89, 1993), and larch (Huang et al., In Vitro Cell 27:201-207, 1991). In a preferred embodiment, the inventive genetic constructs are employed to transform woody plants, herein defined as a tree or shrub whose stem lives for a number of years and increases in diameter each year by the addition of woody tissue. Preferably the target plant is selected from the group consisting of eucalyptus and pine species, most preferably from the group consisting of Eucalyptus grandis and Pinus radiata. Other species which may be usefully transformed with the genetic constructs of the present invention include, but are not limited to: pines such as Pinus banksiana, Pinus brutia, Pinus caribaea, Pinus clausa, Pinus contorta, Pinus coulteri, Pinus echinata, Pinus eldarica, Pinus ellioti, Pinus jeffreyi, Pinus lambertiana, Pinus monticola, Pinus nigra, Pinus palustrus, Pinus pinaster, Pinus ponderosa, Pinus resinosa, Pinus rigida, Pinus serotina, Pinus strobus, Pinus sylvestris, Pinus taeda, Pinus virginiana; other gymnosperms, such as Abies amabilis, Abies balsamea, Abies concolor, Abies grandis, Abies lasiocarpa, Abies magnifica, Abies procera, Chamaecyparis lawsoniona, Chamaecyparis nootkatensis, Chamaecyparis thyoides, Huniperus virginiana, Larix decidua, Larix laricina, Larix leptolepis, Larix occidentalis, Larix siberica, Libocedrus decurrens, Picea abies, Picea engelmanni, Picea glauca, Picea mariana, Picea pungens, Picea rubens, Picea sitchensis, Pseudotsuga menziesii, Sequoia gigantea, Sequoia sempervirens, Taxodium distichum, Tsuga canadensis, Tsuga heterophylla, Tsuga mertensiana, Thuja occidentalis, Thuja plicata; and Eucalypts, such as Eucalyptus alba, Eucalyptus bancroftii, Eucalyptus botyroides, Eucalyptus bridgesiana, Eucalyptus calophylla, Eucalyptus camaldulensis, Eucalyptus citriodora, Eucalyptus cladocalyx, Eucalyptus coccifera, Eucalyptus curtisii, Eucalyptus dalrympleana, Eucalyptus deglupta, Eucalyptus delagatensis, Eucalyptus diversicolor, Eucalyptus dunnii, Eucalyptus ficifolia, Eucalyptus globulus, Eucalyptus gomphocephala, Eucalyptus gunnii, Eucalyptus henryi, Eucalyptus laevopinea, Eucalyptus macarthurii, Eucalyptus macrorhyncha, Eucalyptus maculata, Eucalyptus marginata, Eucalyptus megacarpa, Eucalyptus melliodora, Eucalyptus nicholii, Eucalyptus nitens, Eucalyptus nova-anglica, Eucalyptus obliqua, Eucalyptus obtusiflora, Eucalyptus oreades, Eucalyptus pauciflora, Eucalyptus polybractea, Eucalyptus regnans, Eucalyptus resinifera, Eucalyptus robusta, Eucalyptus rudis, Eucalyptus saligna, Eucalyptus sideroxylon, Eucalyptus stuartiana, Eucalyptus tereticornis, Eucalyptus torelliana, Eucalyptus urnigera, Eucalyptus urophylla, Eucalyptus viminalis, Eucalyptus viridis, Eucalyptus wandoo and Eucalyptus youmanni; and hybrids of any of these species.
Techniques for stably incorporating genetic constructs into the genome of target plants are well known in the art and include Agrobacterium tumefaciens mediated introduction, electroporation, protoplast fusion, injection into reproductive organs, injection into immature embryos, high velocity projectile introduction and the like. The choice of technique will-depend upon the target plant to be transformed. For example, dicotyledonous plants and certain monocots and gymnosperms may be transformed by Agrobacterium Ti plasmid technology, as described, for example by Bevan, Nucleic Acids Res. 12:8711-8721, 1984. Targets for the introduction of the genetic constructs of the present invention include tissues, such as leaf tissue, dissociated cells, protoplasts, seeds, embryos, meristematic regions; cotyledons, hypocotyls, and the like. The preferred method for transforming eucalyptus and pine is a biolistic method using pollen (see, for example, Aronen, Finnish Forest Res. Papers, Vol. 595, 53 pp, 1996) or easily regenerable embryonic tissues.
Once the cells are transformed, cells having the inventive genetic construct incorporated in their genome may be selected by means of a marker, such as the kanamycin resistance marker discussed above. Transgenic cells may then be cultured in an appropriate medium to regenerate whole plants, using techniques well known in the art. In the case of protoplasts, the cell wall is allowed to reform under appropriate osmotic conditions. In the case of seeds or embryos, an appropriate germination or callus initiation medium is employed. For explants, an appropriate regeneration medium is used. Regeneration of plants is well established for many species. For a review of regeneration of forest trees see Dunstan et al., “Somatic embryogenesis in woody plants,” in Thorpe TA, ed., In Vitro Embryogenesis of Plants (Current Plant Science and Biotechnology in Agriculture Vol. 20), Chapter 12, pp. 471-540, 1995. Specific protocols for the regeneration of spruce are discussed by Roberts et al., “Somatic embryogenesis of spruce,” in Redenbaugh K, ed., Synseed: applications of synthetic seed to crop improvement, CRC Press: Chapter 23, pp. 427-449, 1993). Transformed plants having the desired phenotype may be selected using techniques well known in the art. The resulting transformed plants may be reproduced sexually or asexually, using methods well known in the art, to give successive generations of transgenic plants.
As discussed above, the production of RNA in target cells can be controlled by choice of the promoter sequence, or by selecting the number of functional copies or the site of integration of the polynucleotides incorporated into the genome of the target host. A target organism may be transformed with more than one genetic construct of the present invention, thereby modulating the activity of more than gene. Similarly, a genetic construct may be assembled containing more than one open reading frame coding for a polypeptide of interest or more than one untranslated region of a gene coding for such a polypeptide.
The isolated polynucleotides of the present invention also have utility in genome mapping, in physical mapping, and in positional cloning of genes. As detailed below, the polynucleotide sequences identified as SEQ ID NO: 1-14, 20, 22-62, 81-86 and 88-127, and their variants, may be used to design oligonucleotide probes and primers. Oligonucleotide probes designed using the polynucleotides of the present invention may be used to detect the presence and examine the expression patterns of genes in any organism having sufficiently similar DNA and RNA sequences in their cells using techniques that are well known in the art, such as slot blot DNA hybridization techniques. Oligonucleotide primers designed using the polynucleotides of the present invention may be used for PCR amplifications. Oligonucleotide probes and primers designed using the polynucleotides of the present invention may also be used in connection with various microarray technologies, including the microarray technology of Affymetrix (Santa Clara, Calif.).
As used herein, the term “oligonucleotide” refers to a relatively short segment of a polynucleotide sequence, generally comprising between 6 and 60 nucleotides, and comprehends both probes for use in hybridization assays and primers for use in the amplification of DNA by polymerase chain reaction.
An oligonucleotide probe or primer is described as “corresponding to” a polynucleotide of the present invention, including one of the sequences set out as SEQ ID NO: 1-14, 20, 22-62, 81-86 and 88-127, or a variant, if the oligonucleotide probe or primer, or its complement, is contained within one of the sequences set out as SEQ ID NO: 1-14, 20, 22-62, 81-86 and 88-127, or a variant of one of the specified sequences. Oligonucleotide probes and primers of the present invention are substantially complementary to a polynucleotide disclosed herein.
Two single stranded sequences are said to be substantially complementary when the nucleotides of one strand, optimally aligned and compared, with the appropriate nucleotide insertions and/or deletions, pair with at least 80%, preferably at least 90% to 95% and more preferably at least 98% to 100% of the nucleotides of the other strand. Alternatively, substantial complementarity exists when a first DNA strand will selectively hybridize to a second DNA strand under stringent hybridization conditions. Stringent hybridization conditions for determining complementarity include salt conditions of less than about 1 M, more usually less than about 500 mM, and preferably less than about 200 mM. Hybridization temperatures can be as low as 5° C., but are generally greater than about 22° C., more preferably greater than about 30° C., and most preferably greater than about 37° C. Longer DNA fragments may require higher hybridization temperatures for specific hybridization. Since the stringency of hybridization may be affected by other factors such as probe composition, presence of organic solvents and extent of base mismatching, the combination of parameters is more important than the absolute measure of any one alone.
