US20090083877A1

US20090083877A1 - Transcription Factors, DNA and Methods for Introduction of Value-Added Seed Traits and Stress Tolerance

Info

Publication number: US20090083877A1
Application number: US12/238,920
Authority: US
Inventors: Christopher Dale Rock; Srinivas Satyalinga Gampala
Original assignee: Individual
Current assignee: Texas Tech University TTU
Priority date: 2002-07-30
Filing date: 2008-09-26
Publication date: 2009-03-26
Also published as: US20050193443A1; US7446241B2

Abstract

Abscisic acid-inducible gene expression in different plant tissues is enhanced synergistically by the co-expression of a B3-domain transcription factor and various bZIP-domain transcription factors, or a different B3-domain transcription factor. Using these transcription factors in novel formulations, as shown by examples, will confer value-added traits to transgenic plants, including, but not limited to, higher levels of heterologous gene expression, drought and salt tolerance, viability and productivity under stress, and enhanced nutrient reserves and seed properties.

Description

CROSS-REFERENCE TO RELATED APPLICATION

This is a divisional application of pending U.S. application Ser. No. 10/996,058 filed Nov. 24, 2004, the contents of which are incorporated herein by reference. This is a continuation-in-part of pending U.S. application Ser. No. 10/629,907, filed Jul. 30, 2003, which is based upon Provisional Application No. 60/399,565 filed Jul. 30, 2002, both of which are incorporated fully herein by reference

REFERENCE TO SEQUENCE LISTING SUBMITTED ELECTRONICALLY

The official copy of the sequence listing is submitted electronically via EFS-Web as an ASCII formatted sequence listing with a file named rocksequence.txt, created on Jul. 30, 2003, and having a size of 173 KB and is filed concurrently with the specification. The sequence listing contained in this ASCII formatted document is part of the specification and is herein incorporated by reference in its entirety.

BACKGROUND OF THE INVENTION

1. Field of the Invention
A variety of stress-related traits in plants are enhanced by the synergistic effects on abscisic acid (ABA)-inducible gene expression of co-expressed basic leucine zipper (bZIP)-domain transcription factors and B3-domain transcription factors. Additionally, two different B3-domain transcription factors may be used to synergistically regulate ABA-inducible gene expression.
2. Description of Related Art
The growth in the world's population combined with a general increase in global prosperity is creating an increasing demand for food, fiber and sustainable agriculture. It is estimated that the world's population will increase by 80% to 10.8 billion people by 2050, with a concomitant decrease in arable land of 20%. A worthwhile future can only be guaranteed through sustainable agriculture and a protective relationship with nature. For example, rice is the staple food for two-thirds of the world's population and is the primary cereal crop in the world, with worldwide production in 2000 of 600 million tons. 92% of the world's rice is produced in Asia, and 40% of the cultivated area is rain-fed and experiences environmental stress, with losses estimated at 200 million tons/yr. Another example is impacts of drought on maize production in the southwest United States. Based on data from the USDA National Agricultural Statistics Service (http://www.usda.gov/nass/), in 2003 the geographical region spanning southern CA, AZ, NM, TX High Plains and trans-Pecos regions produced 1.2% (127 mil bushels) of the nation's grain corn, valued at >$310 million. It is noteworthy that only 78% of grain corn planted in these regions of the Southwest were subsequently harvested, whereas on average 90% of the planted acreage was harvested throughout the United States. Significantly, for AZ and NM from 1999-2003, the percentages of grain corn harvested ranged from only 35-58%, while the national average over that time period was 90.2%. The basis for these differences between the southwest and the “Corn Belt” harvests, valued at >$48 million in losses last year alone, is due to reductions in yield due to drought stress typically experienced by crops in the southwest. Genetic engineering of maize for increased vegetative drought stress adaptation should result in increased yields and profits for producers. A third example is dryland cotton; estimates of the value-added worth of cotton with increased photosynthetic and water use efficiencies and improved seed qualities exceed $200 million/yr in west Texas, $1 billion/yr in the USA, and $5 billion/yr globally.
Yield enhancement to increase crop production is one of the essential strategies to meet the demand for food by the growing population. In order to supply the world's population in 20 years' time with enough to eat, today's food production will have to be doubled on a third less land and water. For example, due to traditional rice breeding advances, with which germplasm from wild relatives was transferred to cultivated strains, production of rice doubled between 1966 and 1990, but it is estimated that production must increase 60% by 2025 to meet demand. The rate at which growers have been able to further improve crop productivity has declined as improved farming practices have become more fully implemented around the world, as land in developed countries available for conversion to farming has declined, and as concerns about the environmental impact of farming have increased.
While the rate of yield increases from hybrids has slowed in the last two decades, the application of biotechnology and genomics is dramatically increasing innovation in the agricultural and seed industries. Biotechnology as a means of sustainable agriculture is a crucial component to meeting the challenges posed by the interrelated global issues of poverty, hunger, population growth, and environmental degradation in the twenty-first century. Biotechnology enables gene-by-gene analysis and enhancement of crops and is augmenting traditional breeding by enabling faster, targeted development of performance-enhancing traits. These traits currently are designed to create higher-quality animal feed and in the future are expected to include nutritional benefits for humans.
Growers have rapidly adopted the first generation of genetically engineered seed traits, with significant numbers of acres planted. The number of global planted acres of herbicide-tolerant and insect-resistant crops grew from less than 5 million acres in 1995 to approximately 120 million acres in 1999. Despite this rapid growth, the total number of acres covered currently represents only a small fraction of the approximately 3 billion acres of crops cultivated worldwide. Additional growth will come from further adoption of currently available traits and the development of new input and output traits.
Improvement of crop plants for a variety of traits, including disease and pest resistance, adaptation to abiotic stresses, and grain quality improvements such as oil, starch or protein composition, has been achieved by introducing new or modified genes into plant genomes. It has recently been shown that the “Green Revolution” of the 1960s that resulted in large increases in wheat yields was due to adoption of varieties that contain a dominant allele of a gene that controls transcription factor expression by modulating microRNAs, a newly discovered mechanism of gene regulation in mesozoans. Transcription factors control virtually all significant plant traits, including yield, disease resistance, freezing and drought protection, as well as the production of chemicals and proteins used as pharmaceuticals, nutriceuticals and consumer products, by coordinate regulation of multiple target genes whose functions in many cases are not yet known.
The expression of target transgenes and endogenous genes is controlled through a complex set of protein/DNA and protein/protein interactions. Promoters and enhancers can impart patterns of expression that are either constitutive or limited to specific tissues or times during development, or in response to environmental stimuli. There are limitations in the types of expression achievable using existing promoters for transgene expression. One limitation is in the expression level achievable. It is difficult to obtain traits that require relatively high expression of an introduced gene, due to limitations in promoter strength. A second limitation is that the pattern of expression conferred by the particular promoter employed is inflexible in that the same promoter-dependent pattern of expression is conferred from generation to generation. It is desirable to have the ability to regulate trait-conferring transgene expression differently in successive generations. One example would be a trait that has a side effect of being detrimental to seed quality, but which is desired for use in fodder. In this case, it would be desirable to carry the trait-conferring transgene in an inactive state in separate breeding stocks.
Plants are sessile and therefore must perpetually develop in response to their changing environment. Plants have evolved complex, integrated, and overlapping signaling pathways to maintain a plastic growth habit in response to stresses such as drought, salt, cold, as well as hormonal cues such as abscisic acid (ABA). ABA mediates a myriad of physiological processes in growth and development, including cell division, water use efficiency, and gene expression during seed development and in response to environmental stresses such as drought, chilling, salt, pathogen attack, and UV light. Despite the complex multitude of physiological, molecular, genetic, biochemical, and pharmacological data that implicate ABA in stress responses, the adaptive responses to ABA and stresses, and the pathways that trigger them, are largely unknown. Seed maturation and freezing/drought/salt tolerance may have certain protective mechanisms in common, since they share the common phenomenon of dehydration stress.
It would be advantageous for genetic engineering of plants with environmental stress resistance to regulate multiple genes in a particular metabolic or response pathway via a single transgene. Cloning and overexpression of Drought Response Element Binding (DREB)/Cold Binding Factor (CBF) subfamily of the AP2-domain family of transcription factors responsible for cold-inducible gene expression has demonstrated the practical benefits of coordinated activation of uncharacterized gene sets that can confer non-specific protection to transgenic plants by up-regulation or pre-activation of stress-response pathways. The ABA-INSENSITIVE-4 gene (ABI4) is most closely related to the DREB/CBF subfamily of the AP2-domain family. Transgenic overexpression of the transcription factor ALFIN1 enhances expression of the endogenous MsPRP2 gene in alfalfa and improves salinity tolerance of the plants. Over-expression of a single Ca²⁺-dependent protein kinase confers both cold and salt/drought tolerance on rice plants. A multi-component transcription factor/target promoter system that regulates hormone and stress responses could be used to address the limitations of single transgene expression and tap into the natural defense systems of crop plants.
Although hundreds of ABA-regulated genes have been identified to date, many of them homologs from a broad range of species, these are likely to represent a somewhat anecdotal sampling of the full spectrum of ABA-responsive genes. Preliminary genome profiling in Arabidopsis has allowed estimation of the number of plant genes modulated by ABA, with current estimates at about 2000-6000 genes. A number of plant gene products have been identified that may function in desiccation tolerance. The COR genes are cold-, drought-, salt-, and ABA-responsive genes whose protein products are heat stable and hydrophilic; some COR genes have structural similarities to the late embryogenesis-abundant (LEA) proteins. LEA homologues in wheat, maize, barley, carrot, and the resurrection plant Craterostigma plantagineum are induced by ABA and dehydration stress. The exact roles of COR and LEA genes in cold and desiccation tolerance are not yet known, but there is strong evidence that they have an adaptive function in desiccation, freezing, and salt tolerance. Altered expression of ABA signal transduction genes can have beneficial effects on stress adaptation of plants.
The RY-G-box-RY regulatory element is commonly found in seed storage protein gene promoters and is necessary for seed-specific expression of the β-phaseolin and Em promoters. The sequences of the Ry-G-box-RY elements that are found in different natural promoters have variations, but can be recognized by the presence of particular nucleotide sequences: CATGCAW (the “RY” feature) and CACGTG (the “G-box”). There is substantial diversity in the cis sequences shown to confer ABA-inducible expression. The smallest promoter units (called ABA-Response Elements; ABREs) that are both necessary and sufficient for ABA induction of gene expression appear to consist of at least two essential cis elements, one of which is usually a G-box and the other a “coupling” element.
A seed-specific regulatory factor, Viviparous-1 (VP1), was first described in 1931 and was cloned by transposon tagging in 1989. The ABA-INSENSITIVE3 (ABI3) gene of Arabidopsis is the genetic equivalent of maize VP1 and was cloned by chromosome walking. VP1/ABI3 is expressed in developing seeds and precedes ABA-inducible storage protein and late-embryogenesis-abundant (LEA) gene expression. Rice and maize protoplasts that transiently overexpress the VP1 cDNA can transactivate ABA-inducible promoters from numerous species. Similar transactivation results have been obtained in homologous transient gene expression systems with the rice VP1 and bean Pv-ALF orthologs. Remarkably, VP1 also has repressor activity towards the germination-specific alpha-amylase genes, but repression is non-cell-autonomous and requires embryo-specific factors other than ABA and VP1.
Structure/function studies with VP1 and PvALF in transient gene expression assays demonstrate that the highly conserved N-terminal acidic domain (A1, VP1 amino acids [aa] 51-163) functions as a transcriptional activator and acts in synergy with ABA. The acidic domain of VP1 is not required for germination-specific alpha-amylase gene repression. The conserved basic B2 region (aa 508-544 of VP1) is required for transactivation of the ABA-inducible Em promoter and for enhancing the in vitro binding of various basic leucine zipper (bZIP) factors to their cognate targets, but not for alpha-amylase gene repression. The B3 domain (aa 632-760) binds specifically to promoter sequences required for transactivation but not to ABA-responsive cis-elements. Furthermore, the B3 domain is not required for synergistic effects of transactivation with ABA or for alpha-amylase gene repression. Pv-ALF facilitates chromatin modification of the ABA-inducible β-Phas promoter, which in turn potentiates ABA-mediated transcription. Carrot and Arabidopsis Pv-ALF orthologs can also direct ABA-inducible seed storage protein expression in leaves when expressed ectopically. The exact molecular mechanisms of ABI3/VP1/Pv-ALF are not known, but the predicted FUS3 and LEAFY COTYLEDON-2 class of regulators that control embryo maturation have a continuous stretch of more than 100 amino acids showing significant sequence similarity to the conserved B3 domains of ABI3/VP1/Pv-ALF. Taken together with genetic results that show FUSCA3 and LEC2 interact with ABI3, these correlations suggest that ABI3, LEC2, and FUS3 may act in partially redundant pathways. The Arabidopsis genome encodes 43 members of the B3-domain family, 19 of them within the ABI3/VP1-related subfamily, and their functions are largely unknown.
There are 81 predicted bZIP factor genes in Arabidopsis, but only one bZIP subfamily has been genetically or functionally linked to ABA response: that composed of ABI5 and its homologs, including the ABRE Binding Factors (ABFs and AREBs), Enhanced Em Level (EEL/AtbZIP12), and AtbZIP13-15, 27, and 67, which include the AtDPBFs (Arabidopsis thaliana Dc3 Promoter Binding Factors). Homologs of these genes have been characterized in sunflower and rice, where they are also correlated with ABA-, seed- or stress-induced gene expression. However, studies of bZIPs from other species have shown that in vitro binding of ABREs need not reflect action in ABA signaling in vivo. A rice homolog of ABI5, TRAB1, was identified by a yeast two-hybrid screen using the basic domains of OsVP1 as “bait” and shown to interact with ABREs in vitro and activate ABA-inducible transcription in rice protoplasts. AREBs and ABFs both share with ABI5 three conserved charged domains (C1-C3) in their amino-halves as well as the bZIP domain and another conserved (C4) domain at the C-terminus. In vitro studies with the DPBFs and other ABI5-family members have demonstrated that this subfamily binds to G-box promoter elements (ABREs) required for ABA regulation. However, the ABI5/DPBF/ABF/AREB subfamily has a broader consensus sequence for its binding site than the other bZIP proteins in that its members tolerate variability in the ACGT core element essential to the ABRE G-box. ABI5 and its homolog DPBF4/EEL were shown to compete for the same binding sites in the AtEM1 promoter and a model was proposed, based on single and double mutant phenotypes of altered gene expression, that EEL directly antagonized ABI5 transactivation. Analyses of transcript accumulation in abi5 mutants suggest that, similar to ABI3, ABI5 has both activator and repressor functions, but that ABI5 and ABI3 may have either synergistic or antagonistic effects on gene expression, depending on the gene. ABI5 protein accumulation is further enhanced by ABA-induced phosphorylation and resulting stabilization of the protein, at least during the early phases of germination.
As indicated above, it has been previously shown that maize VP1 is functionally redundant with ABI3 and that other orthologues of VP1/ABI3 could substitute for VP1 in a multi-component heterologous transactivation system. Consistent with this, expression of an Arabidopsis GIBBERELLIN-INSENSITIVE (GAI) orthologue (the same gene responsible for the “Green Revolution” in wheat; see above) in transgenic rice resulted in desirable dwarfing traits, suggesting that heterologous regulatory genes can be used to affect traits in a wide range of crop species. Transgenic rice plants that express the maize phosphoenolpyruvate carboxylase (PEPC) and pyruvate orthophosphate dikinase (PPDK) exhibit a higher photosynthetic capacity (up to 35%) than untransformed plants, mainly associated with an enhanced stomatal conductance and a higher internal CO₂concentration. An additional benefit of using heterologous genes is that they may minimize artifacts such as co-suppression and posttranscriptional transgene silencing.
Coordinated regulation of multiple endogenous genes is important for stress adaptation. New methods which genetically engineer value-added vegetative traits for stress adaptation and seed qualities by directed expression of ABA-related transcription factors would be beneficial to supply the world with the increased amounts of food needed by future generations. By overcoming the limitations of targeted gene expression and by transactivation of endogenous plant stress adaptation pathways, the volume and quality of plant products, especially from environments under stress, will be improved.

