Plant having altered environmental stress tolerance

FIELD OF THE INVENTION

[0002] The present invention relates to the regulatory response of plants to environmental stresses such as cold and to drought. More specifically, the present invention relates to genes which regulate the response of a plant to environmental stresses such as cold or drought and their use to enhance the stress tolerance of recombinant plants into which these genes are introduced.

BACKGROUND OF THE INVENTION

[0003] Environmental factors serve as cues to trigger a number of specific changes in plant growth and development. One such factor is low temperature. Prominent examples of cold-regulated processes include cold acclimation, the increase in freezing tolerance that occurs in response to low non-freezing temperatures (Guy, C. L., Annu. Rev. Plant Physiol. Plant Mol. Biol. 41:187-223 (1990)); vernalization, the shortening of time to flowering induced by low temperature (Lang, A., in Encyclopedia of Plant Physiology, Vol. 15-1, ed. Ruhland, W. (Springer, Berlin), pp. 1489-1536 (1965)); and stratification, the breaking of seed dormancy by low temperature (Berry, J. A. and J. K. Raison, in Encyclopedia of Plant Physiology, Vol. 12A, eds. Lange, O. L., Nobel, P. S., Osmond, C. B. and Ziegler, H. (Springer, Berlin), pp. 277-338 (1981)). Due to the fundamental nature and agronomic importance of these processes, there is interest in understanding how plants sense and respond to low temperature. One approach being taken is to determine the signal transduction pathways and regulatory mechanisms involved in cold-regulated gene expression.

[0004] Strong evidence exists for calcium having a role in low temperature signal transduction and regulation of at least some COR (cold-regulated) genes. Dhindsa and colleagues (Monroy, A. F., et al, Plant Physiol. 102:1227-1235 (1993); Monroy, A. F., and R. S., The Plant Cell, 7:321-331 (1995)) have shown that, in alfalfa, calcium chelators and calcium channel blockers prevent low temperature induction of COR genes and that calcium ionophores and calcium channel agonists induce expression of COR genes at normal growth temperatures. Similarly, Knight et al (The Plant Cell 8:489-503 (1996)) have shown that cold-induced expression of the Arabidopsis thaliana COR gene KINI is inhibited by calcium chelators and calcium channel blockers. These results suggest that low temperature triggers an influx of extracellular calcium that activates a signal transduction pathway that induces the expression of COR genes. Consistent with this notion is the finding that low temperature evokes transient increases in cytosolic calcium levels in plants (Knight, M. R. et al, Nature 352:524-526 (1991); Knight, H., et al., The Plant Cell 8:489-503 (1996)). In addition, low temperatures have been shown to stimulate the activity of mechanosensitive calcium-selective cation channels in plants (Ding, J. P. and B. G. Pickard, Plant J. 3:713-720 (1993)).

[0005] Recent efforts have led to the identification of a cis-acting cold-regulatory element in plants, the C-repeat/DRE (Yamaguchi-Shinozaki, et al., The Plant Cell 6:251-264 (1994); Baker, S. S., et al., Plant. Mol. Biol. 24:701-713 (1994); Jiang, C., et al., Plant Mol. Biol. 30:679-684 (1996)). The element, which has a 5 base pair core sequence for CCGAC, is present once to multiple times in all plant cold-regulated promoters that have been described to date; these include the promoters of the COR15a (Baker, S. S., et al, Plant. Mol. Biol. 24:701-713 (1994)), COR78/RD29A (Horvath, D. P., et al, Plant Physiol. 103:1047-1053 (1993); Yamaguchi-Shinozaki, K., et al., The Plant Cell 6:251-264 (1994)), COR6.6 (Wang, H., et al., Plant Mol. Biol. 28:605-617 (1995)) and KINI (Wang, H., et al, Plant Mol. Biol. 28:605-617 (1995)) genes of Arabidopsis and the BN115 gene of Brassica napus (White, T. C., et al, Plant Physiol. 106:917-928 (1994)). Deletion analysis of the Arabidopsis COR15a gene suggested that the CCGAC sequence, designated the C-repeat, might be part of a cis-acting cold-regulatory element (Baker, S. S., et al., Plant Mol. Biol. 24:701-713 (1994)). That this was the case was first demonstrated by Yamaguchi-Shinozaki and Shinozaki (Yamaguchi-Shinozaki, K., et al., The Plant Cell 6:251-264 (1994)) who showed that two of the C-repeat sequences present in the promoter of COR78/RD29A induced cold-regulated gene expression when fused to a reporter gene. It was also found that these two elements stimulate transcription in response to dehydration and high salinity and thus, was designated the DRE (dehydration, low temperature and high salt regulatory element). Recent studies by Jiang et al (Jiang, C., et al., Plant Mol. Biol. 30:679-684 (1996)) indicate that the C-repeats (referred to as low temperature response elements) present in the promoter of the B. napus BN115 gene also impart cold-regulated gene expression.