In specific embodiments, the oligonucleotide probes and/or primers comprise at least about 6 contiguous residues, more preferably at least about 10 contiguous residues, and most preferably at least about 20 contiguous residues complementary to a polynucleotide sequence of the present invention. Probes and primers of the present invention may be from about 8 to 100 base pairs in length or, preferably from about 10 to 50 base pairs in length or, more preferably from about 15 to 40 base pairs in length. The probes can be easily selected using procedures well known in the art, taking into account DNA-DNA hybridization stringencies, annealing and melting temperatures, and potential for formation of loops and other factors, which are well known in the art. Preferred techniques for designing PCR primers are disclosed in Dieffenbach, C W and Dyksler, GS. PCR Primer: a laboratory manual, CSHL Press: Cold Spring Harbor, N.Y., 1995. A software program suitable for designing probes, and especially for designing PCR primers, is available from Premier Biosoft International, 3786 Corina Way, Palo Alto, Calif. 94303-4504.
A plurality of oligonucleotide probes or primers corresponding to a polynucleotide of the present invention may be provided in a kit form. Such kits generally comprise multiple DNA or oligonucleotide probes, each probe being specific for a polynucleotide sequence. Kits of the present invention may comprise one or more probes or primers corresponding to a polynucleotide of the present invention, including a polynucleotide sequence identified in SEQ ID NO: 1-14, 20, 22-62, 81-86 and 88-120.
In one embodiment useful for high-throughput assays, the oligonucleotide probe kits of the present invention comprise multiple probes in an array format, wherein each probe is immobilized at a predefined, spatially addressable location on the surface of a solid substrate. Array formats which may be usefully employed in the present invention are disclosed, for example, in U.S. Pat. Nos. 5,412,087 and 5,545,451; and PCT Publication No. WO 95/00450, the disclosures of which are hereby incorporated by reference.
The polynucleotides of the present invention may also be used to tag or identify an organism or reproductive material therefrom. Such tagging may be accomplished, for example, by stably introducing a non-disruptive non-functional heterologous polynucleotide identifier into an organism, the polynucleotide comprising one of the polynucleotides of the present invention.
The following examples are offered by way of illustration and not by way of limitation.
EXAMPLE 1
Isolation and Characterization of a Ubiguitin Gene Promoter from Pinus radiata 
Pinus radiata cDNA expression libraries were constructed and screened as follows. mRNA was extracted from plant tissue using the protocol of Chang et al., Plant Molecular Biology Reporter 11:113-116, 1993 with minor modifications. Specifically, samples were dissolved in CPC-RNAXB (100 mM Tris-Cl, pH 8,0; 25 mM EDTA; 2.0 M NaCl; 2% CTAB; 2% PVP and 0.05% Spermidine*3HCl) and extracted with chloroform:isoamyl alcohol, 24:1. mRNA was precipitated with ethanol and the total RNA preparate was purified using a Poly(A) Quik mRNA Isolation Kit (Stratagene, La Jolla, Calif.). A cDNA expression library was constructed from the purified mRNA by reverse transcriptase synthesis followed by insertion of the resulting cDNA clones in Lambda ZAP using a ZAP Express cDNA Synthesis Kit (Stratagene), according to the manufacturer's protocol. The resulting cDNAs were packaged using a Gigapack II Packaging Extract (Stratagene) employing 1 μl of sample DNA from the 5 μl ligation mix. Mass excision of the library was done using XL1-Blue MRF' cells and XLOLR cells (Stratagene) with ExAssist helper phage (Stratagene). The excised phagemids were diluted with NZY broth (Gibco BRL, Gaithersburg, Md.) and plated out onto LB-kanamycin agar plates containing X-gal and isopropylthio-beta-galactoside (IPTG).
Of the colonies plated and picked for DNA miniprep, 99% contained an insert suitable for sequencing. Positive colonies were cultured in NZY broth with kanamycin and cDNA was purified by means of alkaline lysis and polyethylene glycol (PEG) precipitation. Agarose gel at 1% was used to screen sequencing templates for chromosomal contamination. Dye primer sequences were prepared using a Turbo Catalyst 800 machine (Perkin Elmer/Applied Biosystems Division, Foster City, Calif.) according to the manufacturer's protocol.
DNA sequence for positive clones was obtained using a Perkin Elmer/Applied Biosystems Division Prism 377 sequencer. cDNA clones were sequenced first from the 5' end and, in some cases, also from the 3' end. For some clones, internal sequence was obtained using subcloned fragments. Subcloning was performed using standard procedures of restriction mapping and subcloning to pBluescript II SK+ vector.
As described below, one of the most abundant sequences identified was a ubiquitin gene, hereinafter referred to as the “Super-Ubiquitin or SU” gene.
Isolation of cDNA Clones Containing the Ubiquitin Gene
Sequences of cDNA clones with homology to the ubiquitin gene were obtained from high-throughput cDNA sequencing as described above. Sequences from several independent clones were assembled in a contig and a consensus sequence was generated from overlapping clones. The determined nucleotide sequence of the isolated Super Ubiquitin clone, comprising the promoter region (including an intron), coding region and 3' untranslated region (UTR) is provided in SEQ ID NO: 1. The 5' UTR is represented by residues 1 to 2,064, the intron by residues 1,196 to 2,033, and the coding region of the gene, which contains three direct repeats, by residues 2,065 to 2,751. The 3' UTR is 328 residues long (residues 2,755 to 3,083). The nucleotide sequence of the Super Ubiquitin promoter region only, including the intron, is given in SEQ ID NO: 2. The nucleotide sequence of the Super Ubiquitin promoter region only, excluding the intron, is given in SEQ ID NO: 3. The predicted amino acid sequence for the Pinus radiata Super Ubiquitin is provided in SEQ ID NO: 80.
Ubiquitin proteins function as part of a protein degradation pathway, in which they covalently attach to proteins, thereby targeting them for degradation (for a review, see Belknap and Garbarino, Trends in Plant Sciences 1:331-335, 1996). The protein is produced from a precursor polypeptide, encoded by a single mRNA. The Super Ubiquitin mRNA contains three copies of the ubiquitin monomer.
Cloning of the Super Ubiquitin Promoter
Fragments of the Super Ubiquitin promoter were cloned by two different PCR-based approaches.
Method 1: Long Distance Gene Walking PCR
Using “Long Distance Gene Walking” PCR (Min and Powell, Biotechniques 24:398-400, 1998), a 2 kb fragment was obtained that contained the entire coding region of the ubiquitin gene, a 900 bp intron in the 5' UTR and approximately 100 bp of the promoter.
To generate this fragment, 2 nested primers were designed from the 3' UTR of the Super Ubiquitin cDNA sequence isolated from pine. Generally, the 5' UTR is used for primer design to amplify upstream sequence. However, the available 5' UTR of Super Ubiquitin was very short, and two initial primers derived from this region failed to amplify any fragments. Therefore, the primers of SEQ ID NO: 15 and 16 were designed from the 3' UTR.