BRIEF SUMMARY OF THE INVENTION

Transgenic plants that ectopically express a B3-domain transcription factor, preferably VP1, ABI3, RAV2 and homologues from various species, in combination with at least one different B3-domain transcription factor or a bZIP-domain transcription factor, preferably ABI5 and ABI5-like family members ABF1 and ABF3 and homologues from various species, will respond to abiotic stressors such as salt, drought, and cold by activating ABA-inducible target promoters as well as endogenous promoters that coordinate expression of genes involved in stress adaptation, such as LEA and COR genes. In preferred embodiments, the B3-domain transcription factor and the bZIP-domain transcription factor are those found in members of the genus Arabidopsis and Zea mays. This multi-component expression system may be expanded by modifying the regulatory sequences of the target promoter or the promoter driving the transcription factor effectors to include tissue-specific enhancer elements or stress-response elements to further direct the expression of the target gene of interest. It is known in animal systems that targeting of some combinations of transcription factors to the same promoter may produce synergistic effects on the expression level. The strategy disclosed herein amplifies the expression level from an ABA-inducible promoter. For example, recent results have shown that grain-filling in rice is critically dependent on water status and ABA levels, suggesting that amplification of ABA response pathways by ectopic transcription factor expression in appropriate tissues and at critical times during development could have beneficial effects. The multi-component benefits of transcription factor synergy may be realized by genetic crossing of two lines harboring separate transcription factor components.
Abscisic acid (ABA) signaling pathways are highly conserved among monocots and dicots (See Gampala et al., J. Biol. Chem. 277: 1689 (2002)). Therefore, a multi-component transgenic approach to engineering stress tolerance with effectors from diverse plant species is practical. Evidence presented herein with overexpressed Arabidopsis bZIP domain transcription factors called ABFs, AREB3, DPBF4/EEL, ABI5 and maize B3 domain transcription factor VP1 in rice embryonic and maize mesophyll protoplasts further extends this claim. Since it has been shown that maize VP1 is functionally redundant with ABI3, other orthologues of VP1/ABI3 from various species could substitute for VP1 in a multi-component heterologous transactivation system. Further, evidence is presented herein that a VP1/ABI3-related B3 domain homologue from Arabidopsis, RAV2, functions in synergy with VP1 and the bZIPs ABI5 and ABF3 in maize mesophyll protoplasts, demonstrating a novel combinatorial phenomenon of synergy that extends the scope of this invention. One potential drawback to overexpressing regulatory factors that confer stress tolerance to transgenic crops is reduced yields through pleiotropic “knock on” effects that indeed may be the direct consequence of stress adaptation mechanisms triggered by the transgene effector. In this scenario, the present invention would still find application in horticultural plants like turf grasses where yields, per se, may be less important. Likewise, in ornamental species the slow-growth, stress-adapted phenotype would be a value-added trait. Some novel activities of ABI5-like family members and ABI5 alone and in combination with maize VP1 have been demonstrated. Ectopic or controlled, e.g. inducible, expression of these and related effectors in any plant species should result in conditionally altered stress responses and higher levels of engineered target gene expression than otherwise possible. The present invention also relates to polynucleotides which contain the complete gene with the polynucleotide sequence corresponding to SEQ ID NO:.1, SEQ ID NO.:3, or SEQ ID NO: 5 or fragments thereof, and which can be obtained by screening by means of the hybridization of a corresponding gene bank with a probe which contains the sequence of said polynucleotide corresponding to SEQ ID NO:.1, SEQ ID NO.:3, or SEQ ID NO: 5 or a fragment thereof, and isolation of said DNA sequence.
Given the efficacy of ABA in regulating such basic processes as seed development, dormancy vs. germination, transpiration and stress responses, the present invention can pave the way to important biotechnological applications.

BRIEF DESCRIPTION OF THE DRAWINGS

The features and advantages of the present invention will become apparent from the following detailed description of a preferred embodiment thereof, taken in conjunction with the accompanying drawings, in which:

FIG. 1. depicts two graphs showing that A) the overexpression of ABF3 and ABF4 in rice protoplasts is sufficient to transactivate ABA-inducible Em-GUS expression; and B) that overexpressed ABF3 interacts synergistically with ABA and VP1, but not ABI5.

FIG. 2 depicts two graphs showing that A) ABI5, ABF3, ABF4, AREB3, or DPBF4/EEL overexpression in maize mesophyll protoplasts is sufficient to transactivate Em-GUS expression, while B) ABI5, ABF1, and ABF3 but not ABF2, AREB3, ABF4, or DPBF4/EEL can synergize with co-transformed VP1; and

FIG. 3 is a graph in two parts showing that A) RAV2 interacts synergistically with the bZIP transcription factors ABI5 and ABF3; and B) that RAV2 interacts synergistically with VP1 in maize mesophyll protoplasts.