[0006] U.S. Pat. Nos. 5,296,462 and 5,356,816 to Thomashow describe the genes encoding the proteins involved in cold adaptation in Arabidopsis thaliana. In particular the DNA encoding the COR15 proteins is described. These proteins are significant in promoting cold tolerance in plants.

[0007] A need exists for the identification of genes which regulate the expression of cold tolerance genes and drought tolerance genes. A further need exists for DNA constructs useful for introducing these regulatory genes into a plant in order to cause the plant to begin expressing or enhance their expression of native or non-native cold tolerance genes and drought tolerance genes. These and other needs are provided by the present invention.

SUMMARY OF THE INVENTION

[0008] DNA in isolated form is provided which includes a sequence encoding a binding protein capable of selectively binding to a DNA regulatory sequence which regulates expression of one or more environmental stress tolerance genes in a plant. The binding protein is preferably capable of regulating expression of one or more environmental stress tolerance genes in a plant by selectively binding to a DNA regulatory sequence which regulates the one or more environmental stress tolerance genes. In one embodiment, the binding protein is a non-naturally occurring protein formed by combining an amino acid sequence capable of binding to a CCG regulatory sequence, preferably a CCGAC regulatory sequence with an amino acid sequence which forms a transcription activation region which regulates expression of one or more environmental stress tolerance genes in a plant by regulating expression of one or more environmental stress tolerance genes when the binding protein binds to the regulatory region.

[0009] DNA in isolated form is also provided which includes a promoter and the sequence encoding the binding protein. In one variation, the promoter causes expression of the binding protein in a manner which is different than how the binding protein is expressed in its native state. For example, the promoter may increase the level at which the binding protein is expressed, express the binding protein without being induced by an environmental stress and/or express the binding protein in response to a different form or degree of environmental stress than would otherwise be needed to induce expression of the binding protein. The promoter may also be inducible by an exogenous agent. The promoter can also be selected with regard to the type or types of plant tissues that the binding protein will be expressed as well as when in the plant's life the promoter will function to regulate expression of the binding protein.

[0010] A nucleic acid construct capable of transforming a plant is also provided which includes a sequence encoding a binding protein capable of selectively binding to a DNA regulatory sequence which regulates expression of one or more environmental stress tolerance genes in a plant. The binding protein is preferably capable of regulating expression of one or more environmental stress tolerance genes in a plant by selectively binding to a DNA regulatory sequence which regulates the one or more environmental stress tolerance genes. The nucleic acid construct may be an RNA or DNA construct. Examples of types of constructs include, but are not limited to DNA and RNA viral vectors and plasmids.

[0011] A nucleic acid construct capable of transforming a plant is also provided which includes a sequence which when transformed into a plant expresses a binding protein capable of selectively binding to a DNA regulatory sequence which regulates one or more environmental stress tolerance genes in the plant. The binding protein preferably regulates expression of one or more environmental stress tolerance genes in the plant by selectively binding to a DNA regulatory sequence which regulates the one or more environmental stress tolerance genes.

[0012] In one variation of the above constructs, the construct also includes a promoter which regulates expression of the binding protein encoding sequence. The promoter may optionally be homologous or heterologous relative to the binding protein encoding sequence. The promoter and binding protein encoding sequence may also optionally be native to the same or a different plant species. In one variation, the promoter causes expression of the binding protein in a manner which is different than how the binding protein is expressed in its native state. For example, the promoter may increase the level at which the binding protein is expressed, express the binding protein without being induced by an environmental stress and/or express the binding protein in response to a different form or degree of environmental stress than would otherwise be needed to induce expression of the binding protein. The promoter may also be inducible by an exogenous agent. The promoter can also be selected with regard to the type or types of plant tissues that the binding protein will be expressed as well as when in the plant's life the promoter will function to regulate expression of the binding protein.