The method involved an initial, linear PCR step with pine genomic DNA as template using the primer of SEQ ID NO: 15, and subsequent C-tailing of the single stranded DNA product using terminal transferase. The second PCR-step used these fragments as template for amplification with the primer of SEQ ID NO: 16 and primer AP of SEQ ID NO: 17. The AP primer was designed to bind to the polyC tail generated by the terminal transferase. Both primers (SEQ ID NO: 16 and 17) contained a 5'-NotI restriction site for the cloning of products into the NotI site of a suitable vector. The final PCR product contained fragments of different sizes. These fragments were separated by electrophoresis and the largest were purified from the gel, digested with restriction endonuclease NotI and cloned in the NotI site of expression vector pBK-CMV (Stratagene, La Jolla, Calif.). The largest of these clones contained the complete coding region of the gene (no introns were found in the coding sequence) and a 5' UTR which contained a 900 bp intron.
Method 2: “Genome Walker” Kit
The Super Ubiquitin gene promoter was cloned using a “Genome Walker” kit (Clontech, Palo Alto, Calif.). This is also a PCR-based method, which requires two PCR primers to be constructed, one of which must be gene-specific. Although the ubiquitin coding region is highly conserved, the 5' UTR from different ubiquitin genes is not conserved and could therefore be used to design a gene-specific primer. A 2.2 kb fragment was amplified and subcloned in pGEM-T-easy (Promega, Madison, Wis.). Analysis by PCR and DNA sequencing showed that the clone contained 5' UTR sequence of the Super Ubiquitin gene, including the 900 bp intron and approximately 1 kb of putative promoter region. An intron in the 5' UTR is a common feature of plant polyubiquitin genes and may be involved in determining gene expression levels.
The gene specific primers used for these PCR reactions are provided in SEQ ID NO: 18 and 19.
Expression of Super Ubiguitin
Using primers derived from the gene-specific 5' and 3' UTR sequences, expression levels of Super Ubiquitin in different plant tissues was examined by means of RT-PCR. Super Ubiquitin was found to be expressed in all plant tissues examined, including branch phloem and xylem, feeder roots, fertilized cones, needles, one year old cones, pollen sacs, pollinated cones, root xylem, shoot buds, structural roots, trunk phloem and trunk. Expression of Super Ubiquitin in plant tissues was also demonstrated in a Northern blot assay using a PCR probe prepared from the 5'UTR.
Functional Analysis of the Super Ubiguitin Promoter
To test the function of the Super Ubiquitin promoter in plants, Arabidopsis thaliana was transformed with constructs containing the reporter gene for Green Fluorescent Protein (GFP) operably linked to either the Super Ubiquitin promoter of SEQ ID NO: 2 or SEQ ID NO: 3 (i.e., either with or without the intron). Constructs lacking a promoter were used as a negative control, with a plant T-DNA vector carrying a CaMV 35S promoter cloned in front of GFP being used as a positive control. The constructs were introduced into Arabidopsis via Agrobacterium-mediated transformation.
All the plant culture media were according to the protocol of Valvekens and Van Montagu, Proc. Natl. Acad. Sci. USA 85:5536-5540, 1988 with minor modifications. For root transformation, sterilized seeds were placed in a line on the surface of germination medium, the plates were placed on their sides to facilitate root harvesting, and the seeds were grown for two weeks at 24° C. with a 16 h photoperiod.
Expression of the constructs was measured by determining expression levels of the reporter gene for Green Fluorescent Protein (GFP). Preliminary GFP expression (transient) was detected in early transgenic roots during T-DNA transfer. Transgenic roots that developed green callus, growing on shoot-inducing medium containing 50 μg/ml Kanamycin and 100 μg/ml Timentin, were further tested for GFP expression. After several weeks of stringent selection on Kanamycin medium, several independent transgenic Arabidopsis lines were engineered and tested for GFP expression.
Expression was seen both with the Super Ubiquitin promoter including intron and the Super Ubiquitin promoter without the intron. However, preliminary results indicated that the levels of expression obtained with the Super Ubiquitin intron-less promoter construct were significantly higher than those seen with the promoter including intron, suggesting that the intron may contain a repressor. The sequence of the intron is provided in SEQ ID NO: 21.
EXAMPLE 2
Isolation of a CDC Promoter from Pinus radiata 
Plant polynucleotide sequences homologous to the Cell Division Control (CDC) protein gene were isolated from a Pinus radiata cDNA expression library as described in Example 1. Using the “Genome Walker” protocol described above and gene specific primers designed from these plant polynucleotide sequences, 5'UTR sequence containing the putative promoter of the P. radiata CDC gene was isolated from genomic DNA. The determined nucleotide sequence is given in SEQ ID NO: 4.
EXAMPLE 3
Isolation of a Xylogenesis-Specific Promoter from Pinus radiata 
Plant polynucleotide sequences specific for plant xylogenesis were isolated from Pinus radiata cDNA expression libraries prepared from xylem, essentially as described in Example 1. Using the “Genome Walker” protocol described above and gene specific primers designed from these plant polynucleotide sequences, sequences containing putative Pinus radiata xylogenesis-specific promoters were isolated from genomic DNA. The determined nucleotide sequences are provided in SEQ ID NO: 5 and 41-44. An extended cDNA sequence for the clone of SEQ ID NO: 41-44 is provided in SEQ ID NO: 92.
EXAMPLE 4
Isolation of a 4-Coumarate-CoA Ligase Promoter from Pinus radiata 
Plant polynucleotide sequences homologous to the 4-Coumarate-CoA Ligase (4CL) gene were isolated from a Pinus radiata cDNA expression library as described in Example 1. Using the “Genome Walker” protocol described above and gene specific primers designed from these plant polynucleotide sequences, sequences containing the putative promoter of the P. radiata 4CL gene was isolated from genomic DNA. The determined nucleotide sequence is given in SEQ ID NO: 6.
Genetic constructs comprising the reporter gene for Green Fluorescent Protein (GFP) or GUS reporter genes operably linked to the promoter of SEQ ID NO: 6 were prepared and used to transform Arabidopsis thaliana plants.
EXAMPLE 5
Isolation of a Cellulose Synthase Promoter from Eucalyptus grandis 
Plant polynucleotide sequences homologous to the cellulose synthase gene were isolated from a Eucalyptus grandis cDNA expression library essentially as described in Example 1. Using the “Genome Walker” protocol described above and gene specific primers designed from these plant polynucleotide sequences, 5′UTR sequences containing the putative promoter of the E. grandis cellulose synthase gene were isolated from genomic DNA. Independent PCR experiments using different DNA bands as templates yielded two sequences which contained a number of base differences. One band was 750 bp in length and the nucleotide sequence of this band is given in SEQ ID NO: 7. The other band was 3 kb in length. The sequence of the 3' end of this band corresponded to the sequence given in SEQ ID NO: 7, with a number of base pair differences. The sequence of this 3' end is given in SEQ ID NO: 8. The sequence of the 5' end of this band is given in SEQ ID NO: 20.
EXAMPLE 6
Isolation of a Leaf-Specific Promoter from Eucalyptus grandis 
Plant polynucleotide sequences specific for leaf were isolated from Eucalyptus grandis cDNA expression libraries prepared from leaf tissue, essentially as described in Example 1. Using the “Genome Walker” protocol described above and gene specific primers designed from these plant polynucleotide sequences, 5'UTR sequence containing a leaf-specific promoter of a novel E. grandis gene (of unknown function) was isolated from genomic DNA. Independent PCR experiments using different DNA bands as templates yielded three sequences which contained a number of base differences and deletions. The determined nucleotide sequences of the three PCR fragments are given in SEQ ID NO: 9-11.
EXAMPLE 7
Isolation of an O-Methyl Transferase Promoter from Eucalyptus grandis 
Plant polynucleotide sequences homologous to an O-methyl transferase (OMT) gene were isolated from a Eucalyptus grandis cDNA expression library essentially as described in Example 1. Using the “Genome Walker” protocol described above and gene specific primers designed from these plant polynucleotide sequences, 5'UTR sequences containing the putative promoter of the E. grandis OMT gene was isolated from genomic DNA. The determined nucleotide sequence is given in SEQ ID NO: 12. This promoter sequence was extended by further sequencing. The extended cDNA sequences are given in SEQ ID NO: 60 and 113.