DETAILED DESCRIPTION OF THE INVENTION

Definitions

Unless otherwise indicated, all technical and scientific terms used herein have the same meaning as they would to one of ordinary skill in the art of the present invention. It is to be understood that this invention is not limited to the particular methodology, protocol, and reagents described, as these may vary.
All publications cited herein are expressly incorporated herein by reference for the purpose of describing and disclosing compositions and methodologies which might be used in connection with the invention.
Optimal alignment of sequences for comparison may be conducted by the local homology algorithm of Smith and Waterman Adv. Appl. Math. 2:482 (1981), by the homology alignment algorithm of Needleman and Wunsch J. Mol. Biol. 48:443 (1970), by the search for similarity method of Pearson and Lipman Proc. Natl. Acad. Sci. (U.S.A.) 85: 2444 (1988), by computerized implementations of these algorithms (GAP, BESTFIT, BLAST, FASTA, and TFASTA in the Wisconsin Genetics Software Package, Genetics Computer Group (GCG), 575 Science Dr., Madison, Wis.), or by inspection.
“Percentage of sequence identity” is determined by comparing two optimally aligned sequences over a comparison window, wherein the portion of the polynucleotide or polypeptide sequence in the comparison window may comprise additions or deletions (i.e., gaps) as compared to the reference sequence (which does not comprise additions or deletions) for optimal alignment of the two sequences. The percentage is calculated by determining the number of positions at which the identical nucleic acid base or amino acid residue occurs in both sequences to yield the number of matched positions, dividing the number of matched positions by the total number of positions in the window of comparison and multiplying the result by 100 to yield the percentage of sequence identity.
The term “substantial identity” of polynucleotide sequences means that a polynucleotide comprises a sequence that has at least 25% sequence identity. Alternatively, percent identity can be any integer from 25% to 100%. More preferred embodiments include at least: 39%, 45%, 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, or 99% compared to a reference sequence using the programs described herein; preferably BLAST using standard parameters, as described below.
Accordingly, “B3-domain transcription factors” are transcription factors that include a polynucleotide sequence having a B3 domain which is at least 25% identical to the B3 domain of SEQ ID NO:1. More preferably, the B3-domain transcription factor is a transcription factor that includes a polynucleotide sequence having a B3 domain which is at least 45% identical to the B3 domain of SEQ.ID.NO.: 1. Additionally, the B3-domain transcription factors are transcription factors that include a polypeptide sequence having a B3 domain which is at least 40% identical to the B3 domain of SEQ ID NO:2. More preferably, the B3-domain transcription factor is a transcription factor that includes a polypeptide sequence having a B3 domain which is at least 50% identical to the B3 domain of SEQ.ID.NO.: 2. The B3-domain transcription factors also include transcription factors that include a polynucleotide sequence having a B3 domain which is at least 25% identical to the B3 domain of SEQ ID NO:3. More preferably, the B3-domain transcription factor is a transcription factor that includes a polynucleotide sequence having a B3 domain which is at least 45% identical to the B3 domain of SEQ.ID.NO.: 3. Additionally, the B3-domain transcription factors include transcription factors that include a polypeptide sequence having a B3 domain which is at least 40% identical to the B3 domain of SEQ ID NO: 4. More preferably, the B3-domain transcription factor is a transcription factor that includes a polypeptide sequence having a B3 domain which is at least 50% identical to the B3 domain of SEQ.ID.NO.: 4. The “bZIP domain transcription factors” include transcription factors that include a polynucleotide sequence having a bZIP domain which is at least 25% identical to the bZIP domain of SEQ ID NO:5. More preferably, the bZIP domain transcription factor is a transcription factor that includes a polynucleotide sequence having a bZIP domain which is at least 45% identical to the bZIP domain of SEQ.ID.NO.: 5. Additionally, the bZIP domain transcription factors include transcription factors that include a polypeptide sequence having a bZIP domain that is at least 40% identical to the bZIP domain of SEQ ID NO: 6. More preferably, the bZIP domain transcription factor is a transcription factor that includes a polypeptide sequence having a bZIP domain which is at least 60% identical to the bZIP domain of SEQ.ID.NO.: 6. One of skill will recognize that these values can be appropriately adjusted to determine corresponding identity of proteins encoded by two nucleotide sequences by taking into account codon degeneracy, amino acid similarity, reading frame positioning and the like. Substantial identity of amino acid sequences for these purposes normally means sequence identity of at least 60%. Preferred percent identity of polypeptides can be any integer from 40% to 100%. More preferred embodiments include at least 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, or 99%. Most preferred embodiments include at least 60% polypeptide identity.
The phrase “nucleic acid” refers to a single or double-stranded polymer of deoxyribonucleotide or ribonucleotide bases read from the 5′ to the 3′ end. Nucleic acids may also include modified nucleotides that permit correct read through by a polymerase and do not alter expression of a polypeptide encoded by that nucleic acid.
The phrase “polynucleotide sequence” or “nucleic acid sequence” includes both the sense and antisense strands of a nucleic acid as either individual single strands or in the duplex. It includes, but is not limited to, self-replicating plasmids, chromosomal sequences, and pharmacological application of polymers of DNA or RNA. For example, see “Therapeutic silencing of an endogenous gene by systemic administration of modified siRNAs” Nature 432: 173-178 (Nov. 11, 2004). The present invention also includes small interfering RNAs (siRNAs) homologous to the bZIP domain transcription factors and B3 domain transcription factors.
The phrase “nucleic acid sequence encoding” refers to a nucleic acid which directs the expression of a specific protein or peptide. The nucleic acid sequences include, but are not limited to, both the DNA strand sequence that is transcribed into RNA and the RNA sequence that is translated into protein. The nucleic acid sequences include both the full length nucleic acid sequences as well as non-full length sequences derived from the full length sequences. It should be further understood that the sequence includes the degenerate codons of the native sequence or sequences which may be introduced to provide codon preference in a specific host cell.
A polynucleotide “exogenous to” an individual plant is a polynucleotide which is introduced into the plant by any means other than by a sexual cross. Examples of means by which this can be accomplished are described below, and include Agrobacterium-mediated transformation, biolistic methods, electroporation, in planta techniques, and the like. Such a plant containing the exogenous nucleic acid is referred to here as an R1 generation transgenic plant. Transgenic plants which arise from sexual cross or by selfing are descendants of such a plant.
A “B3 domain polynucleotide” is a nucleic acid sequence comprising a coding region of about 100 to about 900 nucleotides, sometimes from about 200 to about 630 nucleotides, which hybridizes to SEQ ID NO:1 or 3 under stringent conditions, preferably as defined below, or which encodes a B3 domain polypeptide. B3 domain polynucleotides can also be identified by their ability to hybridize under low stringency conditions (e.g., Tm about 40° C.) to nucleic acid probes having a sequence from position 559 to 885 in SEQ ID NO:3 or from position 1560 to 1929 in SEQ ID NO:1.
A “B3 domain polypeptide” is a sequence of about 100 to about 130 amino acid residues encoded by a B3 domain polynucleotide. A full length B3 domain polypeptide can act as a subunit of a protein capable of acting as a transcription factor in plant cells.
A “bZIP domain polynucleotide” is a nucleic acid sequence comprising a coding region of about 190 nucleotides which hybridizes to SEQ ID NO:5 under stringent conditions, preferably as defined below, or which encodes a bZIP domain polypeptide. bZIP domain polynucleotides can also be identified by their ability to hybridize under low stringency conditions (e.g., Tm about 40° C.) to nucleic acid probes having a sequence from position 1057 to 1251 in SEQ ID NO:5.
A “bZIP domain polypeptide” is a sequence of about 60 amino acid residues encoded by a bZIP domain polynucleotide. A full length bZIP domain polypeptide can act as a subunit of a protein capable of acting as a transcription factor in plant cells.
As used herein, a “homolog” of a particular gene (e.g., SEQ ID NO:1) is a second gene in the same plant type or in a different plant type, which has a polynucleotide sequence of at least 50 contiguous nucleotides which are substantially identical (determined as described herein) to a sequence in the first gene. It is believed that, in general, homologs share a common evolutionary past.
“Increased or enhanced B3 domain activity or expression of a B3 domain gene” refers to an augmented change in B3 domain activity. Examples of such increased activity or expression include the following. B3 domain activity or expression of the B3 domain gene is increased above the level of that in wild-type, non-transgenic control plants (i.e. the quantity of B3 domain activity or expression of the B3 domain gene is increased). B3 domain activity or expression of the B3 domain gene is in an organ, tissue or cell where it is not normally detected in wild-type, non-transgenic control plants (i.e. spatial distribution of B3 domain activity or expression of the B3 domain gene is increased). B3 domain activity or expression is increased when B3 domain activity or expression of the B3 domain gene is present in an organ, tissue or cell for a longer period than in a wild-type, non-transgenic controls (i.e. duration of B3 domain activity or expression of the B3 domain gene is increased).
“Increased or enhanced bZIP domain activity or expression of a bZIP domain gene” refers to an augmented change in bZIP domain activity. Examples of such increased activity or expression include the following. bZIP domain activity or expression of the bZIP domain gene is increased above the level of that in wild-type, non-transgenic control plants (i.e. the quantity of bZIP domain activity or expression of the bZIP domain gene is increased). bZIP domain activity or expression of the bZIP domain gene is in an organ, tissue or cell where it is not normally detected in wild-type, non-transgenic control plants (i.e. spatial distribution of bZIP domain activity or expression of the bZIP domain gene is increased). bZIP domain activity or expression is increased when bZIP domain activity or expression of the bZIP domain gene is present in an organ, tissue or cell for a longer period than in a wild-type, non-transgenic controls (i.e. duration of bZIP domain activity or expression of the bZIP domain gene is increased).
Two nucleic acid sequences or polypeptides are said to be “identical” if the sequence of nucleotides or amino acid residues, respectively, in the two sequences is the same when aligned for maximum correspondence as described below. The term “complementary to” is used herein to mean that the sequence is complementary to all or a portion of a reference polynucleotide sequence.
The term “isolated” means separated from its natural environment.
The term “polynucleotide” refers in general to polyribonucleotides and polydeoxyribonucleotides, and can denote an unmodified RNA or DNA or a modified RNA or DNA.
The term “polypeptides” is to be understood to mean peptides or proteins which contain two or more amino acids which are bound via peptide bonds.
The terms “stringent conditions” or “stringent hybridization conditions” includes reference to conditions under which a polynucleotide will hybridize to its target sequence, to a detectably greater degree than other sequences (e.g., at least 2-fold over background). Stringent conditions are sequence-dependent and will be different in different circumstances. By controlling the stringency of the hybridization and/or washing conditions, target sequences can be identified which are 100% complementary to the probe (homologous probing). Alternatively, stringency conditions can be adjusted to allow some mismatching in sequences so that lower degrees of similarity are detected (heterologous probing).
Polypeptides which are “substantially similar” share sequences as noted above except that residue positions which are not identical may differ by conservative amino acid changes. Conservative amino acid substitutions refer to the interchangeability of residues having similar side chains. For example, a group of amino acids having aliphatic side chains is glycine, alanine, valine, leucine, and isoleucine; a group of amino acids having aliphatic-hydroxyl side chains is serine and threonine; a group of amino acids having amide-containing side chains is asparagine and glutamine; a group of amino acids having aromatic side chains is phenylalanine, tyrosine, and tryptophan; a group of amino acids having basic side chains is lysine, arginine, and histidine; and a group of amino acids having sulfur-containing side chains is cysteine and methionine. Preferred conservative amino acids substitution groups are: valine-leucine-isoleucine, phenylalanine-tyrosine, lysine-arginine, alanine-valine, aspartic acid-glutamic acid, and asparagine-glutamine.
An “isolated polynucleotide” or an “isolated DNA segment” having a sequence which encodes a plant transcription factor is a polynucleotide which contains the coding sequence of the plant transcription factor (i) in isolation, (ii) in combination with additional coding sequences, such as fusion protein or signal peptide, in which the plant transcription factor coding sequence is the dominant coding sequence, (iii) in combination with non-coding sequences, such as control elements, such as promoter and terminator elements, effective for expression of the coding sequence in plant cells, and/or (iv) in a vector or host environment in which the plant transcription factor coding sequence is a heterologous gene.
As used herein, the term “plasmid” refers to a circular double-stranded (ds) DNA construct used as a cloning vector, and which forms an extrachromosomal self-replicating genetic element in many bacteria and some eukaryotes.
As used herein, the term “vector” refers to a nucleic acid construct designed for transfer between different host cells. An “expression vector” refers to a vector that has the ability to incorporate and express heterologous DNA fragments in a foreign cell. Many prokaryotic and eukaryotic expression vectors are commercially available. Selection of appropriate expression vectors is within the knowledge of those having skill in the art.
As used herein, the term “promoter” refers to a nucleic acid sequence that functions to direct transcription of a distal gene. The promoter will generally be appropriate to the host cell in which the target gene is being expressed. The promoter together with other transcriptional and translational regulatory nucleic acid sequences (also termed “control sequences”) is necessary to express a given gene. In general, the transcriptional and translational regulatory sequences include, but are not limited to, promoter sequences, ribosomal binding sites, transcriptional start and stop sequences, translational start and stop sequences, enhancer or activator sequences, and regulatory small RNA target-binding sequences. The term “promoter” also refers to a region or sequence determinants located upstream or downstream from the start of transcription and which are involved in recognition and binding of RNA polymerase and other proteins to initiate transcription. A “plant promoter” is a promoter capable of initiating transcription in plant cells. Such promoters need not be of plant origin, for example, promoters derived from plant viruses, such as the CaMV35S promoter, can be used in the present invention. As used herein, the term “promoter” refers to a sequence of DNA that functions to direct transcription of a gene which is operably linked thereto. A promoter may or may not include additional control sequences (also termed “transcriptional and translational regulatory sequences”), involved in expression of a given gene product. In general, transcriptional and translational regulatory sequences include, but are not limited to, promoter sequences, ribosomal binding sites, transcriptional start and stop sequences, translational start and stop sequences, enhancer or activator sequences, and regulatory small RNA target-binding sequences. The promoter may be homologous or heterologous to the cell in which it is found.
A nucleic acid sequence is “heterologous” with respect to a control sequence (i.e. promoter or enhancer) when it does not function in nature to regulate the same gene the expression of which it is currently regulating. Generally, heterologous nucleic acid constructs are introduced into the cell or part of the genome in which they are present, and have been added to the cell by transfection, microinjection, electroporation, or the like. The sequences may contain a control sequence/DNA coding sequence combination that is the same as, or different from, a control sequence/DNA coding sequence combination found in the native plant. A polynucleotide sequence is “heterologous to” an organism or a second polynucleotide sequence if it originates from a foreign species, or, if from the same species, is modified from its original form. For example, a promoter operably linked to a heterologous coding sequence refers to a coding sequence from a species different from that from which the promoter was derived, or, if from the same species, a coding sequence which is different from any naturally occurring allelic variants.
As used herein, the term “operably linked” relative to a recombinant DNA construct or vector means nucleotide components of the recombinant DNA construct or vector are in a functional relationship with another nucleic acid sequence. For example, a promoter or enhancer is operably linked to a coding sequence if it affects the transcription of the sequence; or a ribosome binding site is operably linked to a coding sequence if it is positioned so as to facilitate translation. Generally, “operably linked” means that the DNA sequences being linked are contiguous, and, in the case of a secretory leader, contiguous and in reading phase. However, enhancers do not have to be contiguous.
As used herein, the term “gene” means the segment of DNA involved in producing a polypeptide chain, which may or may not include regions preceding and following the coding region, e.g. 5′ untranslated (5′ UTR) or “leader” sequences and 3′ UTR or “trailer” sequences, as well as intervening sequences (introns) between individual coding segments (exons). The term “gene” may be used interchangeably herein with the term “nucleic acid coding sequence”, and the term “structural gene” which means a DNA coding region.
As used herein, the term “fragment,” when referring to a gene sequence means a polynucleotide having a nucleic acid sequence which is the same as part of, but not all of, the nucleic acid sequence of the full length gene. The fragment preferably includes at least 15 contiguous bases of the gene, preferably at least 20-30 bases. With reference to interaction with a transcription factor, the sequence must be of sufficient length to interact with the transcription factor.
As used herein, the terms “transformed”, “stably transformed” or “transgenic” with reference to a plant cell means the plant cell has a non-native (heterologous) nucleic acid sequence integrated into its genome which is maintained through one or more generations.
As used herein, the term “expression” refers to the process by which a polypeptide is produced based on the nucleic acid sequence of a gene. The process generally includes both transcription, and translation.
The term “introduced” in the context of inserting a nucleic acid sequence into a cell, means “transfection”, or “transformation” or “transduction” and includes reference to the incorporation of a nucleic acid sequence into a eukaryotic or prokaryotic cell where the nucleic acid sequence may be incorporated into the genome of the cell (for example, chromosome, plasmid, plastid, or mitochondrial DNA), converted into an autonomous replicon, or transiently expressed (for example, transfected mRNA).
As used herein, the term “effector” refers to plant transcription factors that “effect” the transcription of genes having the appropriate response sequence.
As used herein, the terms “regulatable promoter” and “inducible promoter” may be used interchangeably and refer to any promoter the activity of which is affected by a cis- or trans-acting factor.
As used herein, the terms “transcriptional regulatory protein”, “transcriptional regulatory factor” and “transcription factor” may be used interchangeably and refer to a cytoplasmic or nuclear protein that binds a DNA response element and thereby transcriptionally regulates the expression of an associated gene or genes. Transcription factors generally bind directly to a DNA response sequence or element, however in some cases may bind indirectly to another protein, which in turn binds to or is bound to the DNA response element.
As used herein, the terms “response sequence” and “response element” refer to the binding site or sequence for a transcriptional regulatory protein (transcription factor) which may be the part of, overlapping, or adjacent to, a promoter sequence.
As used herein, a “plant cell” refers to any cell derived from a plant, including undifferentiated tissue (e.g., callus) as well as plant seeds, pollen, progagules and embryos.
As used herein, the term “mature plant” refers to a fully differentiated plant.
As used herein, the terms “native” and “wild-type” relative to a given plant trait or phenotype refers to the form in which that trait or phenotype is found in the same variety of plant in nature.
As used herein, the term “plant” includes reference to whole plants, shoot vegetative organs/structures (for example, leaves, stems, tubers, etc.), roots, flowers and floral organs/structures (e.g. bracts, sepals, petals, stamens, carpels, anthers and ovules), seed (including embryo, endosperm, and seed coat) and fruit (the mature ovary), plant tissue (e.g. vascular tissue, ground tissue, and the like) and cells (e.g. guard cells, egg cells, trichomes and the like), and progeny of the same. Plant cell, as used herein includes, without limitation, seeds, suspension cultures, embryos, meristematic regions, callus tissue, leaves roots shoots, gametophytes, sporophytes, pollen, and microspores. The class of plants which can be used in the methods of the present invention is generally as broad as the class of higher and lower plants amenable to transformation techniques, including angiosperms (both monocotyledenous and dicotyledenous plants), gymnosperms, ferns, and multicellular algae. It includes plants of a variety of ploidy levels, including aneuploid, polyploid, diploid, haploid and hemizygous.
As used herein, the term “transgenic plant” refers to a plant comprising within its genome a heterologous DNA segment. Generally, the heterologous polynucleotide is stably integrated within the genome such that the polynucleotide is passed on to successive generations. The heterologous polynucleotide may be integrated into the genome alone or as part of a recombinant expression cassette. “Transgenic” is used herein to include any cell, cell line, callus, tissue, plant part or plant, the genotype of which has been altered by the presence of heterologous nucleic acid including those transgenics initially so altered as well as those created by sexual crosses or asexual propagation from the initial transgenic.
As used herein, the term “enhancement” means increasing the intracellular activity of one or more enzymes in a plant cell and/or plant which are encoded by the corresponding DNA. Enhancement can be achieved with the aid of various manipulations of the cell. In order to achieve enhancement, particularly over-expression, the number of copies of the corresponding gene can be increased, a strong promoter can be used, or the promoter and regulation region or the ribosome binding site which is situated upstream of the structural gene can be mutated. Expression cassettes which are incorporated upstream of the structural gene act in the same manner. In addition, it is possible to increase expression by employing inducible promoters. A gene can also be used which encodes a corresponding enzyme with a high activity. Expression can also be improved by measures for extending the life of the mRNA. Furthermore, enzyme activity as a whole is increased by preventing the degradation of the enzyme. Moreover, these measures can optionally be combined in any desired manner. These and other methods for altering gene activity in a plant are known as described, for example, in Methods in Plant Molecular Biology, Maliga et al, Eds., Cold Spring Harbor Laboratory Press, New York (1995).