Genetic constructs comprising the reporter gene for Green Fluorescent Protein (GFP) operably linked to the promoter of SEQ ID NO: 12 were prepared and used to transform Arabidopsis thaliana. 
EXAMPLE 8
Isolation of Root-Specific Promoters from Pinus radiata 
Plant polynucleotide sequences homologous to the root-specific receptor-like kinase gene were isolated from a Pinus radiata cDNA expression library as described in Example 1. Using the “Genome Walker” protocol described above and gene specific primers designed from these plant polynucleotide sequences, 5'UTR sequence containing a putative P. radiata root-specific promoter was isolated from genomic DNA. Two independent PCR experiments yielded sequences that contained a number of base differences. The determined nucleotide sequences from the two experiments are given in SEQ ID NO: 13, 14, 110 and 111.
EXAMPLE 9
Isolation of an EF1-alpha Promoter from Eucalyptus Grandis 
Plant polynucleotide sequences homologous to the Eucalyptus Elongation Factor-alpha (EF1-alpha) gene were isolated from a Eucalyptus grandis cDNA expression library and used to screen a Eucalyptus grandis genomic DNA library as follows.
The Eucalyptus grandis genomic DNA library was constructed using genomic DNA extracted from Eucalyptus nitens ×grandis plant tissue, according to the protocol of Doyle and Doyle, Focus 12:13-15, 1990, with minor modifications. Specifically, plant tissue was ground under liquid nitrogen and dissolved in 2X CTAB extraction buffer (2% CTAB, hexadecyltrimethylammonium bromide; 1.4 M NaCl, 20 mM EDTA pH 8.0, 100 mM Tris.HCl pH 8.0, 1% polyvinylpyrollidone). After extraction with chloroform: isoamylalcohol (24:1), 10% CTAB was added to the aqueous layer and the chloroform:isoamylalcohol extraction repeated. Genomic DNA was precipitated with isopropanol.
The resulting DNA was digested with restriction endonuclease Sau3A1 following standard procedures, extracted once with phenol:chloroform:isoamylalcohol (25:24:1) and ethanol precipitated. The digested fragments were separated on a sucrose density gradient using ultracentrifugation. Fractions containing fragments of 9-23 kb were pooled and ethanol precipitated. The resulting fragments were cloned into the lambda DASH II/BamHI vector (Stratagene, La Jolla, Calif.) following the manufacturer's protocol and packaged using a Gigapack II Packaging Extract (Stratagene). The library was amplified once.
The library was screened with radiolabeled EST fragments isolated from a Eucalyptus grandis library (as described in Example 1), that showed homology to the Eucalyptus EF1-alpha gene. Phage lysates were prepared from positive plaques and genomic DNA was extracted.
From this genomic DNA, the 5'UTR region containing the putative promoter of the Eucalyptus EF1-alpha gene was obtained using the ELONGASE Amplification System (Gibco BRL). A 10 kb fragment was amplified and restriction mapped. The putative promoter region of the Eucalyptus elongation factor A (EF1-alpha) gene was identified on a 4 kb fragment, which was subcloned into a pUC19 vector (Gibco BRL) containing an engineered NotI-site. The determined genomic DNA sequences of the isolated fragment containing the promoter region are provided in SEQ ID NO: 61 and 62, with the amino acid encoded by SEQ ID NO: 61 being provided in SEQ ID NO: 79. An extended sequence of the clone of SEQ ID NO: 61 is provided in SEQ ID NO: 127.
EXAMPLE 10
Isolation of Flower-Specific Promoters from Eucalyptus grandis 
Plant polynucleotide sequences specific for flower-derived tissue were isolated from Eucalyptus grandis cDNA expression libraries prepared from flower tissue, essentially as described in Example 1. Using the “Genome Walker” protocol described above and gene specific primers designed from these plant polynucleotide sequences, several sequences, each containing a putative Eucalyptus grandis flower-specific promoter, were isolated from genomic DNA. The determined nucleotide sequences are given in SEQ ID NO: 29-33 and 59. An extended sequence of the clone of SEQ ID NO: 30-33 is provided in SEQ ID NO: 89. An extended sequence of the clone of SEQ ID NO: 29 is provided in SEQ ID NO: 90.
EXAMPLE 11
Isolation of Pollen-Specific Promoters from Eucalyptus grandis and Pinus radiata 
Plant polynucleotide sequences specific for pollen were isolated from Eucalyptus grandis and Pinus radiata cDNA expression libraries prepared from pollen, essentially as described in Example 1. Using the “Genome Walker” protocol described above and gene specific primers designed from these plant polynucleotide sequences, several sequences, each containing a putative pollen-specific promoter, were isolated from genomic DNA. The determined nucleotide sequences isolated from Pinus radiata are given in SEQ ID NO: 49-53, with the predicted amino acid sequences encoded by SEQ ID NO: 51-53 being provided in SEQ ID NO: 73-75, respectively. An extended sequence for the clone of SEQ ID NO: 49 is provided in SEQ ID NO: 94.
EXAMPLE 12
Isolation of Bud-Specific and Meristem-Specific Promoter from Pinus radiata 
Plant polynucleotide sequences specific for bud and meristem were isolated from Pinus radiata cDNA expression libraries prepared from bud and meristem, essentially as described in Example 1. Using the “Genome Walker” protocol described above and gene specific primers designed from these plant polynucleotide sequences, two sequences, one containing a putative bud-specific promoter and the other containing a putative meristem-specific promoter, were isolated from genomic DNA. The determined nucleotide sequences for these two promoters are given in SEQ ID NO: 40 and 45, respectively. The predicted amino acid sequences encoded by the DNA sequences of SEQ ID NO: 40 and 45 are provided in SEQ ID NO: 70 and 71, respectively.
EXAMPLE 13
Isolation of Promoters from Eucalyptus grandis 
Plant polynucleotide sequences showing some homology to various known genes were isolated from Eucalyptus grandis cDNA expression libraries essentially as described in Example 1. Using the “Genome Walker” protocol described above and gene specific primers designed from these plant polynucleotide sequences, sequences containing the putative promoters for the following E. grandis genes were isolated from genomic DNA: auxin induced protein (SEQ ID NO: 26-28); carbonic anhydrase (SEQ ID NO: 36); isoflavone reductase (SEQ ID NO: 37 and 38); pollen allergen (SEQ ID NO: 23-25); pollen coat protein (SEQ ID NO: 22), sucrose synthase (SEQ ID NO: 56-58); ubiquitin (SEQ ID NO: 34); glyceraldehyde-3-phosphate dehydrogenase (SEQ ID NO: 35 and 39); O-methyl transferase (OMT; SEQ ID NO: 60); macrophage migration inhibition factor from mammals (MIF; SEQ ID NO: 81-86); UDP glucose 6-dehydrogenase (SEQ ID NO: 103); laccase 1 (SEQ ID NO: 105, 106 and 116); arabinogalactan-like 1 (SEQ ID NO: 107); arabinogalactan-like 2 (SEQ ID NO: 108, 109); a hypothetical protein (SEQ ID NO: 104); constans (SEQ ID NO: 118); Flowering Promoting Factor 1 (FPF1; SEQ ID NO: 119); transcription factor DREB-1 (SEQ ID NO: 121); salt tolerance protein (SEQ ID NO: 123); xylem-specific histidine kinase-like (SEQ ID NO: 125) and root specific (SEQ ID NO: 126). The amino acid sequences encoded by the DNA sequences of SEQ ID NO: 22, 25, 26, 28, 34, 35, 36, 56, 57, 60, 86 and 124 are provided in SEQ ID NO: 63, 64, 65, 66, 67, 68, 69, 76, 77, 78, 87 and 130, respectively. Extended cDNA sequences for the clones of SEQ ID NO: 58, 35, 60, 103, 106 and 107 are provided in SEQ ID NO: 91, 93, 113 and 115-117, respectively.
EXAMPLE 14
Isolation of Promoters from Pinus radiata 
Plant polynucleotide sequences showing some homology to various known genes were isolated from Pinus radiata cDNA expression libraries essentially as described in Example 1. Using the “Genome Walker” protocol described above and gene specific primers designed from these plant polynucleotide sequences, sequences containing the putative promoters for the following Pinus radiata genes were isolated from genomic DNA: senescence-like protein (SEQ ID NO: 46-48); nodulin homolog pollen specific (SEQ ID NO: 54 and 55); chalcone synthase (SEQ ID NO: 88); PrMALE1 (SEQ ID NO: 95, 96); UDP glucose glycosyltransferase (SEQ ID NO: 97); elogation factor 1 alpha (SEQ ID NO: 98, 99); S-adenosylmethionine synthase (SEQ ID NO: 100-102); Pinus radiata lipid transfer protein 2 (PrLTP2; SEQ ID NO: 112); Pinus radiata agamous protein (SEQ ID NO: 120); Drought Induced DI-19 (SEQ ID NO: 122) and low temperature induced protein LTI (SEQ ID NO 124). The amino acid sequences encoded by the polynucleotide sequences of SEQ ID NOS: 46 and 124 are provided in SEQ ID NOS: 72 and 130. An extended cDNA sequence for the clone of SEQ ID NO: 97 is provided in SEQ ID NO: 114.
EXAMPLE 15
Polynucleotide and Amino Acid Analysis
The determined cDNA sequences described above were compared to and aligned with known sequences in the EMBL database (as updated to October 2000). Specifically, the polynucleotides identified in SEQ ID NOS: 22-62 and 88-120 were compared to polynucleotides in the EMBL database using the BLASTN algorithm Version 2.0.6 [Sep.-16-1998] and the polynucleotides identified in SEQ ID NOS: 121-127 were compared to polynucleotides in the EMBL database using the BLASTN algorithm Version 2.0.11 [Jan.-20-2000] set to the following running parameters: Unix running command: blastall -p blastn -d embldb -e 10 -G0 -E0 -r1 -v30 -b30 -i queryseq -o results. Multiple alignments of redundant sequences were used to build up reliable consensus sequences. Based on similarity to known sequences from other plant or non-plant species, the isolated polynucleotides of the present invention identified as SEQ ID NOS: 22-62 and 88-127 were putatively identified as having the functions shown in Table 1, above.
The cDNA sequences of SEQ ID NO: 1-22, 23, 25-42, 45-49, 57-59, 62, 88-99, 101-112 and 114-127 were determined to have less than 40% identity to sequences in the EMBL database using the computer algorithm BLASTN, as described above. The cDNA sequences of SEQ ID NO: 56 and 113 were determined to have less than 60% identity to sequences in the EMBL database using BLASTN, as described above. The cDNA sequences of SEQ ID NO: 43, 52, 60 and 61 were determined to have less than 75% identity to sequences in the EMBL database using BLASTN, as described above. The cDNA sequences of SEQ ID NO: 24, 51 and 100 were determined to have less than 90% identity to sequences in the EMBL database using BLASTN, as described above.
EXAMPLE 16
Modification of a Reporter Gene under Control of the Superubiguitin Promoter
Six independent Arabidopsis thaliana transgenic lines were transformed with Pinus radiata superubiquitin promoter constructs to demonstrate the relative expression of a GUS reporter gene under control of different superubiquitin promoter constructs. The reporter constructs in the plasmid pBI-101 contained the GUS (β-D-glucuronidase) reporter gene in frame with the superubiquitin promoter with the intron (SEQ ID NO: 2), the superubiquitin promoter without the intron (SEQ ID NO: 3), and the CaMV 35S promoter. A reporter gene construct without a promoter sequence was used as control.
Groups of six Arabidopsis thaliana plants were transformed with the reporter constructs described above, using Agrobacterium tumefaciens transformation protocols. A. tumefaciens was transformed with 100 ng of the plasmid DNA according to standard techniques, as described, for example, by Bevan (Nucleic Acids Res. 12:8711-8721, 1984). Fresh plant material was collected from each plant, protein extracted from the whole plant, and the protein concentration determined (Bradford, Anal. Biochem. 72:248-254, 1976). The protein samples were diluted with carrier bovine serum albumin to 100 ng protein to maintain readings on the fluorimeter in the linear part of the standard curve using 4-methyl-umbelliferone (MU). GUS activity was quantified by fluorimetric analysis, using a Victor2 1420 multi-label counter (Wallac, Turku, Finland) as described by Jefferson (Plant Mol. Biol. Rep. 5:387-405, 1987). As shown in FIG. 1, the construct containing the superubiquitin promoter without the intron showed seven times more GUS activity than the CaMV 35S promoter and the construct containing the superubiquitin promoter with the intron showed sixty two times more GUS activity than the CaMV 35S promoter. No activity was detected for the promoter-less control construct.
EXAMPLE 17
Determination of the Activity of Superubiguitin Promoter Constructs in Tobacco Plant Protoplasts
Isolation of Protoplasts
Protoplasts were isolated from sterile tobacco (Nicotiana tabacum) leaf tissue and transformed with superubiquitin promoter constructs. Mesophyll protoplasts were prepared according to the method of Bilang et al., Plant Molecular Biology Manual A1:1-16, 1994. A number of fully expanded leaves were removed from sterile wild type tobacco plants, sliced perpendicular to the midrib and submerged in a digestion enzyme solution containing 1.2% cellulase and 0.4% pectinase (Sigma, St. Louis Mo.). The leaves were left to incubate in the dark without agitation at 26° C. for approximately 18 hours. The leaf strips were then gently agitated for 30 min to release the protoplasts. Protoplasts were further purified by filtration through 100 μm nylon mesh. One ml of W5 solution (154 mM MgCl2, 125 mM CaCl2, 5 mM KCl, 5 mM glucose, pH 5.8-6) was carefully layered on top of the filtrate and centrifuged at 80×g for 10 min. The live protoplast layer was removed with a wide bore pipette, washed twice with 10 ml W5 solution using centrifugation at 70×g for 5 min, with final resuspension in 5 ml W5 solution. Protoplasts were counted in a hemocytometer and viability was determined under the microscope after staining with 5 mg/ml fluoroscein diacetate (FDA) in 100% acetone.
Transformation with Promoter Constructs
The isolated protoplasts were transformed with plasmid DNA using a polyethylene glycol protocol. After centrifugation of the purified protoplasts at 70×g for 5 min, they were resuspended in MMM solution (15 mM MgCl2, 0.1% w/v 2 [N-morpholino]ethanesulfonic acid (MES), 0.5 M mannitol pH 5.8) to a density of 2×106 protoplasts/ml. Aliquots containing 5×105 protoplasts/ml in 250 μl were distributed to 15 ml tubes and mixed with 20 μg plasmid DNA. 250 μl polyethylene glycol-4000 (40%) was gently added and incubated for 5 minutes at room temperature. Ten ml W5 solution was slowly added, the protoplasts centrifuged at 70×g for 5 min and finally resuspended in 2 ml K3 medium (Bilang et al., Plant Molecular Biology Manual A1:1-16, 1994). The transformed protoplasts were incubated in the dark at 26° C. for 24 hours before protein was extracted for reporter enzyme assays using 4-methyl-umbelliferyl-glucuronide (MUG).
Protein was extracted from the protoplasts using the following protocol. Transformed protoplast suspensions were centrifuged at 70×g for 10 min, resuspended in 50 μl extraction buffer (Jefferson, Plant Mol. Biol. Rep. 5:387-405, 1987) and vigorously mixed using a vortex. The homogenate was cleared by centrifugation at 4,300 rpm for 5 min, the supernatant removed and used for protein assays (Bradford, Anal. Biochem. 72:248-254, 1976).
The results shown in FIG. 2 demonstrate the promoter activity of deletion constructs of the superubiquitin promoter without the intron (SEQ ID NO: 3) and the superubiquitin promoter with the intron (SEQ ID NO: 2) in tobacco plant protoplasts transformed as described above. The deletion constructs were made in plasmid pBI-101 that contained the GUS reporter gene, using Endonuclease III (Gibco BRL, Gaithersburg, Md.) according to the manufacturer's protocols. The deletion constructs contained 1,103; 753; 573; 446; 368 and 195 bp of superubiquitin promoter sequence, respectively, upstream of the TATA sequence (bp numbers 1,104-1,110 of SEQ ID NO: 2). A control construct containing no sequence upstream of the TATA sequence was also made. These results show that the construct containing the entire superubiquitin promoter with the intron had the highest MU activity in the protoplasts.
In FIG. 3, the tobacco protoplasts were transformed with four different promoter constructs in plasmid pBI-101 containing the GUS reporter gene. These included the superubiquitin promoter without the intron (SEQ ID NO: 3), an elongation factor 1α promoter (SEQ ID NO: 99) and a 5-adenosylmethionine synthetase promoter (SEQ ID NO: 100). A promoterless control was included in the experiment, and is referred to in FIG. 3 as pBI-101.