Method and Composition of the Invention

The invention provides transgenic plant cells and transgenic plants which express at least two transcription factors that interact synergistically: 1) a first B3-domain transcription factor and 2) a second B3-domain transcription factor or a bZIP domain transcription factor. Expression of the transcription factors is correlated with increased expression of a gene under the control of a promoter with which the transcription factors interact. The two transcription factors are expressed in the same cell and act in concert to modulate expression of the gene to which they are operably linked. Expression of two transcription factors in the same plant results in a level of transgene expression which is greater than the expression of each transcription factor alone, when the transgene is under the control of a promoter with which the transcription factors interact. In other words, as exemplified herein, the level of expression observed when a transgene is expressed under the control of a promoter with which both 1) the B3-domain transcription factor and 2) the bZIP and/or B3-domain transcription factors interact is greater than the expression level observed due to the additive effects of each individual transcription factor.
The invention provides expression cassettes comprising a promoter operably linked to a heterologous polynucleotide sequence or complement thereof, encoding a B3 or bZIP domain-containing polypeptide comprising a sequence which is at least 50% identical to the B3 domain of SEQ ID NO:2 or SEQ ID NO:4 and 60% identical to SEQ ID NO 6. In some embodiments, the polynucleotide sequence is heterologous to any element in the expression cassette. In a preferred embodiment, the B3 domain comprises a polypeptide between about amino acid residue 496 and amino acid residue 619 of SEQ ID NO:2. In a more preferred embodiment, the B3 domain comprises a polypeptide sequence between about amino acid residue 187 and amino acid residue 295 of SEQ ID NO:4. In yet another preferred embodiment, the bZIP domain comprises a polypeptide between about amino acid residue 353 and amino acid residue 417 of SEQ. ID NO: 6.
In particularly preferred embodiments, the B3 domain polypeptide is shown in SEQ ID NO:2, 4, 30, 32, 34, 36, 38, 40, 42, 44, 46, 48, 50, 52, 54, 56, 58, 60, 62, 64 or 66. Such B3 domain polypeptides can be encoded by the polynucleotide sequences shown in SEQ ID NO:1, 3, 31, 33, 35, 37, 39, 41, 43, 45, 47, 49, 51, 53, 55, 57, 59, 61, 63 or SEQ ID NO:65, respectively. In another embodiment the B3 domain polypeptide is a fusion between two or more B3 domain polypeptides or polypeptide subsequences. The polynucleotide sequence can be heterologous to any element in the expression cassette. Such expression cassettes can encode fusions of two or more B3 domain polypeptides or polypeptide subsequences.
In particularly preferred embodiments, the bZIP domain polypeptide is shown in SEQ ID NO: 6, 8, 10, 12, 14, 16, 18, 20, 22, 24, 26 or 28. Such bZIP domain polypeptides can be encoded by the polynucleotide sequences shown in SEQ ID NO: 5, 7, 9 11, 13, 15, 17, 19, 21, 23, 25 or 27. In another embodiment the bZIP domain polypeptide is a fusion between two or more bZIP domain polypeptides or polypeptide subsequences. The polynucleotide sequence can be heterologous to any element in the expression cassette. Such expression cassettes can encode fusions of two or more bZIP domain polypeptides or polypeptide subsequences.
The invention also provides an isolated nucleic acid or complement thereof, encoding a B3 domain polypeptide comprising a sequence at least 50% identical to the B3 domain of SEQ ID NO: 2 or 4. In a preferred embodiment, the B3 domain comprises a polypeptide sequence from about amino acid 187 to about amino acid 295 of SEQ ID NO:4. In another embodiment, the B3 domain polypeptide comprises a polypeptide sequence at least 50% identical to the B3 domain of SEQ ID NO:2 Such B3 domain polypeptides can be encoded by polynucleotide sequences at least 39% identical to B3 domain sequences shown in SEQ ID NO: 1 (nucleotide position 1560 to 1929) or SEQ ID NO:3 (nucleotide position 559-885), respectively. In another embodiment, the B3 domain polypeptide is a fusion between two or more B3 domain polypeptides or polypeptide subsequences.
The invention also provides an isolated nucleic acid or complement thereof, encoding a bZIP domain polypeptide comprising a subsequence at least 60% identical to the bZIP domain of SEQ ID NO: 6. In a preferred embodiment, the bZIP domain comprises a polypeptide sequence between about amino acid residue 353 and amino acid residue 417 of SEQ ID NO:6. Such bZIP domain polypeptides can be encoded by the polynucleotide at least 39% identical to sequences shown in SEQ ID NO:5 (nucleotide position 1057 to 1251). In another embodiment, the bZIP domain polypeptide is a fusion between two or more bZIP domain polypeptides or polypeptide subsequences.
In one embodiment, it may be advantageous for propagating or expressing the polynucleotide to carry it in a bacterial or fungal strain with the appropriate vector suitable for the cell type. Common methods of propagating polynucleotides and producing proteins in these cell types are known in the art and are described, for example, in Maniatis et al., Molecular Cloning: A Laboratory Manual, Cold Spring Harbor Laboratory Press, New York (1982) and Sambrook et al., Molecular Cloning: A Laboratory Manual, Cold Spring Harbor Laboratory Press, New York (1989).
The invention also provides isolated polypeptides comprising amino acid sequences at least 50% identical to the B3 domain of SEQ ID NO:2 or 4 and capable of exhibiting at least one of the biological activities of the polypeptides encoded in SEQ ID NO:2, SEQ ID NO:4 or a fragment thereof. Antibodies capable of binding the above described polypeptides are also provided.
The invention also provides isolated polypeptides comprising amino acid sequences at least 60% identical to the bZIP domain of SEQ ID NO:6 and capable of exhibiting at least one of the biological activities of the polypeptides encoded in SEQ ID NO:6 or a fragment thereof. Antibodies capable of binding the above described polypeptides are also provided. The invention also provides transgenic plant cells or plants comprising an expression cassette comprising a promoter operably linked to a heterologous polynucleotide sequence, or complement thereof, encoding a B3 domain polypeptide comprising a sequence which is at least 50% identical to the B3 domain of SEQ ID NO:2 or 4. Such B3 domain polypeptides can be encoded by the polynucleotide sequences shown in SEQ ID NO:1 or SEQ ID NO:3 respectively. The invention also provides plants that are regenerated from the plant cells discussed above.
The invention also provides transgenic plant cells or plants comprising an expression cassette comprising a promoter operably linked to a heterologous polynucleotide sequence, or complement thereof, encoding a bZIP domain polypeptide comprising a sequence which is at least 60% identical to the bZIP domain of SEQ ID NO:6. Such bZIP domain polypeptides can be encoded by the polynucleotide sequences shown in SEQ ID NO:5. The invention also provides plants that are regenerated from the plant cells discussed above.
In activating transcription of a nucleic acid coding sequence, the transcription factors described herein may interact with (1) a native promoter or (2) a non-native, recombinant or heterologous promoter. In either case, all or part of the promoter sequence is operably linked to a native nucleic acid coding sequence or a heterologous nucleic acid coding sequence (e.g., a transgene) and may be from the same or a different species from that of the plant in which it is present. The transgene may be a reporter gene, such as luciferase (LUC) or β-glucuronidase (GUS), or a gene encoding a recombinant protein that is expressed in the plant.
In practicing the invention, a plant cell may be transformed with one or more vectors, each comprising the coding sequence for one or more plant transcription factors, each operably linked to a tissue specific promoter, wherein the tissue specific promoters may be the same or different. It will be understood by those of skill in the art that once expressed a recombinant transcription factor may act on the promoter which is regulating expression of the transcription factor itself, one or more heterologous target promoters, in addition to acting on multiple native promoters.
In the case where the inserted polynucleotide sequence is transcribed and translated to produce a functional polypeptide, one of skill will recognize that because of codon degeneracy a number of polynucleotide sequences will encode the same polypeptide. These variants are specifically covered by the term “polynucleotide sequence from” a particular B3 and/or bZIP domain gene. In addition, the term specifically includes sequences (e.g., full length sequences) substantially identical (determined as described below) with a B3 and/or bZIP domain gene sequence and that encode proteins that retain the function of a B3 and/or bZIP domain polypeptide.
In the case of polynucleotides used to inhibit expression of an endogenous or heterologous gene, the introduced sequence need not be perfectly identical to a sequence of the target gene. The introduced polynucleotide sequence will typically be at least substantially identical (as determined below) to the target sequence.
Polynucleotide sequences according to the invention are suitable as hybridization probes for RNA, cDNA and DNA, in order to isolate those cDNAs or genes which exhibit a high degree of similarity to the sequence of the B3 and/or bZIP domain gene.
Polynucleotide sequences according to the invention are also suitable as primers for polymerase chain reaction (PCR) for the production of DNA which encodes a protein having activity of a B3 and/or bZIP domain polypeptide.
Oligonucleotides such as these, which serve as probes or primers, can contain more than 30, preferably up to 30, more preferably up to 20, most preferably at least 15 successive nucleotides. Oligonucleotides with a length of at least 40 or 50 nucleotides are also suitable.
The polypeptides according to the invention include polypeptides corresponding to SEQ ID NO. 2 or 4, particularly those with the biological activity of a B3 domain protein, and also includes those, at least 50% of which, preferably at least 60% of which, are homologous with the B3 domain of the polypeptides corresponding to SEQ ID NO. 2 and 4 and which have the cited activity.
The polypeptides according to the invention include polypeptides corresponding to SEQ ID No. 6, particularly those with the biological activity of a bZIP domain protein, and also includes those, at least 60% of which are homologous with the bZIP domain of the polypeptide corresponding to SEQ ID NO. 6 and which have the cited activity.
Another indication that nucleotide sequences are substantially identical is if two molecules hybridize to each other, or a third nucleic acid, under stringent conditions. In the present invention, mRNA encoded by B3 and/or bZIP domain genes of the invention can be identified in RNA blots under stringent conditions using cDNAs of the invention or fragments of at least about 100 nucleotides. Genomic DNA or cDNA comprising genes of the invention can be identified using the same cDNAs specified in SEQ ID NO 1, 3, or 5 (or fragments of at least about 100 nucleotides) under low stringency conditions for heterologous probing of samples.
Typically, stringent conditions will be those in which the salt concentration is less than about 1.5 M Na ion, typically about 0.01 to 1.0 M Na ion concentration (or other salts) at pH 7.0 to 8.3 and the temperature is at least about 30° C. for short probes (e.g., 10 to 50 nucleotides) and at least about 60° C. for long probes (e.g., greater than 50 nucleotides). Stringent conditions may also be achieved with the addition of destabilizing agents such as formamide. Exemplary low stringency conditions include hybridization with a buffer solution of 30 to 35% formamide, 1 M NaCl, 1% SDS (sodium dodecyl sulphate) at 37° C., and a wash in 1× to 2×SSC (20×SSC=3.0 M NaCl/0.3 M trisodium citrate) at 50 to 55° C. Exemplary moderate stringency conditions include hybridization in 40 to 45% formamide, 1 M NaCl, 1% SDS at 37° C., and a wash in 0.5× to 1×SSC at 55 to 60° C. Exemplary high stringency conditions include hybridization in 50% formamide, 1 M NaCl, 1% SDS at 37° C., and a wash in 0.1×SSC at 60 to 65° C.
Specificity is typically the function of post-hybridization washes, the critical factors being the ionic strength and temperature of the final wash solution. For DNA-DNA hybrids, the Tm can be approximated from the equation of Meinkoth and Wahl, Anal. Biochem., 138:267-284 (1984): Tm=81.5° C.+16.6(log M)+0.41(% GC)-0.61 (% form)-500/L; where M is: the molarity of monovalent cations, % GC is the percentage of guanosine and cytosine nucleotides in the DNA, % form is the percentage of formamide in the hybridization solution, and L is the length of the hybrid in base pairs. The Tm is the temperature (under defined ionic strength and pH) at which 50% of a complementary target sequence hybridizes to a perfectly matched probe. Tm is reduced by about 1° C. for each 1% of mismatching; thus, Tm, hybridization and/or wash conditions can be adjusted to hybridize to sequences of the desired identity. For example, if sequences with approximately 90% identity are sought, the Tm can be decreased 10° C. Generally, stringent conditions are selected to be about 5° C. lower than the thermal melting point (Tm) for the specific sequence and its complement at a defined ionic strength and pH. However, severely stringent conditions can utilize a hybridization and/or wash at 1, 2, 3, or 4° C. lower than the thermal melting point (Tm); moderately stringent conditions can utilize a hybridization and/or wash at 6, 7, 8, 9, or 10° C. lower than the thermal melting point (Tm); low stringency conditions can utilize a hybridization and/or wash at 11, 12, 13, 14, 15, or 20° C. lower than the thermal melting point (Tm). Using the equation, hybridization and wash compositions, and desired Tm, those of ordinary skill will understand that variations in the stringency of hybridization and/or wash solutions are inherently described. If the desired degree of mismatching results in a Tm of less than 45° C. (aqueous solution) or 32° C. (formamide solution), it is preferred to increase the SSC concentration so that a higher temperature can be used. An extensive guide to the hybridization of nucleic acids is found in Current Protocols in Molecular Biology, Chapter 2, Ausubel, et al., Eds., Greene Publishing and Wiley-Interscience, New York (2000). Thus, with the foregoing information, the skilled artisan can identify and isolate polynucleotides which are substantially similar to the present polynucleotides. In so isolating such a polynucleotide, the polynucleotide can be used as the present polynucleotide in, for example, increasing the stress tolerance of a plant.
The invention also relates to coding DNA sequences which result from SEQ ID NO. 1, SEQ ID NO: 3 and SEQ ID NO: 5 by degeneration of the genetic code. In the same manner, the invention further relates to DNA sequences which hybridize with SEQ ID NO. 1, 3, or 5 or with parts of SEQ ID NOs. 1, 3, or 5. Moreover, one skilled in the art is also aware of conservative amino acid replacements such as the replacement of glycine by alanine or of aspartic acid by glutamic acid in proteins as “sense mutations” which do not result in any fundamental change in the activity of the protein, i.e. which are functionally neutral. It is also known that changes at the N- and/or C-terminus of a protein do not substantially impair the function thereof, and may even stabilise said function.
In the same manner, the present invention also relates to DNA sequences which hybridize with SEQ ID NO. 1, 3, or 5 or with parts of SEQ ID NOs. 1, 3, or 5. Finally, the present invention relates to DNA sequences which are produced by polymerase chain reaction (PCR) using oligonucleotide primers which result from SEQ ID NOs. 1, 3, or 5. Oligonucleotides of this type typically have a length of at least 15 nucleotides.
In one preferred embodiment, the plant transcription factor is operably linked to a tissue-specific promoter, preferably an inducible promoter.
In a preferred embodiment the polynucleotides of the present invention are in a vector and/or a host cell. Preferably, the polynucleotides are in a plant cell or transgenic plant. In a preferred embodiment, transgenic plant lines, e.g., rice, wheat, corn, barley, oat, rape, cotton, peanut, and soybean are developed and genetic crosses carried out using conventional plant breeding techniques. In one exemplary approach, a first stable transgenic plant line is generated where the plants express two transcription factors, e.g. 1) a B3-domain transcription factor and a bZIP domain transcription factors, or 2) two different B3-domain transcription factors, under the control of a tissue-specific promoter. A number of such lines may be generated with varying levels of transcription factor expression. In practicing the method, these plants may be crossed with a parental transgenic rice, wheat, corn, barley, oat, rape, cotton, peanut, or soybean line that expresses a heterologous protein coding sequence (e.g., a recombinant protein) under the control of a tissue-specific promoter that is responsive to the transcription factors expressed in the first plant line. Plants derived from the resulting cross (F2) have a higher expression level of the heterologous protein in one or more particular seed tissues, than a corresponding non-transgenic plant. In a preferred embodiment, the B3 domain transcription factor(s) and/or bZIP domain transcription factor may be incorporated into the same (original) plant or into two separate transcription factor-expressing lines that are crossed together to make a double transcription factor line wherein the transcription factors will synergize with each other to control the expression of endogenous genes and/or a third recombinant “target”. The “target” can also be crossed in and selected for “triple-expressing” lines.
In another preferred embodiment, the present invention provides methods of increasing the stress tolerance of a plant in need thereof, comprising introducing the polynucleotides of the invention into said plant.
In another preferred embodiment, the present invention provides an isolated polypeptide comprising the amino acid sequence in SEQ ID NO:2 or 4 or 6 or those proteins that are at least 40%, preferably 50%, preferably 60% and preferably 95% identity to SEQ ID NO:2, 4, or 6. Preferably, the polypeptides have B3 domain or bZIP activity to effect expression driven by an ABA-inducible promoter.
In another preferred embodiment, the present invention provides a method for making B3 or bZIP domain proteins, comprising culturing the host cell carrying the polynucleotides of the invention for a time and under conditions suitable for expression of the B3 or bZIP, and collecting the B3 or bZIP protein.
In another preferred embodiment the present invention provides a process for screening for polynucleotides which encode a B3 domain and bZIP domain proteins comprising hybridizing the polynucleotide of the invention to the polynucleotide to be screened; expressing the polynucleotide to produce a protein; and detecting the presence or absence of B3 domain activity in said protein.
One embodiment of the present invention is methods of screening for polynucleotides in a sample which have substantial homology to the polynucleotides of the present invention, preferably those polynucleotides encoding a protein having B3 domain activity. The method comprises providing an isolated B3 domain nucleic acid molecule comprising a polynucleotide sequence, or complement thereof, encoding a B3 domain polypeptide with a subsequence at least 50% identical to the B3 domain of SEQ ID NO:2 or 4, contacting the isolated nucleic acid molecule with a sample under conditions which permit a comparison of the sequence of the isolated nucleic acid molecule with the sequence of DNA in the sample; and analyzing the result of the comparison. In some embodiments, the isolated nucleic acid molecule and the sample are contacted under conditions which permit the formation of a duplex between complementary nucleic acid sequences.
One embodiment of the present invention is methods of screening for polynucleotides in a sample which have substantial homology to the polynucleotides of the present invention, preferably those polynucleotides encoding a protein having bZIP domain activity. The method comprises providing an isolated bZIP domain nucleic acid molecule comprising a polynucleotide sequence, or complement thereof, encoding a bZIP domain polypeptide with a subsequence at least 60% identical to the bZIP domain of SEQ ID NO:6, contacting the isolated nucleic acid molecule with a sample under conditions which permit a comparison of the sequence of the isolated nucleic acid molecule with the sequence of DNA in the sample; and analyzing the result of the comparison. In some embodiments, the isolated nucleic acid molecule and the sample are contacted under conditions which permit the formation of a duplex between complementary nucleic acid sequences.
In a preferred embodiment the B3 domain polypeptide and the bZIP domain polypeptide have functional assays for B3 or bZIP transacting activity on ABA-inducible gene expression.
In another preferred embodiment, the present invention includes a process for screening in a transient functional assay for polynucleotides which encode a protein having B3 or bZIP transacting activity on ABA-inducible gene expression comprising hybridizing the polynucleotides of the invention to the polynucleotide to be screened; expressing the polynucleotide to produce a protein; and detecting the presence or absence of B3 or bZIP trans-acting activity on ABA-inducible gene expression in said functional assay. In another preferred embodiment, the present invention provides a method for making B3 or bZIP proteins, comprising culturing the host cell carrying the polynucleotides of the invention for a time and under conditions suitable for expression of B3 or bZIP proteins, and collecting the B3 or bZIP proteins protein.
In the case of both expression of transgenes and inhibition of endogenous genes (e.g., by antisense, or sense suppression) one of skill will recognize that the inserted polynucleotide sequence need not be identical and may be “substantially identical” to a sequence of the gene from which it was derived. As explained below, these variants are specifically covered by this term.
In another preferred embodiment, the present invention provides a method for detecting a nucleic acid with at least 48% homology to the B3 domain nucleotide SEQ ID NO:1 or 3 or 5, sequences which are complimentary to SEQ ID NO:1 or 3 or 5 and/or which encode a protein having substantial identity with the amino acid sequence in SEQ ID NO:2, 4 or 6 respectively, comprising contacting a nucleic acid sample with a probe or primer comprising at least 15 consecutive nucleotides of the nucleotide sequences of SEQ ID NO:1, 3, or 5 or at least 15 consecutive nucleotides of the complement thereof.
Thus, in one embodiment of the present invention, the stress tolerance of a plant can be enhanced or increased by increasing the amount of protein available in the plant, preferably by the enhancement of the B3 and/or bZIP domain gene expression in the plant. Thus, one embodiment of the present invention are plant cells carrying the polynucleotides of the present invention, and preferably transgenic plants carrying the isolated polynucleotides of the present invention.

Plant Transcription Factors

Transcription factors are capable of sequence-specific interaction with a gene sequence or gene regulatory sequence. The interaction may be direct sequence-specific binding in that the transcription factor directly contacts the gene or gene regulatory sequence, or indirect sequence-specific binding mediated by interaction of the transcription factor with other proteins. In these cases, the binding and/or effect of the B3-domain transcription factor is influenced in a synergistic manner by another B3-domain transcription factor or a bZIP-domain transcription factor.
The gene or gene regulatory region and transcription factor may be derived from the same type of plant (e.g., the same species or genus) or a different type of plant. The transcription factors used herein produce synergistic results related to the ability of the plant to respond to stress. The B3-domain transcriptions factors and the bZIP transcriptions factors are described in detail above.

Constructs for Expression of a Transcription Factor in a Plant Cell

A heterologous nucleic acid construct or expression vector designed for operation in plants comprising the coding sequence for a plant transcription factor may be used to transiently or stably transform a plant, e.g. a monocot plant. An exemplary heterologous nucleic acid construct or expression vector designed for operation in plants, includes (i) a promoter (transcriptional regulatory region) induced in particular tissue (“tissue-specific”), (ii) the coding sequence for a plant transcription factor operably linked to the promoter, (iii) companion sequences upstream and downstream which are of plasmid or viral origin and provide necessary characteristics to the vector to permit the vector to move the DNA from bacteria to the desired plant host; (iv) a selectable marker sequence; and (v) a transcriptional termination region generally at the opposite end of the vector from the transcription initiation regulatory region. Suitable transformation vectors for the preparation of such constructs are known in the art and many are commercially available.
Vector components may also include a signal sequence. The desired recombinant protein or polypeptide may be produced directly, or as a fusion polypeptide with a heterologous polypeptide, which may be a signal sequence or other polypeptide having a specific cleavage site at the N-terminus of the mature protein or polypeptide. Included in heterologous nucleic acid constructs for use in the methods of the invention are signal sequences that allow processing and translocation of the protein, as appropriate.
In some cases, the recombinant protein may be produced as a precursor protein, which may be further processed in the plant cell culture or following extraction from the plant.

Tissue-Specific Promoters

The transcription regulatory or promoter region of the chimeric gene or heterologous nucleic acid construct is preferably a tissue-specific promoter, for example, a promoter capable of directing expression of a gene product under its control, which is specific to the seed embryo, aleurone, outer layer of the endosperm, mesophyll cells, vascular cells, guard cells, and the like.
Promoter sequences for regulating transcription of operably linked coding sequences include naturally-occurring promoters, or regions thereof capable of directing tissue-specific transcription, and hybrid promoters, which combine elements of more than one promoter. Methods for construction of hybrid promoters are well known in the art. In some cases, the promoter is derived from the same plant species as the plant in which the nucleic acid construct is to be introduced. Promoters for use in the invention are typically derived from crops such as rice, barley, wheat, corn, sunflower, carrot, bean, rape, and model species such as Arabidopsis.
Alternatively, a tissue-specific promoter from one type of monocot may be used to regulate transcription of a gene coding sequence from a different monocot or dicot. Numerous types of appropriate expression vectors, and suitable regulatory sequences are known in the art for a variety of plant host cells. In general, the transcriptional and translational regulatory sequences may include, but are not limited to, promoter sequences, ribosomal binding sites, transcriptional start and stop sequences, translational start and stop sequences, and enhancer or activator sequences.
Effective inducible or tissue-specific transcriptional initiation regions, e.g., promoters, may be isolated from various tissues and/or at various stages of development by a variety of techniques routinely used by those of skill in the art, including, but not limited to: (1) conventional hybridization techniques using known coding sequences from a different species, tissue and/or developmental stage, followed by characterizing the region 5′ of the homologous gene to identify the associated transcriptional initiation sequence; (2) subtractive hybridization, (3) differential display, and (4) selective amplification via biotin- and restriction-mediated enrichment, SABRE.

Expression Vector Components

Expression vectors or heterologous nucleic acid constructs, designed for operation in plants, comprise companion sequences upstream and downstream from the expression cassette. The companion sequences are of plasmid or viral origin and provide necessary characteristics to the vector to permit the vector to move DNA from bacteria to the plant host, such as, sequences containing an origin of replication and a selectable marker. Typical secondary hosts include bacteria and yeast.
The transcriptional termination region may be taken from a gene where it is normally associated with the transcriptional initiation region or may be taken from a different gene.
The particular marker gene employed is one that allows for selection of transformed cells as compared to cells lacking the DNA that has been introduced. Preferably, the selectable marker gene is one that facilitates selection at the tissue culture or seedling stages.
In general, a selected nucleic acid sequence is inserted into an appropriate restriction endonuclease site or sites in the vector. Standard methods for cutting, ligating and E. coli transformation, known to those of skill in the art, are used in constructing vectors for use in the present invention. Generally, vectors for use in practicing the present invention are constructed using methods known to those skilled in the art.

Plants

The plants used in practicing the invention are of both monocot and dicot origin. The Graminaceae family includes all members of the grass family of which the edible varieties are known as cereals or grains. The cereals include a wide variety of species such as wheat (Triticum sps.), rice (Oryza sps.), barley (Hordeum sps.), oats (Avena sps.), rye (Secale sps.), corn (Zea sps.), and millet (Pennisettum sps.). In one embodiment of the invention, preferred family members are rice, wheat, corn, barley, oat, rape, cotton, peanut, and soybean.
Plant cells or tissues derived from the members of the family may be transformed with expression vectors (i.e., plasmid DNA into which the gene of interest has been inserted) using a variety of standard techniques (e.g., microparticle bombardment, electroporation, protoplast fusion or infection with Agrobacterium).
Transgenic plant cells obtained as a result of such transformation express the coding sequence for one or more plant transcription factor, e.g. a B3-domain transcription factor and bZIP or B3-domain transcription factors. The transgenic plant cells are cultured in medium containing the appropriate selection agent to identify and select for plant cells which express the heterologous nucleic acid sequence. After plant cells that express the heterologous nucleic acid sequence are selected, whole plants are regenerated from the selected transgenic plant cells. Techniques for regenerating whole plants from transformed plant cells are generally known in the art.
In one embodiment of the invention, transgenic plant lines, e.g., rice, wheat, corn, barley, oat, rape, cotton, peanut, and soybean are developed and genetic crosses carried out using conventional plant breeding techniques. In one example of this approach, a first stable transgenic plant line is generated where the plants express two of the transcription factors under the control of a tissue-specific promoter. A number of such lines may be generated with varying levels of transcription factor expression. The plants are crossed with a second transgenic plant line that expresses a heterologous protein coding sequence (e.g., a recombinant protein) under the control of a tissue-specific promoter that is responsive to the transcription factors expressed in the first plant line. The resulting cross (F2) has a higher expression level of the heterologous protein in one or more particular tissues, dependent upon the promoter used.

Transformation of Plant Cells

Vectors useful in the practice of the present invention may be microinjected directly into plant cells by use of micropipettes to mechanically transfer the nucleic acid construct or cassette. Such nucleic acid constructs or cassettes may also be transferred into the plant cell using polyethylene glycol. In addition, high velocity ballistic penetration by small particles with the nucleic acid either within the matrix of small beads or particles, or on the surface may also be used for introduction of nucleic acid sequences into plant cells.
Additional methods for introduction of nucleic acid sequences into plant cells include fusion of protoplasts with other entities, either minicells, cells, lysosomes or other fusible forms for introduction of nucleic acid sequences into plant cells with lipid surfaces; and electroporation. In this technique, electrical impulses of high field strength reversibly permeabilize biomembranes allowing the introduction of plasmids into plant cells or protoplasts. Electroporated plant protoplasts will reform the cell wall, divide, and form plant callus.
Another preferred method of introducing a nucleic acid construct into plant cells is to infect a plant cell, explant, meristem or seed with Agrobacterium, in particular Agrobacterium tumefaciens. A nucleic acid construct comprising such a sequence of interest can be introduced into appropriate plant cells.
Standard Agrobacterium binary vectors are known to those of skill in the art and many are commercially available. Expression vectors typically include polyadenylation sites, translation regulatory sequences (e.g., translation start sites), introns and splice sites, enhancer sequences (which can be inducible, tissue-specific or constitutive), and may further include 5′ and 3′ regulatory and flanking sequences.
Suitable selectable markers for selection in plant cells are described above and the particular marker gene employed is one which allows for selection of transformed cells as compared to cells lacking the DNA which has been introduced. Preferably, the selectable marker gene is one which facilitates selection at the tissue culture or seedling stages.
Transformed explant cells are screened for the ability to be cultured in selective media having a threshold concentration of selective agent. Explants that can grow on the selective media are typically transferred to a fresh supply of the same media and cultured again. The explants are then cultured under regeneration conditions to produce regenerated plant shoots. After shoots form, the shoots are transferred to a selective rooting medium to provide a complete plantlet. The plantlet may then be grown to provide seed, cuttings, or the like for propagating the transformed plants. The method provides for efficient transformation of plant cells with expression of modified native or non-native plant genes and regeneration of transgenic plants, which can produce a recombinant protein or polypeptide of interest.
The expression of a recombinant protein or polypeptide can be confirmed using any of a number of standard analytical techniques such as Western blot, ELISA, PCR, HPLC, NMR, or mass spectroscopy.

PREFERRED EMBODIMENT

Strong and novel activities in rice embryonic and maize mesophyll protoplasts of the transcription factors VP1 (see SEQ. ID. NO: 1 and SEQ. ID. NO.:2), RAV2 (see SEQ. ID. NO.:3 and SEQ. ID. NO.:4), ABI5 (see SEQ. ID. NO.:5 and SEQ.ID.NO.: 6), ABF1, ABF3, ABF4, AREB3 and DPBF4 genes from maize (VP1) and Arabidopsis (all others) are demonstrated herein. As shown in the Examples below, the ABA INSENSITIVE-5 (ABI5) basic leucine zipper (bZIP) domain transcription factor and closely related ABI-5-like homologues have been tested for transactivation of the ABA-inducible wheat Em promoter in transiently transformed rice and maize protoplasts. The functional interactions of co-expressed ABI5 and the ABI5-like ABA-Response Element-Binding Factors, such as ABF1, ABF2, ABF3, ABF4, AREB3, and DPBF4/EEL, which have highly conserved domains (C1-C3, bZIP), were tested with each other and with co-expressed maize VIVIPAROUS-1 (VP1) B3-domain transcription factor. Overexpressed Arabidopsis ABI5, ABF3, ABF4, AREB3, DPBF4, and maize VP1, but not ABF1 and ABF2, individually show synergy with ABA in rice embryonic and/or maize mesophyll protoplasts. However, when ABI5 and ABF3 are co-expressed in rice protoplasts, they show no synergistic interactions with each other, in contrast to strong synergy observed with ABI5, or ABF3 co-expressed with VP1 in rice or maize. Furthermore, AREB3, DPBF4/EEL, and ABF4 do not work in synergy with co-transformed maize VP1, whereas ABI5, ABF3 and ABF1 can synergize with VP1 in maize mesophyll protoplasts. This latter result is in contrast to the observation that ABF1 does not appear to interact with ABA alone. Taken together, these functional data provide several examples to support the claim that formulations of bZIP domain transcription factors with B3-domain transcription factors will provide novel and useful means to effect stress- and ABA-inducible gene expression that in turn will enhance valuable traits such as productivity, yields, and stress tolerance of commercial varieties of plants. The data provides strong evidence that expression of these and homologous transgenes from, and into, various plant species in target tissues such as leaves or seeds will render transgenic horticultural and ornamental plants and crops to be better able to withstand environmental stress via coordinated regulation of multiple endogenous gene sets in stress tolerance pathways.
In the Examples and previously published results, it has been demonstrated that over-expression of maize VP1, Arabidopsis ABI5, or several ABI5-related family members transactivate various ABA-inducible promoters from both monocots and dicots in rice or maize protoplasts, proving that these transcription factors are key targets of a conserved ABA signaling pathway in plants. Others have shown that ectopic expression of ABI3, ABI4, or ABI5 transcription factors results in ABA hypersensitivity of vegetative tissues which is partly dependent on increased ABI5 expression. Taken together, these results show that these transcription factors participate in combinatorial control of gene expression, possibly by forming a regulatory complex mediating seed-specific and/or ABA-inducible expression.
Table 1 documents the polypeptide and nucleotide similarities of the bZIP domains of select Arabidopsis genes compared to ABI5. Significant functional effects have been shown on transactivation of the Em promoter for most of these family members. The percentage identity and similarity results for polypeptides are relative, since the BLASTP alignment algorithm does not necessarily take into account all residues of the bZIP. The E values are directly comparable measures of significant homologies between and among pairs of genes. (Altschul et al., Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res. 25:3389-3402 (1997)). For example, the difference in E values between ABF3.2 and ABF3.1 is 1000-fold relatively higher homology of ABF3.2 to ABI5 than ABF3.1.