EXAMPLE 18
Determination of the Activity of P. radiata Pollen-Specific Promoter and E. grandis Pollen Specific Promoter Constructs in Transformed Arabidopsis thaliana cv Columbia
Arabidopsis thaliana transgenic lines were transformed with A. tumefaciens containing constructs of the P. radiata pollen specific promoter (SEQ ID NO: 94) and E. grandis pollen specific promoter (SEQ ID NO: 22) to demonstrate the relative expression of a GUS reporter gene under control of these promoter constructs. The promoter sequences were cloned into plasmid pBI-101 containing a GUS reporter gene.
Agrobacterium tumefaciens Transformation
Agrobacterium tumefaciens strain GV3101 was transformed with these constructs using electroporation. Electrocompetent A. tumefaciens cells were prepared according to the method of Walkerpeach and Velten, Plant Mol. Biol. Man. B1:1-19, 1994. Construct DNA (4 ng) was added to 40 μl competent A. tumefaciens GV3101 cells and electroporation was done using a BTX Electro Cell Manipulator 600 at the following settings: Mode: T 2.5 kV Resistance high voltage (HV), Set Capacitance: C (not used in HV mode), Set Resistance: R R5 (129 Ohm), Set charging voltage: S 1.44 kV, Desired field strength: 14.4 kV/cm and Desired pulse strength: t 5.0 msec. 400 μl YEP liquid media (20 g/l yeast, 20 g/l peptone and 10 g/l sodium chloride) was added to the cuvette and left to recover for one hour at room temperature. Transformed bacteria in YEP medium were spread out on solid YEP medium containing 50 mg/l kanamycin and 50 mg/l rifampicin and incubated at 29° C. for two days to allow colony growth.
Confirmation of Transformation of Constructs into A. tumefaciens 
To confirm that the constructs have been transformed into A. tumefaciens, DNA from the A. tumefaciens colonies from the YEP plates were isolated using standard protocols and amplified using the polymerase chain reaction (PCR) with primers designed from the pBI-101 vector sequence. The primer sequences are given in SEQ ID NOS: 128 and 129. PCR reactions were set up following standard protocols and 30 PCR cycles were done with extension temperature of 72° C.
Transformation of A. thaliana with Transformed A. tumefaciens 
The optical density of the A. tumefaciens bacterial culture was adjusted to 0.7 with infiltration medium (5% sucrose, 0.05% Silwett L-77 surfactant). A. thaliana cv. Columbia plants (6 punnets per construct and 10-12 plants per punnet) were pruned by removing secondary bolts. Pruned A. thaliana plants in punnets were dipped into infiltration solution and moved back and forth for 5 seconds. Punnets were put on their side to allow excess infiltration medium to drain covered with a top tray and wrapped in plastic wrap to maintain humidity. Plants were placed in a growth room at ambient conditions for 24 hours. After this period, the top tray and plastic wrap were removed and plants were set upright until siliques formed.
Seeds were harvested and sterilized with a 5% sodium hypochlorite solution to destroy any residual A. tumefaciens bacteria and fungal contamination.
Under sterile conditions, 100 μl seeds from the transformed A. thaliana plants were placed into an Eppendorf tube. One ml sterile water was added and the seeds left to imbibe the water for no longer than an hour. The water was remove by centrifugation, 1 ml 70% ethanol added to the seeds and gently mixed. This step was not allowed to last longer than one minute. The ethanol was removed by centrifugation, 1 ml 5% sodium hypochlorite solution was added to the seeds and gently mixed for up to 5 min. The sodium hypochlorite solution was removed by centrifugation and the seeds washed with sterile water for 1 min. The washing step was repeated three more times with centrifugation. Seeds were finally resuspended in sterile water. 500 μl of seeds in solution were pipetted onto half-strength Murashige and Skoog medium (MS; Gibco BRL) agar plates containing 50 mg/l kanamycin and 250 mg/l timentin and spread evenly with a flamed wire-loop. The Petri dishes were placed in a refrigerator for 3 days to allow the seeds to stratify. Thereafter the plates were placed in growth room and grown under lights at 22° C. with a 14 hour photoperiod until germination. Putative transformant seedlings were selected as those growing on the antibiotic-containing medium, with large, healthy-looking dark green leaves and a strong root system. These transgenic plants were removed and placed into soil culture at 22° C. with a 12 hour photoperiod.
Staining of Plant Tissues
Tissue were taken from the flower, leaf, stem and root of A. thaliana transformed with constructs of P. radiata unknown pollen specific promoter and E. grandis pollen specific promoter and stained histochemically to determine the expression of the GUS gene under control of the pollen specific promoters. The GUS staining protocol is described by Campisi et al., Plant J. 17:699-707, 1999.
A. thaliana flower, leaf, stem and root tissue were immersed in staining solution (50 mM NaPO4 pH 7.2; 0.5% Triton X-100; 1 mM X Glucuronide sodium salt (Gibco BRL)) for immunochemical staining. Vacuum was applied twice for 5 min to infiltrate the tissue with the staining solution. The tissue was left in the staining solution for 2 days (with agitation) at 37° for color development and then destained in 70% ethanol for 24 hours at 37° C. (with agitation). The tissues were examined for blue GUS staining using a light microscope. GUS expression was observed only in the flower buds of plants transformed with the P. radiata pollen specific promoter construct, and not in the leaf, stem or root tissue. With the E. grandis pollen specific promoter construct, Gus expression was observed in the floral buds as well as in the hydathodes of the leaves. No expression was observed in the stem or root tissues.
To determine in which cell layers the GUS gene was expressed, flower buds were fixed for thin sectioning. The flower buds were fixed with formaldehyde acetic acid (FAA) in an Eppendorf tube and vacuum was applied twice for 15 min. After incubation for 2 hours at room temperature, vacuum was again applied for 15 min and the tissue left overnight at 4° C. The tissues were then dehydrated using a series of ethanol and then passed into a xylene series. Paraffin wax (Sigma) was added slowly and the tissues left for 72 hours with wax changes every 12 hours. Sections of 8 to 10 μm thickness were prepared using a microtome.
The thin sections illustrated that GUS expression was restricted to the tapetum cell layer in the anther of the floral bud of A. thaliana transformed with the P. radiata construct (SEQ ID NO: 49). No staining was observed in other tissues from the floral bud. GUS expression was confined to the pollen grains within the flower bud of A. thaliana transformed with the E. grandis pollen specific promoter construct, with low levels of GUS expression in the fibrous and connective tissue of the anther. No GUS expression was observed in other organs of the floral bud.
EXAMPLE 19
Determination of the Activity of an E. grandis EF1 Alpha Promoter Deletion Construct in Transformed Arabidopsis thaliana cv Columbia
Protoplasts from Nicotiana tabacum Bright Yellow 2 (BY-2) cell suspension were transformed with a deletion construct of the E. grandis EF1-alpha promoter to determine GUS expression. Base pairs 2,174 to 3,720 of SEQ ID NO: 127 were cloned into expression vector pART9, containing the reporter gene GUS and an OCS termination sequence.
Preparation of Protoplasts
Sterile Nicotiana tabacum Bright Yellow-2 (BY-2) suspension cultures were prepared as described in Example 17. After incubation for 3 to 5 days, 3 g of the N. tabacum BY-2 cell suspension were suspended in an enzyme solution containing 1% cellulase, 0.3% pectinase and 0.5% driselase in 0.4 M mannitol. These were left to digest in the dark, with agitation at 26° C., for 3-4 hours. Protoplasts were purified by filtration through a 63 μm nylon mesh. Protoplasts were centrifuged at 80×g for 5 min, washed twice with 10 ml FMS medium (Fukuda, Murashige and Skoog medium; Hasezawa & Syono, Plant Cell Physiol. 24:127-132, 1983) and finally resuspended in 5 ml FMS medium. Protoplasts were counted in a hemocytometer and viability determined by staining with 5 mg/ml FDA (fluorescein deacetate; Sigma St Louis Mich.) in 100% acetone by viewing under the fluorescent microscope.