TABLE 1

Pairwise comparison of polypeptide and nucleotide homologies between ABI5-Like
Family members and ABI5 bZIP domains.

		Percent	Percent		% n.t. Identity with	SEQ. ID. NO.
		Identity of ABI5bZIP	Similarity		ABI5 bZIP (n.t. 1057-1251,	1) nucleotides
AGI	Annotation	(aa 353-417, SEQ. NO. 6)	ABI5 bZIP	E	SEQ NO. 5)	2) protein

At2g36270

ABI5

	100	—	4.E−30	100	1) SEQ. ID. NO. 5
						2) SEQ.ID.NO.: 6
At1g49720	ABF1	62	72	1.E−14	52	1) SEQ.ID.NO.: 7
						2) SEQ.ID.NO.: 8
At5g42910	ABF2-Like	50	69	6.E−10	53	1) SEQ.ID.NO.: 9
						2) SEQ.ID.NO.: 10
At1g45249	ABF2	71	81	3.E−17	62	1) SEQ.ID.NO.: 11
						2) SEQ.ID.NO.: 12
At4g34000	ABF3.2	66	80	8.E−18	56	1) SEQ ID. NO.: 13
						2) SEQ.ID.NO.: 14
At4g34000	ABF3.1	80	93	8.E−15	52	1) SEQ.ID.NO.: 15
						2) SEQ ID. NO.: 16
At3g19290	ABF4	63	80	1.E−16	58	1) SEQ.ID.NO.: 17
						2) SEQ.ID.NO.: 18
At3g56850	AREB3	61	73	3.E−13	39	1) SEQ.ID.NO.: 19
						2) SEQ.ID.NO.: 20
At3g44460	DPBF2	67	80	6.E−18	52	1) SEQ.ID.NO.: 21
						2) SEQ.ID.NO.: 22
At2g41070	DPBF4/EEL	69	87	1.E−13	48	1) SEQ.ID.NO.: 23
						2) SEQ.ID.NO.: 24
At1g03970	GBF4	60	72	4.E−12	48	1) SEQ.ID.NO.: 25
						2) SEQ.ID.NO.: 26
At5g44080	GBF4-Like	63	73	1.E−12	54	1) SEQ.ID.NO.: 27
						2) SEQ.ID.NO.: 28

Table 2 documents that the VP1 B3-domain protein sequence can be used to claim Arabidopsis ABI3, LEC2, FUS3, and At4g21550(=AB3L3), whereas the RAV2 protein and/or its B3 domain can be used to claim “more preferred embodiments” (>50% identity or similarity) with At1g13260=RAV1, At3g25730=RAV1-Like, At1g25560=RAV2-Like, 2g30470=B3L1, At4g32010=AB3L2, At4g01500=AB3L4, At1g51120=AB3L5, At2g46870=AB3L6, At1g01030=AB3L7, At2g36080=AB3L8, At 1 g50680=AB3L9, At3g61970=AB3L10, At5g06250=AB3L11, At3g11580=AB3L12, and At2g28350=AB3L16.
The AGI indications in both Table 1 and Table 2 can be used to obtain additional information about the specific proteins and polynucleotides on the website www.arabidopsis.org.

TABLE 2

Pairwise homologies between Arabidopsis ABI3-Like family members
and the VIVIPAROUS1 B3 domain or RAV2 protein.*

		Percent Identity with VP1b3			Percent Identity with RAV2
AGI number	Annotation	(aa496-619 SEQ ID NO. 2)	Percent Similar VP1b3	E	SEQ. ID NO. 4)	Percent Similar with RAV2

At3g24650	ABI3	84	90	2.E−56
At3g26790	FUS3	57	74	7.E−32
At1g28300	LEC2	52	70	1.E−29
At1g13260	RAV1	36	54	2.E−09	67	78
At3g25730	RAV1-	35	51	2.E−09	62	75
	Like
At1g68840	RAV2	33	46	6.E−11	100	—
At1g25560	RAV2-	35	50	9.E−10	75	83
	Like
At2g30470	AB3L1	42	60	2.E−17	43	65
at4g32010	AB3L2	40	60	6.E−17	40	65
At4g21550	AB3L3	38	62	6.E−14
At4g01500	AB3L4	31	51	2.E−09	60	73
At1g51120	AB3L5	34	51	2.E−08	39	58
At2g46870	AB3L6	32	52	2.E−09	65	80
At1g01030	AB3L7	32	55	9.E−08	54	70
At2g36080	AB3L8	31	48	4.E−07	66	79
At1g50680	AB3L9	32	47	3.E−07	39	56
At3g61970	AB3L10	31	49	1.E−07	67	83
At5g06250	AB3L11	29	45	3.E−07	63	77
At3g11580	AB3L12	28	43	3.E−07	57	71
At2g28350	AB3L16	29§	38§	0.42	35	53

					% n.t. identity with RAV2 B3	SEQ.ID. NO:
		Percent Identity with RAC2b3			domain (nt. 559-885 SEQ ID	1) nucleotides
AGI number	E	87-295, SEQ ID NO. 4)	Percent Similar with RAV2b3	E	NO. 3)	2) protein

At3g24650		34	49	3.E−10	48	1) SEQ.ID.NO.: 29
						2) SEQ.ID.NO.: 30
At3g26790		39	58	1.E−10	47	1) SEQ.ID.NO.: 31
						2) SEQ.ID.NO.: 32
At1g28300		34	50	1.E−09	49	1) SEQ.ID.NO.: 33
						2) SEQ.ID.NO.: 34
At1g13260	1.E−111	86	92	3.E−50	65	1) SEQ.ID.NO.: 35
						2) SEQ.ID.NO.: 36
At3g25730	1.E−101	73	85	6.E−43	62	1) SEQ.ID.NO.: 37
						2) SEQ.ID.NO.: 38
At1g68840	0.E+00	100	—	4.E−61	100	1) SEQ.ID.NO.: 3
						2) SEQ.ID.NO.: 4
At1g25560	1.E−135	83	86	2.E−50	66	1) SEQ.ID.NO.: 39
						2) SEQ.ID.NO.: 40
At2g30470	1.E−13	43	65	1.E−14	61	1) SEQ.ID.NO.: 41
						2) SEQ.ID.NO.: 42
at4g32010	5.E−13	40	65	5.E−14	50	1) SEQ.ID.NO.: 43
						2) SEQ.ID.NO.: 44
At4g21550		40	59	4.E−11	56	1) SEQ.ID.NO.: 45
						2) SEQ.ID.NO.: 46
At4g01500	2.E−33	59	73	1.E−33	74	1) SEQ.ID.NO.: 47
						2) SEQ.ID.NO.: 48
At1g51120	3.E−39	51	67	6.E−22	68	1) SEQ.ID.NO.: 49
						2) SEQ.ID.NO.: 50
At2g46870	4.E−39	68	83	6.E−39	78	1) SEQ.ID.NO.: 51
						2) SEQ.ID.NO.: 52
At1g01030	3.E−40	69	82	3.E−39	59	1) SEQ.ID.NO.: 53
						2) SEQ.ID.NO.: 54
At2g36080	6.E−38	68	79	5.E−37	58	1) SEQ.ID.NO.: 55
						2) SEQ.ID.NO.: 56
At1g50680	7.E−41	50	65	8.E−22	68	1) SEQ.ID.NO.: 57
						2) SEQ.ID.NO.: 58
At3g61970	3.E−38	67	83	2.E−38	76	2) SEQ.ID.NO.: 59
						1) SEQ.ID.NO.: 60
At5g06250	8.E−37	64	77	3.E−37	74	1) SEQ.ID.NO.: 61
						2) SEQ.ID.NO.: 62
At3g11580	2.E−38	62	77	8.E−36	48	1) SEQ.ID.NO.: 63
						2) SEQ.ID.NO.: 64
At2g28350	7.E−10	36	54	1.E−10	51	1) SEQ.ID.NO.: 65
						2) SEQ.ID.NO.: 66

*Altschul SF, Madden TL, Schaffer AA, Zhang J, Zhang Z, Miller W, Lipmann DJ (1997) Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res 25: 3389-3402. See http://www.arabidopsis.org/
{circumflex over ( )} Higgins D, Thompson J, Gibson T, Thompson JD, Higgins DG, Gibson TJ (1994) CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res. 22: 4673-4680. See European Bioinformatics Institute http://www.ebi.ac.uk/clustalw
§Compared to ABI3 B3 domain (aa551-674, SEQ ID NO. 30).

Example 1

Materials and Methods

Plant Materials. Maize mesophyll protoplasts were isolated from 20-hr illuminated leaves of 10 day old maize seedlings that had been kept in the dark at 25° C. The middle part of the second leaves (about 6 cm in length) was cut into 0.5 mm strips with a razor blade and digested in an enzyme solution containing 1% (w/v) cellulose RS, 0.1% (w/v) macerozyme R10 (Yakult Honsha, Nishinomiya, Japan), 0.6 M mannitol, 10 mM MES (pH 5.7), 1 mM CaCl₂, 1 mM MgCl₂, 10 mM β-mercaptoethanol, and 0.1% BSA (w/v) for 3 hr at room temperature. Protoplasts were released by shaking on a rotary shaker at 80 rpm for 10 min and were filtered through a 70 μm nylon filter. Protoplasts were collected by centrifugation at 100 g for 2 min, washed in cold 0.6 M mannitol solution, centrifuged, and resuspended at 2×10⁶/mL in cold 0.6 M mannitol. Electroporation conditions were 400 V/cm, 200 μF, 10 msec, and two pulses with a Biorad GenePulser apparatus. Each sample contained 5×10⁴protoplasts and about 50 μg DNA in 0.3 mL of 0.6 M mannitol and 20 mM KCl.
Embryonic rice (Oryza sativa) callus cultures (Radon 6 from the International Rice Research Institute, Los Bafios, Phillipines) were obtained. Embryonic rice callus cultures were grown as suspensions in liquid culture as well as on phytagel plates containing MS medium supplemented with 2.0 mg/L 2,4-D. Cultures were propagated and digested for making protoplasts as previously described except that 10 mM HEPES (Sigma, St. Louis, Mo., USA), pH 5.6, was substituted for phosphate in the Krens'F medium, and 2% (weight/volume; w/v) cellulase YC, 0.35% (w/v) macerozyme, and 0.1% (w/v) pectolyase Y23 were used for overnight digestion (Karlan Research Products, Santa Rosa, CA, USA). Protoplasts were transformed with various mixtures of DNA reporter and effector constructs using polyethylene glycol precipitation. Transformed protoplasts were incubated with or without 100 μM ABA for 16 h in the dark in Krens solution before quantifying β-glucuronidase (GUS) and luciferase (LUC) reporter enzyme activities as previously described. ABA was dissolved and stored in absolute ethanol at −20° C. as a 0.1 M stock solution. Prior to use, required dilutions of ABA were made in Krens solution, and control samples received the same volume of solvent as in ABA treatments.

Plasmid Constructs

Plasmid pBM207 contains the wheat (Triticum aestivum) Early Methionine-labeled (Em) promoter driving the expression of GUS, encoded by uida from Escherichia coli. Plasmid pDH359 contains ABI5 cDNA driven by Ubiquitin promoter. Plasmid pCR349.13S contains the 35S promoter driving the VP1 sense cDNA. Plasmid pDirect2.6 contains the Ubi promoter in a reverse orientation and was used as control construct to balance the total amount of input plasmid DNA between various treatments. Plasmid pAHC 18 contains the Ubi promoter driving firefly (Photinus pyralis) LUC cDNA and was included in transformations to provide an internal reference for non-ABA-inducible transient transcription in reporter enzyme assays. ABF1-ABF4, AREB3, and DPBF4 were amplified by PCR using gene-specific primers from an Arabidopsis cDNA library (Minet et al. Plant J. 2:417 (1992)) and were cloned into plasmid pDH349 (Gampala et al. J. Biol. Chem. 277: 1689 (2002)) containing the maize Ubiquitin promoter and nopaline synthase 3′ termination signals. Primers used for PCR amplification are listed in Table 3.

TABLE 3

Gene-specific PCR primers used to clone
Arabidopsis ABI5-like cDNAs used herein.