Transformation of Protoplasts
Protoplasts were transformed according to the protocol described by Morgan and Ow (In: Methods in Plant Molecular Biology: a laboratory course manual, pp. 1-16. P. Maliga, D. Klessig, A. R. Cashmore, W. Gruissem, and J. E. Varner, eds. Cold Spring Harbor Laboratory, CSHP, NY). Briefly, the protocol is as follows. Following the counting step, protoplasts were centrifuged at 80×g for 5 min and resuspended in 1×MaMg solution (0.4 M manniotol, 15 mM MgCl2.6H2O, 0.1% 2-(N-Morpholino)ethane sulfonic acid (MES)) to a density of 5×106 protoplasts/ml. Aliquots of 100 μl (0.5×105 protoplasts) were distributed to 15 ml tubes and washed with 5 ml ix MaMg (200 g, 5 min). Pelleted protoplasts were resuspended in 500 ul 1× MaMg solution, and heat shocked by placing at 45° C. for 5 minutes. After incubation at room temperature 5-10 minutes, the transforming DNA was added (10-20 μg DNA+10 μg carrier DNA). To this, 500 μl 40% PEG-3500 was gently added and incubated for 25 minutes at room temperature. 5 ml W5 (154 mM NaCl, 125 mM CaCl2.2H2O, 5 mM KCl, 5 mM Glucose) solution was slowly added stepwise followed by centrifugation at 200× g for 5 min. Pelleted protoplasts were resuspended in 1 ml K3AM medium at approximately 0.5×105 protoplasts/ml. Samples were transferred to 6-well plates and incubated in the dark at 26° C. for 48 hours.
To extract protein, protoplasts were centrifuged at 200×g for 5 min in a microfuge, resuspended in 100 μl GUS extraction buffer (50 mM NaPO4 pH 7.2, 10 mM EDTA pH 8, 0.01% Sarcosyl, 0.1% Triton X-100) containing β-mercaptoethanol (Jefferson et al., Plant Mol. Biol. Rep. 5:387-405, 1987) and vortexed for 1 min. The homogenate was cleared by centrifugation at 5,000 rpm for 5 minutes. The supernatant containing the protein was transferred to a fresh tube and stored at −80° C. The protein concentrations were determined by BioRad protein assay kit (BioRad, Hercules, Calif.) following the manufacturer's protocols. Protein extracts were diluted 1/10 with extraction buffer.
Determination of GUS Expression
GUS expression in the protoplast extracts was determined using a MUG (4-methyl umbelliferyl β-D-glucuronide) assay. Protein samples, containing 1 μg protein made up to a total volume of 45 μl with extraction buffer, were aliquoted onto a microtitre plate and incubated at 37° C. To each sample, 5 μl of 10 mM MUG was added so that the final concentration of MUG was 1 mM. The plate was incubated at 37° C. for 30 min and terminated by adding 150 μl stop solution (0.2 M Na2CO3, pH 11.20), still keeping the plates at 37° C. Plates were read in a Victor2 1420 Multilabel counter with excitation set at 365 nm and emission at 455 nm. The concentration of 4-methyl-umbelliferone (MU) was calculated against a standard curve and the GUS expression calculated.
In FIG. 5, increased expression of the GUS reporter gene in N. tabacum BY-2 protoplasts transformed with an E. grandis EF1 alpha deletion construct was seen compared to the control plasmid without an insert.
EXAMPLE 20
Determination of the Effect of the 3'UTR Super-ubiquitin (SU) Sequences on Gene Expression in Arabidopsis thaliana cv Columbia
In the polynucleotide sequences given in SEQ ID NO: 1 encoding P. radiata superubiquitin (SU) promoter and gene sequences, an 3' untranslated region (UTR) was identified (nucleotides 1,754 to 3,083). To determine the effect of this region on the expression of genes, 250 bp of the 3' UTR (nucleotides 2,755 to 3,073 from SEQ ID NO: 1) was cloned in the sense and antisense orientation into plasmid pBI-121 containing the GUS gene under control of the 35S CaMV promoter and plasmid pBI-101 containing the GUS gene under control of the P. radiata SU promoter (including the intron) given in SEQ ID NO: 2. For controls, constructs were made that contained the SU promoter without an intron (SEQ ID NO: 3) and without the SU 3' UTR sequence, the SU promoter with an intron (SEQ ID NO: 2) and without the SU 3' UTR sequence as well as a construct containing the 35S CaMV promoter but not the SU 3' UTR sequence.
A. thaliana cv Columbia were transformed with these constructs using the floral dip protocol described in Example 18.
Determining the Level of Gene Expression Using a MUG Assay
Six A. thaliana plants were harvested by trimming off the dried tissue and then harvesting the rest of the plant, including the roots. The roots were rinsed in tap water and the samples immersed in liquid nitrogen before storing at −80° C. Six plants from each construct were ground under liquid nitrogen and approximately 100 mg transferred to a microfuge tube. Five samples from each control were included in the assay. Extraction buffer (50 mM NaPO4 pH 7.2, 10 mM EDTA pH 8, 0.01% Sarcosyl, 0.1% Triton X-100) was prepared. To 32 ml of extraction buffer, 8 ml methanol and 28 μl β-mercaptoethanol was added. Of this buffer, 200 μl was added to each sample, vortexed and stored on ice. Samples were spun at 4° C. at 15,000 rpm for 15 min. The supernatant was transferred to a fresh tube and diluted with 800 μl of extraction buffer. Protein concentration was determined using the BioRad Protein Assay Kit.
The expression of GUS by the four constructs was determined using a MUG assay, as follows. To 28 ml extraction buffer (as described in Example 18), 8 ml methanol, 56 μl β-mercaptoethanol and 4 ml of 10 mg/ml bovine serum albumin (BSA) were added. To microtitre plate wells, 100 and 10 ng of protein from each construct was added as well as 25 μl extraction buffer containing BSA and 5 μl 10 mM MUG. The plate was covered in foil and incubated at 37° C. for exactly 20 minutes. The reaction was terminated by adding 150 μl 0.2 M Na2CO3 pH 11.2. Plates were read with a Victor2 1420 Multilabel counter with excitation set at 365 nm and emission at 455 nm. GUS expression levels were determined against a MU standard curve.
In FIG. 4, construct SR34 containing the SU 3'UTR in the sense orientation enhanced the expression of the SU without intron promoter almost to the level of the SU promoter with the intron. In constructs SR33 and SR35 containing the 3'UTR in the antisense orientation, promoter activity was reduced to basal levels.
EXAMPLE 21
Determination of the Activity of P. radiata Ubiquitin Promoter Constructs in Transformed Arabidopsis thaliana cv Columbia and Tobacco Plant Protoplasts
A. Tobacco Plant Protoplasts
1. Isolation of Protoplasts
Protoplasts were isolated from sterile tobacco (Nicotiana tabacum) leaf tissue and transformed with superubiquitin promoter constructs. Mesophyll protoplasts were prepared according to the method of Bilang et al., Plant Molecular Biology Manual A1:1-16, 1994. A number of fully expanded leaves were removed from sterile wild type tobacco plants, sliced perpendicular to the midrib and submerged in a digestion enzyme solution containing 1.2% cellulase and 0.4% pectinase (Sigma, St. Louis Mo.). The leaves were left to incubate in the dark without agitation at 26° C. for approximately 18 hours. The leaf strips were then gently agitated for 30 min to release the protoplasts. Protoplasts were further purified by filtration through 100 μm nylon mesh. One ml of W5 solution (154 mM MgCl2, 125 mM CaCl2, 5 mM KCl, 5 mM glucose, pH 5.8-6) was carefully layered on top of the filtrate and centrifuged at 80×g for 10 min. The live protoplast layer was removed with a wide bore pipette, washed twice with 10 ml W5 solution using centrifugation at 70×g for 5 min, with final resuspension in 5 ml W5 solution. Protoplasts were counted in a hemocytometer and viability was determined under the microscope after staining with 5 mg/ml fluoroscein diacetate (FDA) in 100% acetone.
2. Transformation with Promoter Constructs
The isolated protoplasts were transformed with plasmid BI-101 containing the GUS (β-D-glucuronidase) reporter gene in frame with the specified deletion constructs of the superubiquitin promoter, with and without the intron. The deletion constructs contained 753, 573, 446, 368 and 195 bp of superubiquitin promoter sequence, respectively, upstream of the TATA sequence (bp numbers 1104-1,110 of SEQ ID NO: 2. The constructs tested, and the results, are described in the table, below.