	Primer sequence (5′->3′;
Gene	F = forward, R = reverse)

ABF1
SEQ ID NO 67	F:
	cccaagcttggatccaaagggtctgattcgtttgt
SEQ ID NO 68	R:
	cggggtaccgttaacgtcacatcttctctatagct

ABF2
SEQ ID NO 69	F:
	cccaagcttggatcccccaaacgaagaaccaaaca
SEQ ID NO 70	R:
	cggggtaccgatatcttcttcaaaattggtaactc

ABF3
SEQ ID NO 71	F:
	ccgctcgagggatccgaagcttgatcctcctagtt
SEQ ID NO 72	R:
	cggggtaccgatatcagatacaagataaattcact

ABF4
SEQ ID NO 73	F:
	cccaagcttggatccgaacaagggttttagggctt
SEQ ID NO 74	R:
	cggggtaccgatatcgttgccactcttaagtaata

AREB3
SEQ ID NO 75	F:
	cccactagtggatccatggattctcagaggggtat
SEQ ID NO 76	R:
	cggggtaccgatatctcagaaaggagccgagcttg

DPBF4
SEQ ID NO 77	F:
	cccggtaccggatccacagtttctaaggcaaaata
SEQ ID NO 78	R:
	cggaggcctgaattcacttgaactagtgtttgtac

Results

Previous results demonstrated that overexpressed ABF1 and ABF3 had positive effects on ABA-inducible Em-GUS reporter gene expression in transiently transformed rice protoplasts, providing functional evidence for the involvement of these proteins in ABA- and stress signal transduction. Simultaneously, it has been shown that ABF2, ABF3 and ABF4 overexpression in transgenic Arabidopsis results in ABA hypersensitivity and other ABA-associated phenotypes such as altered ABA-inducible gene expression and glucose signaling, reduced transpiration, and enhanced drought tolerance. The functional roles of the ABI5-like family members ABF1-ABF4 in regulation of ABA-inducible gene expression in rice protoplasts were tested and the results are shown in FIG. 1. FIG. 1A shows that the overexpression of ABF3 and ABF4 is sufficient to transactivate ABA-inducible Em-GUS expression in rice protoplasts. Protoplasts were transformed with Em-GUS and a “dummy” effector construct (pD2.6 containing only the Ubiquitin promoter used to drive effector expression) or co-transformed with a Ubi-ABF construct and treated with or without 100 μM ABA. The values shown in FIG. 1A are the average (±S.E.M.) of four replicate transformations. Consistent with previous results, overexpressed ABF1 and ABF3 had slight and strong synergy with exogenous ABA, respectively. However, overexpression of ABF2 had no effect on Em-GUS expression (see FIG. 1A). Interestingly, overexpression of ABF3 or ABF4 was sufficient for transactivation of the Em promoter. These results are consistent with those of previous researchers who showed that overexpressed ABF3 or ABF4 resulted in accumulation of the LEA genes rd29A and rab18.
FIG. 1B displays the results of an ABA-inducible reporter gene expression experiment with transiently-transformed rice protoplasts overexpressing ABI5, ABF3, and VP1 transcription factors alone and in pairwise co-transformations. FIG. 1B shows that the overexpressed ABF3 interacts synergistically with ABA and VP1, but not with ABI5. Rice protoplasts were transformed with either Em-GUS alone or in pairwise combinations of Ubi-ABF3, Ubi-ABI5, or 35S-VP1. The values in FIG. 1B are the average (±S.E.M.) of four replicate transformations. ABF3 is a related member of the ABI5-family of bZIP transcription factors. As previously reported, ABI5, ABF3, and VP1 transactivated the Em promoter and acted in synergy with ABA. More importantly, ABF3 and VP1 synergized with each other and with ABA when co-expressed. This activity was about twice the synergistic activity seen between ABI5 and VP1. However, paired expression of ABF3 and ABI5 bZIPs in protoplasts did not result in synergy, see FIG. 1B. Based on these two examples of ABI5-family member synergy with maize VP1, it is proposed that most members of the ABI5 bZIP family can have functional interactions with VP1 and ABI3, including homologues from various species.
To provide evidence to support the claim that transcriptional regulation of ABA signaling is highly conserved among higher plants and in different tissue types, various ABI5-like homologues from Arabidopsis were tested for their ABA signaling activities and functional interactions with VP1 in maize mesophyll protoplasts. The results are shown in FIG. 2. FIG. 2A shows that AREB3 or DPBF4/EEL overexpression in maize mesophyll protoplasts is sufficient to transactivate Em-GUS expression. Furthermore, ABF1 and ABF3, but not ABF2, AREB3, ABF4, or DPBF4/EEL, can synergize with co-transformed VP1 (FIG. 2B). The values in FIG. 2 are the average (±S.E.M.) of four replicate transformations. As previously shown for rice embryonic protoplasts (see FIG. 1), ABI5, ABF3 and ABF4 synergize with exogenous ABA and are sufficient for transactivation of the Em promoter when overexpressed in maize mesophyll protoplasts (FIG. 2A). ABF1 and ABF2 have lower levels of ABA synergy compared to ABF3 and ABF4 in maize (FIG. 2A), similar to activities observed in rice (see FIG. 1). Furthermore, the ABI5-like family members AREB3 and DPBF4/EEL synergize with exogenous ABA and are sufficient when overexpressed to transactivate the Em promoter (see FIG. 2A). This finding demonstrates that ABI5-like family members can function in ABA signaling and suggests they may have novel/unique functions and activities including interactions with VP1 and VP1-like homologues. Indeed, ABF1 showed a strong synergy with VP1 in maize protoplasts despite showing little synergy with ABA (compare FIG. 2B with FIG. 2A), unlike ABI5 and ABF3, which showed similar interactions with ABA and VP1 as seen in rice, (compare FIG. 1 and FIG. 2). Interestingly, ABF4 and AREB3 showed no functional interactions with VP1 in maize mesophyll protoplasts, while DPBF4/EEL showed some antagonism of ABA inducible Em-GUS expression when co-expressed with VP1 (see FIG. 2B). This latter result is consistent with the published genetic and biochemical evidence in Arabidopsis that DPBF4/EEL competes directly with ABI5 for functional interactions with ABI3 in transactivating ABA inducible promoters. Therefore, both similarities and differences are seen in the functional interactions of Arabidopsis ABI5-like genes with VP1. It is proposed that other VP1-like family members of Arabidopsis, of which there are over 20, may be the cognate partners of ABI5-like family members such as ABF2 and ABF4 that may regulate distinct, or tissue-specific aspects of ABA and stress signaling.

Example 2

To test the involvement of ABI3-Like B3 domain transcription factors in ABA signaling, ABA-inducible reporter gene transactivation by the B3 domain-containing RAV2 was assayed in maize mesophyll protoplasts transiently co-transformed with a full length cDNA under transcriptional control of the Ubiquitin promoter. Activation of Em-GUS reporter gene expression by RAV2, relative to non-ABA inducible Ubi-LUC reference reporter as internal control, and functional interactions of RAV2 with VP1, ABI5, and the ABI5-Like ABF3 were compared in protoplasts treated with or without 100 uM ABA (see FIG. 3). The results in FIG. 3A show that: 1) the novel B3 domain transcription factor RAV2, ABI5, and ABF3 are sufficient for specific Em-GUS transactivation; and 2) RAV2 synergizes with ABI5 and ABF3, similar to the results in FIGS. 1 and 2 provided above. Furthermore, results shown in FIG. 3B demonstrate that maize VP1 and Arabidopsis RAV2, a ABI3-Like B3 domain transcription factor, act synergistically to activate Em-GUS expression, demonstrating that these novel interactions involve mechanisms conserved between monocots and dicots. Furthermore, this synergism is enhanced by ABA, as shown in FIG. 3B. RAV2 transactivation is antagonized by co-transformation of the ABA-INSENSITIVE-1 dominant negative allele (data not shown), which support the notion that the RAV2 mechanism reported here is specific to ABA signaling.
Although the present invention has been disclosed in terms of a preferred embodiment, it will be understood that numerous additional modifications and variations could be made thereto without departing from the scope of the invention as defined by the following claims:

Claims

1. A method of producing a transgenic plant comprising

a) transforming a plant cell with an expression vector comprising

i) a B3-domain transcription factor having a polynucleotide sequence with a B3 domain which is at least 25% identical to the B3 domain of SEQ. ID NO:1 or SEQ. ID. NO.: 3 and

ii) a bZIP transcription factor having a polynucleotide sequence with a bZIP domain which is at least 25% identical to the bZIP domain of SEQ. ID NO: 5, and

b) generating from the plant cell a transgenic plant with an increased tolerance to environmental stress as compared to a wild type variety of the plant.

2. The method of claim 1, wherein said B3-domain transcription factor is VP1 as defined by SEQ.ID.NO.: 1.

3. The method of claim 2, wherein said bZIP domain transcription factor is ABI5 as defined by SEQ.ID.NO.: 5 or ABF1 as defined by SEQ.ID.NO.: 7.

4. The method of claim 1, wherein said bZIP domain transcription factor is ABI5 as defined by SEQ.ID.NO.: 5 or ABF1 as defined by SEQ.ID.NO.: 7.

5. The method of claim 1, wherein said bZIP domain transcription factor is selected from a group of polynucleotides consisting of SEQ.ID.NO. 9, SEQ.ID.NO. 11, SEQ.ID.NO. 15, SEQ.ID.NO. 17, SEQ.ID.NO.19, SEQ.ID.NO. 21, SEQ.ID.NO. 23, SEQ.ID.NO.25, and SEQ.ID.NO. 27.

6. The method of claim 1, wherein said B3 domain transcription factors are selected from a group of polynucleotides consisting of SEQ.ID.NO. 29, SEQ.ID.NO.31, SEQ.ID.NO. 33, SEQ.ID.NO. 35, SEQ.ID.NO. 37, SEQ.ID.NO. 39, SEQ.ID.NO. 41, SEQ.ID.NO. 43, SEQ.ID.NO.45, SEQ.ID.NO. 47, SEQ.ID.NO. 49, SEQ.ID.NO.51, SEQ.ID.NO. 53, SEQ.ID.NO. 55, SEQ.ID.NO. 57, SEQ.ID.NO. 59, SEQ.ID.NO. 61 SEQ.ID.NO. 63, and SEQ.ID.NO.65.

7. The method of claim 1, wherein said transgenic plant is a monocot plant or a dicot plant.

8. The method of claim 1, wherein said expression vector is a tissue-specific expression vector.

9. A method of producing a transgenic plant comprising

a) transforming a plant cell with an expression vector comprising

i) a B3-domain transcription factor having a polypeptide sequence with a B3 domain which is at least 40% identical to the B3 domain of SEQ. ID NO:2 or SEQ. ID. NO.: 4 and

ii) a bZIP transcription factor having a polypeptide sequence with a bZIP domain which is at least 40% identical to the bZIP domain of SEQ. ID NO: 6, and

10. The method of claim 9, wherein said B3-domain transcription factor is VP1 as defined by SEQ.ID.NO.: 2.

11. The method of claim 10, wherein said bZIP domain transcription factor is ABI5 as defined by SEQ.ID.NO.: 6 or ABF1 as defined by SEQ.ID.NO.: 8.

12. The method of claim 9, wherein said bZIP domain transcription factor is ABI5 as defined by SEQ.ID.NO.: 6 or ABF1 as defined by SEQ.ID.NO.: 8.

13. The method of claim 9, wherein said bZIP domain transcription factor is selected from a group of polypeptides consisting of SEQ.ID.NO. 10, SEQ.ID.NO. 12, SEQ.ID.NO. 16, SEQ.ID.NO. 18, SEQ.ID.NO.20, SEQ.ID.NO. 22, SEQ.ID.NO. 24, SEQ.ID.NO.26, and SEQ.ID.NO. 28.

14. The method of claim 9, wherein said B3 domain transcription factors are selected from a group of polypeptides consisting of SEQ.ID.NO. 30, SEQ.ID.NO.32, SEQ.ID.NO. 34, SEQ.ID.NO. 36, SEQ.ID.NO. 38, SEQ.ID.NO. 40, SEQ.ID.NO. 42, SEQ.ID.NO. 44, SEQ.ID.NO.46, SEQ.ID.NO. 48, SEQ.ID.NO. 50, SEQ.ID.NO.52, SEQ.ID.NO. 54, SEQ.ID.NO. 56, SEQ.ID.NO. 58, SEQ.ID.NO. 60, SEQ.ID.NO. 62 SEQ.ID.NO. 64, and SEQ.ID.NO.66.

15. The method of claim 9, wherein said transgenic plant is a monocot plant or a dicot plant.

16. The method of claim 9, wherein said expression vector is a tissue-specific expression vector.

17. A method of producing a transgenic plant comprising

a) transforming a plant cell with an expression vector comprising

i) a first B3-domain transcription factor having a polynucleotide sequence with a B3 domain which is at least 25% identical to the B3 domain of SEQ. ID NO:1 and

ii) a second B3-domain transcription factor having a polynucleotide sequence with a B3 domain which is at least 25% identical to the B3 domain of SEQ. ID NO: 3, and

18. The method of claim 17, wherein said first B3 domain transcription factor is VP1 as defined by SEQ. ID. NO.: 1.

19. The method of claim 18, wherein said second B3 domain transcription factor is RAV2 as defined by SEQ. ID. NO.: 3.

20. The method of claim 17, wherein said first B3 domain transcription factor is RAV2 as defined by SEQ. ID. NO.: 3.

21. The method of claim 17, wherein said first B3 domain transcription factor or said second B3 domain transcription factor is selected from a group of polynucleotides consisting of SEQ. ID. NO.: 29. SEQ. ID. NO.:31, SEQ. ID. NO.:33, SEQ. ID. NO.:35, SEQ. ID. NO.:37, SEQ. ID. NO.:39, SEQ. ID. NO.:41, SEQ. ID. NO.:43, SEQ. ID. NO.:45, SEQ. ID. NO.:47, SEQ. ID. NO.:49, SEQ. ID. NO.:51, SEQ. ID. NO.:53, SEQ. ID. NO.:55, SEQ. ID. NO.:57, SEQ. ID. NO.:59, SEQ. ID. NO.:61, SEQ. ID. NO.:63 and SEQ. ID. NO.:65.

22. The method of claim 17, wherein said transgenic plant is a monocot plant or a dicot plant.

23. The method of claim 17, wherein said expression vector is a tissue-specific expression vector.

24. A method of producing a transgenic plant comprising

a) transforming a plant cell with an expression vector comprising

i) a first B3-domain transcription factor having a polypeptide sequence with a B3 domain which is at least 40% identical to the B3 domain of SEQ. ID NO:2 and

ii) a second B3-domain transcription factor having a polypeptide sequence with a B3 domain which is at least 40% identical to the B3 domain of SEQ. ID NO: 4, and

25. The method of claim 24, wherein said first B3-domain transcription factor is VP1 as defined by SEQ.ID.NO.: 2.

26. The method of claim 25, wherein said second B3-domain transcription factor is RAV2 as defined by SEQ.ID.NO.: 4.

27. The method of claim 24, wherein said first B3 domain transcription factor is RAV2 as defined by SEQ. IS. NO.: 4.

28. The method of claims 24, wherein said first B3 domain transcription factor or said second B3 domain transcription factor is selected from a group of polypeptides consisting of SEQ.ID.NO.: 30, SEQ.ID.NO.:32, SEQ.ID.NO.:34, SEQ.ID.NO.:36, SEQ. ID.NO.:38, SEQ.ID.NO.:40, SEQ.ID.NO.:42, SEQ.ID.NO.:44, SEQ.ID.NO.:46, SEQ. ID.NO.:48, SEQ.ID.NO.:50, SEQ.ID.NO.:52, SEQ.ID.NO.:54, SEQ.ID.NO.:56, SEQ. ID.NO.:58, SEQ.ID.NO.:60, SEQ.ID.NO.:62, SEQ.ID.NO.:64, and SEQ.ID.NO.:66.

29. The method of claim 24, wherein said transgenic plant is a monocot plant or a dicot plant.

30. The method of claim 24, wherein said expression vector is a tissue-specific expression vector.

31. A transgenic plant, comprising

a) a B3-domain transcription factor having a polynucleotide sequence with a B3 domain which is at least 25% identical to the B3 domain of SEQ. ID. NO: 1 or SEQ. ID. NO. 3 operably linked to a tissue specific promoter, and

b) a bZIP domain transcription factor having a polynucleotide sequence with a bZIP domain which is at least 25% identical to the bZIP domain of SEQ. ID. NO.:5 operably linked to a tissue specific promoter,

wherein expression of the B3-domain transcription factor and the bZIP domain transcription factor in the tissue of said plant is effective to activate transcription of a gene operably linked to a promoter with which said transcription factor interacts.

32. The transgenic plant of claim 31, wherein said B3-domain transcription factor is VP1 as defined by SEQ.ID.NO.: 1.

33. The transgenic plant of claim 32, wherein said bZIP domain transcription factor is ABI5 as defined by SEQ.ID.NO.: 5 or ABF1 as defined by SEQ.ID.NO.: 7.