Construct
Deletion
SEQ ID
Annotated
GUS staining


Ref.
construct
NO:
Fig.
constitutive?







S38
195 bp
131
FIG. 7
No


S39
368 bp
132
FIG. 8
Yes


S40
446 bp
133
FIG. 9
Yes


S41
573 bp
134
FIG. 10
Yes


S48
753 bp
135
FIG. 11
yes


S52
195 bp
136
FIG. 12
No


S53
446 bp
138
FIG. 14
Yes


S54
368 bp
137
FIG. 13
Yes


S55
573 bp
139
FIG. 15
Yes


S56
753 bp
140
FIGS. 16A, B
Yes









Transformation was carried out using a polyethylene glycol protocol. After centrifugation of the purified protoplasts at 70×g for 5 min, they were resuspended in MMM solution (15 mM MgCl2, 0.1% w/v 2[N-morpholino]ethanesulfonic acid (MES), 0.5 M mannitol pH 5.8) to a density of 2×106 protoplasts/ml. Aliquots containing 5×105 protoplasts/ml in 250 μl were distributed to 15 ml tubes and mixed with 20 μg plasmid DNA. 250 μl polyethylene glycol-4000 (40%) was gently added and incubated for 5 minutes at room temperature. Ten ml W5 solution was slowly added, the protoplasts centrifuged at 70×g for 5 min and finally resuspended in 2 ml K3 medium (Bilang et al., Plant Molecular Biology Manual A1:1-16, 1994).
For quantitation of GUS activity, the transformed protoplasts are incubated in the dark at 26° C. for 24 hours before protein is extracted for reporter enzyme assays using 4-methyl-umbelliferyl-glucuronide (MUG). GUS activity is quantified by fluorimetric analysis, as described by Jefferson (Plant Mol. Biol. Rep. 5: 387-405, 1987).
Protein is extracted from the protoplasts using the following protocol. Transformed protoplast suspensions were centrifuged at 70×g for 10 min, resuspended in 50 μl extraction buffer (Jefferson, Plant Mol. Biol. Rep. 5:387-405, 1987) and vigorously mixed using a vortex. The homogenate is cleared by centrifugation at 4,300 rpm for 5 min, the supernatant removed and used for protein assays (Bradford, Anal. Biochem. 72:248-254, 1976).
B. Arabidopsis thaliana Transgenic Lines
Arabidopsis thaliana plants were transformed with A. tumefaciens containing deletion constructs of the P. radiate ubiquitin promoter described above.
1. Agrobacterium tumefaciens Transformation
Agrobacterium tumefaciens strain GV3101 was transformed with the above-described deletion constructs using electroporation. The deletion constructs were prepared using restriction digestion and PCR. The deletion constructs were made in plasmid pBI-101 that contained the GUS reporter gene, using Endonuclease III (Gibco BRL, Gaithersburg, Md.) according to the manufacturer's protocols. A control construct containing no sequence upstream of the TATA sequence was also made.
Electrocompetent A. tumefaciens cells were prepared according to the method of Walkerpeach and Velten, Plant Mol. Biol. Man. B1:1-19, 1994. Construct DNA (4 ng) was added to 40 μl competent A. tumefaciens GV3101 cells and electroporation was done using a BTX Electro Cell Manipulator 600 at the following settings: Mode: T 2.5 kV Resistance high voltage (HV), Set Capacitance: C (not used in HV mode), Set Resistance: R R5 (129 Ohm), Set charging voltage: S 1.44 kV, Desired field strength: 14.4 kV/cm and Desired pulse strength: t 5.09 msec. 400 μl YEP liquid media (20 g/l yeast, 20 g/l peptone and 10 g/l sodium chloride) was added to the cuvette and left to recover for one hour at room temperature. Transformed bacteria in YEP medium were spread out on solid YEP medium containing 50 mg/l kanamycin and 50 mg/l rifampicin and incubated at 29° C. for two days to allow colony growth.
2. Confirmation of Transformation of Constructs into A. tumefaciens 
To confirm that the constructs have been transformed into A. tumefaciens, DNA from the A. tumefaciens colonies from the YEP plates were isolated using standard protocols and amplified using the polymerase chain reaction (PCR) with primers designed from the pBI-101 vector sequence. The primer sequences are given in SEQ ID NOS: 128 and 129. PCR reactions were set up following standard protocols and 30 PCR cycles were done with extension temperature of 72° C.
3. Transformation of A. thaliana with Transformed A. tumefaciens 
The optical density of the A. tumefaciens bacterial culture was adjusted to 0.7 with infiltration medium (5% sucrose, 0.05% Silwett L-77 surfactant). A. thaliana cv. Columbia plants (6 punnets per construct and 10-12 plants per punnet) were pruned by removing secondary bolts. Pruned A. thaliana plants in punnets were dipped into infiltration solution and moved back and forth for 5 seconds. Punnets were put on their side to allow excess infiltration medium to drain covered with a top tray and wrapped in plastic wrap to maintain humidity. Plants were placed in a growth room at ambient condition for 24 hours. After this period, the top tray and plastic wrap were removed and plants were set upright until siliques formed.
Seeds were harvested and sterilized with a 5% sodium hypochlorite solution to destroy any residual A. tumefaciens bacteria and fungal contamination.
Under sterile conditions, 100 μl seeds from the transformed A. thaliana plants were placed into an Eppendorf tube. One ml sterile water was added and the seeds left to imbibe the water for no longer than an hour. The water was remove by centrifugation, 1 ml 70% ethanol added to the seeds and gently mixed. This step was not allowed to last longer than one minute. The ethanol was removed by centrifugation, 1 ml 5% sodium hypochlorite solution was added to the seeds and gently mixed for up to 5 min. The sodium hypochlorite solution was removed by centrifugation and the seeds washed with sterile water for 1 min. The washing step was repeated three more times with centrifugation. Seeds were finally resuspended in sterile water. 500 μl of seeds in solution were pitpetted onto half-strength Murashige and Skoog medium (MS; Gibco BRL) agar plates containing 50 mg/l kanamycin and 250 mg/l timentin and spread evenly with a flamed wire-loop. The Petri dishes were placed in a refrigerator for 3 days to allow the seeds to stratify. Thereafter the plates were placed in growth room and grown under lights at 22° C. with a 14 hour photoperiod until germination. Putative transformant seedlings were selected as those growing on the antibiotic-containing medium, with large, healthy-looking dark green leaves and a strong root system. These transgenic plants were removed and placed into soil culture at 22° with a 12 hour photoperiod.
4. Staining of Plant Tissues
Tissue were taken from the flower, leaf, stem and root of A. thaliana transformed with constructs of P. radiata ubiquitin promoter and stained histochemically to determine the expression of the GUS gene under control of the pollen specific promoters. The GUS staining protocol is described by Campisi et al., Plant J 17:699-707, 1999.
A. thaliana flower, leaf, stem and root tissue were immersed in a staining solution (50 mM NaPO4 pH 7.2; 0.5% Triton X-100; 1 mM X Glucuronide sodium salt (Gibco BRL)) for immunochemical staining. Vacuum was applied twice for 5 min to infiltrate the tissue with the staining solution. The tissue was left in the staining solution for 2 days (with agitation) at 37° for color development and then destained in 70% ethanol for 24 hours at 37° C. (with agitation). The tissues were examined for blue GUS staining using a light microscope.
The results showed that constitutive expression was lost in the smallest deletion constructs (SEQ ID NOS: 131 AND 136) but was observed in all the other constructs tested, including both the intronless and intron-containing deletion constructs. These results demonstrate that the sequences described in SEQ ID NOS: 132-135 and 138-140 have constitutive promoter activity in both Arabidopsis and tobacco plants.

## Claims

1. An isolated polynucleotide comprising a sequence selected from the group consisting of:
(a) a sequence recited in SEQ ID NO: 117, wherein the polynucleotide has arabinogalactan promoter activity;
(b) a sequence recited in SEQ ID NO: 107, wherein the polynucleotide has arabinogalactan promoter activity; and
(c) a sequence comprising the E. grandis arabinogalactan promoter contained in SEQ ID NO: 117 or SEQ ID NO: 107, wherein the polynucleotide has arabinogalactan promoter activity.

2. A genetic construct comprising a polynucleotide of claim 1.

3. A genetic construct comprising, in the 5′-3′ direction:
(a) a promoter sequence;
(b) a DNA sequence of interest; and
(c) a gene termination sequence, wherein the promoter sequence comprises an isolated polynucleotide of claim 1.

4. The genetic construct of claim 3, wherein the DNA sequence of interest comprises an open reading frame encoding a polypeptide of interest.

5. A transgenic plant cell comprising a genetic construct of claim 3.

6. A plant or a part or propagule or progeny thereof comprising a transgenic cell of claim 5.

7. A method for modifying gene expression in a target plant comprising stably incorporating into the genome of the plant a genetic construct according to claim 3.

8. A method for producing a plant having modified gene expression comprising:
(a) transforming a plant cell with a genetic construct to provide a transgenic cell, wherein the genetic construct comprises: (i) a promoter sequence comprising a sequence of claim 1; (ii) a DNA sequence of interest; and (iii) a gene termination sequence; and
(b) cultivating the transgenic cell under conditions conducive to regeneration and mature plant growth.

9. A method for modifying a phenotype of a target plant, comprising stably incorporating into the genome of the target plant a genetic construct comprising:
(a) a promoter sequence of claim 1;
(b) a DNA sequence of interest; and
(c) a gene termination sequence.

10. An isolated polynucleotide comprising a sequence selected from the group consisting of:
(a) complements of the entire length of the sequence recited in SEQ ID NO: 117 or 107; and
(b) reverse complements of the entire length of the sequence recited in SEQ ID NO: 117 or 107.

11. A genetic construct comprising a polynucleotide of claim 10.