34. The transgenic plant of claim 31, wherein said bZIP domain transcription factor is ABI5 as defined by SEQ.ID.NO.: 5 or ABF1 as defined by SEQ.ID.NO.: 7.

35. The transgenic plant of claim 31, wherein said bZIP domain transcription factor is selected from a group of polynucleotides consisting of SEQ.ID.NO. 9, SEQ.ID.NO. 11, SEQ.ID.NO. 15, SEQ.ID.NO. 17, SEQ.ID.NO.19, SEQ.ID.NO. 21, SEQ.ID.NO. 23, SEQ.ID.NO.25, and SEQ.ID.NO. 27.

36. The transgenic plant of claim 31, wherein said B3 domain transcription factors are selected from a group of polynucleotides consisting of SEQ.ID.NO. 29, SEQ.ID.NO.31, SEQ.ID.NO. 33, SEQ.ID.NO. 35, SEQ.ID.NO. 37, SEQ.ID.NO. 39, SEQ.ID.NO. 41, SEQ.ID.NO. 43, SEQ.ID.NO.45, SEQ.ID.NO. 47, SEQ.ID.NO. 49, SEQ.ID.NO.51, SEQ.ID.NO. 53, SEQ.ID.NO. 55, SEQ.ID.NO. 57, SEQ.ID.NO. 59, SEQ.ID.NO. 61 SEQ.ID.NO. 63, and SEQ.ID.NO.65.

37. The transgenic plant of claim 31, wherein said transgenic plant is a monocot plant or a dicot plant.

38. A transgenic plant, comprising

a) a B3-domain transcription factor having a polypeptide sequence with a B3 domain which is at least 40% identical to the B3 domain of SEQ. ID. NO:2 or SEQ. ID. NO. 4 operably linked to a tissue specific promoter, and

b) a bZIP domain transcription factor having a polypeptide sequence with a bZIP domain which is at least 40% identical to the bZIP domain of SEQ. ID. NO.:6 operably linked to a tissue specific promoter,

39. The transgenic plant of claim 38, wherein said B3-domain transcription factor is VP1 as defined by SEQ.ID.NO.: 2.

40. The transgenic plant of claim 39, wherein said bZIP domain transcription factor is ABI5 as defined by SEQ.ID.NO.: 6 or ABF1 as defined by SEQ.ID.NO.: 8.

41. The transgenic plant of claim 38, wherein said bZIP domain transcription factor is ABI5 as defined by SEQ.ID.NO.: 6 ABF1 as defined by SEQ.ID.NO.: 8.

42. The transgenic plant of claim 38, wherein said bZIP domain transcription factor is selected from a group of polypeptides consisting of SEQ.ID.NO. 10, SEQ.ID.NO. 12, SEQ.ID.NO. 16, SEQ.ID.NO. 18, SEQ.ID.NO.20, SEQ.ID.NO. 22, SEQ.ID.NO. 24, SEQ.ID.NO.26, and SEQ.ID.NO. 28.

43. The transgenic plant of claim 38, wherein said B3 domain transcription factors are selected from a group of polypeptides consisting of SEQ.ID.NO. 30, SEQ.ID.NO.32, SEQ.ID.NO. 34, SEQ.ID.NO. 36, SEQ.ID.NO. 38, SEQ.ID.NO. 40, SEQ.ID.NO. 42, SEQ.ID.NO. 44, SEQ.ID.NO.46, SEQ.ID.NO. 48, SEQ.ID.NO. 50, SEQ.ID.NO.52, SEQ.ID.NO. 54, SEQ.ID.NO. 56, SEQ.ID.NO. 58, SEQ.ID.NO. 60, SEQ.ID.NO. 62 SEQ.ID.NO. 64, and SEQ.ID.NO.66.

44. The transgenic plant of claim 38, wherein said transgenic plant is a monocot plant or a dicot plant.

45. A transgenic plant, comprising

a) a first B3-domain transcription factor having a polynucleotide sequence with a B3 domain which is at least 25% identical to the B3 domain of SEQ. ID. NO: 1 operably linked to a tissue specific promoter, and

b) a second B3-domain domain transcription factor having a polynucleotide sequence with a B3 domain which is at least 25% identical to the B3 domain of SEQ. ID. NO.:3 operably linked to a tissue specific promoter,

wherein expression of the first B3-domain transcription factor and the second B3 domain transcription factor in the tissue of said plant is effective to activate transcription of a gene operably linked to a promoter with which said transcription factor interacts.

46. The transgenic plant of claim 45, wherein said first B3 domain transcription factor is VP1 as defined by SEQ. ID. NO.: 1.

47. The transgenic plant of claim 46, wherein said second B3 domain transcription factor is RAV2 as defined by SEQ. ID. NO.: 3.

48. The transgenic plant of claim 45, wherein said first B3 domain transcription factor is RAV2 as defined by SEQ. ID. NO.: 3.

49. The transgenic plant of claim 45, wherein said first B3 domain transcription factor or said second B3 domain transcription factor is selected from a group of polynucleotides consisting of SEQ. ID. NO.: 29. SEQ. ID. NO.:31, SEQ. ID. NO.:33, SEQ. ID. NO.:35, SEQ. ID. NO.:37, SEQ. ID. NO.:39, SEQ. ID. NO.:41, SEQ. ID. NO.:43, SEQ. ID. NO.:45, SEQ. ID. NO.:47, SEQ. ID. NO.:49, SEQ. ID. NO.:51, SEQ. ID. NO.:53, SEQ. ID. NO.:55, SEQ. ID. NO.:57, SEQ. ID. NO.:59, SEQ. ID. NO.:61, SEQ. ID. NO.:63 and SEQ. ID. NO.:65.

50. The transgenic plant of claim 45, wherein said transgenic plant is a monocot plant or a dicot plant.

51. A transgenic plant, comprising

a) a first B3-domain transcription factor having a polypeptide sequence with a B3 domain which is at least 40% identical to the B3 domain of SEQ. ID. NO:2 operably linked to a tissue specific promoter, and

b) a second B3-domain domain transcription factor having a polypeptide sequence with a B3 domain which is at least 40% identical to the B3 domain of SEQ. ID. NO.:4 operably linked to a tissue specific promoter,

52. The transgenic plant of claim 51, wherein said first B3-domain transcription factor is VP1 as defined by SEQ.ID.NO.: 2.

53. The transgenic plant of claim 52, wherein said second B3-domain transcription factor is RAV2 as defined by SEQ.ID.NO.: 4.

54. The transgenic plant of claim 51, wherein said first B3 domain transcription factor is RAV2 as defined by SEQ. IS. NO.: 4.

55. The transgenic plant of claims 51, wherein said first B3 domain transcription factor or said second B3 domain transcription factor is selected from a group of polypeptides consisting of SEQ.ID.NO.: 30, SEQ.ID.NO.:32, SEQ.ID.NO.:34, SEQ.ID.NO.:36, SEQ. ID.NO.:38, SEQ.ID.NO.:40, SEQ.ID.NO.:42, SEQ.ID.NO.:44, SEQ.ID.NO.:46, SEQ. ID.NO.:48, SEQ.ID.NO.:50, SEQ.ID.NO.:52, SEQ.ID.NO.:54, SEQ.ID.NO.:56, SEQ. ID.NO.:58, SEQ.ID.NO.:60, SEQ.ID.NO.:62, SEQ.ID.NO.:64, and SEQ.ID.NO.:66.

56. The transgenic plant of claim 51, wherein said transgenic plant is a monocot plant or a dicot plant.

57. A method of screening for a polynucleotide which encodes a B3 domain protein or a bZIP domain protein comprising,

a) hybridizing a polynucleotide having at least 25% identical to the B3 domain of SEQ. ID. NO:1 or SEQ. ID. NO.: 3 or a polynucleotide having at least 25% identity to the bZIP domain of SEQ. ID. NO. 5: to the polynucleotide to be screened;

b) expressing the polynucleotide to produce a protein; and

c) detecting the presence or absence of B3 domain activity or bZIP domain activity in said protein.

58. A vector comprising an isolated polynucleotide having a polynucleotide sequence with a B3 domain which is at least 25% identical to the B3 domain of SEQ. ID. NO. 1 or SEQ. ID. NO.: 3 and an isolated polynucleotide having a polynucleotide sequence with a bZIP domain which is at least 25% identical to the bZIP domain of SEQ. ID. NO.: 5.

59. The vector of claim 58, wherein said B3-domain transcription factor is VP1 as defined by SEQ.ID.NO.: 1.

60. The vector of claim 59, wherein said bZIP domain transcription factor is selected from a group of polynucleotides consisting of SEQ. ID. NO. 5, and SEQ. ID. NO. 7.

61. The vector of claim 58, wherein said bZIP domain transcription factor is selected from a group of polynucleotides consisting of SEQ. ID. NO. 5. and SEQ. ID. NO. 7.

62. The vector of claim 58 wherein said bZIP domain transcription factor is selected from a group of polynucleotides consisting of SEQ. ID. NO. 9, SEQ. ID. NO. 11, SEQ. ID. NO. 15, SEQ. ID. NO. 17, SEQ. ID. NO. 19, SEQ. ID. NO. 21, SEQ. ID. NO. 23, SEQ. ID. NO. 25 and SEQ. ID. NO. 27.

63. The vector of claim 58 wherein said B3 domain transcription factor is selected from a group of polynucleotides consisting of SEQ. ID. NO. 29, SEQ. ID. NO. 31, SEQ. ID. NO. 33, SEQ. ID. NO. 35, SEQ. ID. NO. 37, SEQ. ID. NO. 39, SEQ. ID. NO. 41, SEQ. ID. NO. 43, SEQ. ID. NO. 45, SEQ. ID. NO. 47, SEQ. ID. NO. 49, SEQ. ID. NO. 51, SEQ. ID. NO. 53, SEQ. ID. NO. 55, SEQ. ID. NO. 57, SEQ. ID. NO. 59, SEQ. ID. NO. 61, SEQ. ID. NO. 63, and SEQ. ID. NO. 65.

64. A host cell comprising an isolated polynucleotide having a polynucleotide sequence with a B3 domain which is at least 25% identical to the B3 domain of SEQ. ID. NO. 1 or SEQ. ID. NO.: 3 and an isolated polynucleotide having a polynucleotide sequence with a bZIP domain which is at least 25% identical to the bZIP domain of SEQ. ID. NO.: 5.

65. The host cell of claim 64, wherein said B3-domain transcription factor is VP1 as defined by SEQ.ID.NO.:1.

66. The host cell of claim 65, wherein said bZIP domain transcription factor is selected from a group of polynucleotides consisting of SEQ. ID. NO. 5. and SEQ. ID. NO. 7.

67. The host cell of claim 64, wherein said bZIP domain transcription factor is selected from a group of polynucleotides consisting of SEQ. ID. NO. 5. and SEQ. ID. NO. 7.

68. The host cell of claim 64 wherein said bZIP domain transcription factor is selected from a group of polynucleotides consisting of SEQ. ID. NO. 9, SEQ. ID. NO. 11, SEQ. ID. NO. 15, SEQ. ID. NO. 17, SEQ. ID. NO. 19, SEQ. ID. NO. 21, SEQ. ID. NO. 23, SEQ. ID. NO. 25 and SEQ. ID. NO. 27.

69. The host cell of claim 64 wherein said B3 domain transcription factor is selected from a group of polynucleotides consisting of SEQ. ID. NO. 29, SEQ. ID. NO. 31, SEQ. ID. NO. 33, SEQ. ID. NO. 35, SEQ. ID. NO. 37, SEQ. ID. NO. 39, SEQ. ID. NO. 41, SEQ. ID. NO. 43, SEQ. ID. NO. 45, SEQ. ID. NO. 47, SEQ. ID. NO. 49, SEQ. ID. NO. 51, SEQ. ID. NO. 53, SEQ. ID. NO. 55, SEQ. ID. NO. 57, SEQ. ID. NO. 59, SEQ. ID. NO. 61, SEQ. ID. NO. 63, and SEQ. ID. NO. 65.

70. A vector comprising a first isolated polynucleotide having a polynucleotide sequence with a B3 domain which is at least 25% identical to the B3 domain of SEQ. ID. NO. 1 and a second isolated polynucleotide having a polynucleotide sequence with a B3 domain which is at least 25% identical to the B3 domain of SEQ. ID. NO.: 3.

71. The vector of claim 70, wherein said first isolated polynucleotide is VP1 as defined by SEQ. ID. NO. 1.

72. The vector of claim 71, wherein said second isolated polynucleotide is RAV2 as defined by SEQ. ID. NO.: 3.

73. The vector of claim 70, wherein said second isolated polynucleotide is RAV2 as defined by SEQ. ID. NO.: 3.

74. The vector of claim 70, wherein said first isolated polynucleotide or said second isolated polynucleotide is selected from a group of polynucleotides consisting of SEQ. ID. NO.: 29, SEQ. ID. NO.:31, SEQ. ID. NO.:33, SEQ. ID. NO.:35, SEQ. ID. NO.:37, SEQ. ID. NO.:39, SEQ. ID. NO.:41, SEQ. ID. NO.:43, SEQ. ID. NO.:45, SEQ. ID. NO.:47, SEQ. ID. NO.:49, SEQ. ID. NO.:51, SEQ. ID. NO.:53, SEQ. ID. NO.:55, SEQ. ID. NO.: 57, SEQ. ID. NO.:59, SEQ. ID. NO.:61, SEQ. ID. NO.:63, and SEQ. ID. NO.:65.

75. A host cell comprising a first isolated polynucleotide having a polynucleotide sequence with a B3 domain which is at least 25% identical to the B3 domain of SEQ. ID. NO. 1 and a second isolated polynucleotide having a polynucleotide sequence with a B3 domain which is at least 25% identical to the B3 domain of SEQ. ID. NO.: 3.

76. The vector of claim 75, wherein said first isolated polynucleotide is VP1 as defined by SEQ. ID. NO. 1.

77. The vector of claim 76, wherein said second isolated polynucleotide is RAV2 as defined by SEQ. ID. NO.: 3.

78. The vector of claim 75, wherein said second isolated polynucleotide is RAV2 as defined by SEQ. ID. NO.: 3.

79. The vector of claim 75, wherein said first isolated polynucleotide or said second isolated polynucleotide is selected from a group of polynucleotides consisting of SEQ. ID. NO.: 29, SEQ. ID. NO.:31, SEQ. ID. NO.:33, SEQ. ID. NO.:35, SEQ. ID. NO.:37, SEQ. ID. NO.:39, SEQ. ID. NO.:41, SEQ. ID. NO.:43, SEQ. ID. NO.:45, SEQ. ID. NO.:47, SEQ. ID. NO.:49, SEQ. ID. NO.:51, SEQ. ID. NO.:53, SEQ. ID. NO.:55, SEQ. ID. NO.: 57, SEQ. ID. NO.:59, SEQ. ID. NO.:61, SEQ. ID. NO.:63, and SEQ. ID. NO.:65.