[0013] A binding protein in isolated form is also provided which is capable of selectively binding to a DNA regulatory sequence which regulates expression of one or more environmental stress tolerance genes in a plant. The binding protein is preferably capable of regulating expression of one or more environmental stress tolerance genes in the plant by selectively binding to a DNA regulatory sequence which regulates the one or more environmental stress tolerance genes.

[0014] A recombinant binding protein expressed within a plant is also provided which is capable of selectively binding to a DNA regulatory sequence in the plant which regulates expression of one or more environmental stress tolerance genes in the plant. The recombinant binding protein is preferably capable of regulating expression of one or more environmental stress tolerance genes in the plant by selectively binding to a DNA regulatory sequence which regulates the one or more environmental stress tolerance genes. The recombinant binding protein may be native or non-native to the plant. Further, the recombinant binding protein may be homologous or heterologous relative to the DNA binding protein present in the plant in which the binding protein is expressed.

[0015] A transformed cell of an organism is also provided which includes a recombinant sequence encoding a binding protein capable of selectively binding to a DNA regulatory sequence which regulates expression of one or more environmental stress tolerance genes in a plant. The binding protein is preferably capable of regulating expression of one or more environmental stress tolerance genes in a plant by selectively binding to a DNA regulatory sequence which regulates the one or more environmental stress tolerance genes. The transformed cell may be a unicellular organism such as a bacterium, yeast or virus, or from a multicellular organism such as a fungus or a plant.

[0016] A transformed cell is also provided which includes a promoter and a sequence encoding a binding protein where at least one of the promoter and sequence under regulatory control of the promoter is recombinant. Optionally, one or both of the promoter and sequence under regulatory control of the promoter is not native to the cell. In one variation, the promoter causes expression of the binding protein in a manner which is different than how the binding protein is expressed in its native state. For example, the promoter may increase the level at which the binding protein is expressed, express the binding protein without being induced by an environmental stress and/or express the binding protein in response to a different form or degree of environmental stress than would otherwise be needed to induce expression of the binding protein. The promoter may also be inducible by an exogenous agent. The promoter can also be selected with regard to the type or types of plant tissues that the binding protein will be expressed as well as when in the plant's life the promoter will function to regulate expression of the binding protein.

[0017] A transformed cell is also provided which includes a recombinant binding protein expressed within the cell which is capable of selectively binding to a DNA regulatory sequence in the plant which regulates expression of one or more environmental stress tolerance genes in the plant. The binding protein is preferably capable of regulating expression of one or more environmental stress tolerance genes in the plant by selectively binding to a DNA regulatory sequence which regulates the one or more environmental stress tolerance genes. The binding protein may be native or non-native to the cell.

[0018] A transformed plant with modified environmental stress tolerance gene expression is also provided. In one embodiment, the transformed plant includes one or more environmental stress tolerance genes; a DNA regulatory sequence which regulates expression of the one or more environmental stress tolerance genes; and a recombinant sequence encoding a binding protein capable of selectively binding to the DNA regulatory sequence.

[0019] In another embodiment, the transformed plant includes one or more environmental stress tolerance genes; a DNA regulatory sequence which regulates expression of the one or more environmental stress tolerance genes; a sequence encoding a binding protein capable of selectively binding to the DNA regulatory sequence; and a recombinant promoter which regulates expression of the sequence encoding the binding protein.

[0020] In yet another embodiment, the transformed plant includes one or more environmental stress tolerance genes; a recombinant DNA regulatory sequence which regulates expression of the one or more environmental stress tolerance genes; and a sequence encoding a binding protein capable of selectively binding to the DNA regulatory sequence.

[0021] In yet another embodiment, the transformed plant includes at least one recombinant environmental stress tolerance gene; a DNA regulatory sequence which regulates expression of the at least one environmental stress tolerance gene; and a sequence encoding a binding protein capable of selectively binding to the DNA regulatory sequence.

[0022] In yet another embodiment, the transformed plant includes at least one recombinant environmental stress tolerance gene; a DNA regulatory sequence which regulates expression of the at least one environmental stress tolerance gene; and a recombinant binding protein expressed by the plant which is capable of selectively binding to the DNA regulatory sequence.

[0023] A method for altering an environmental stress tolerance of a plant is also provided. In one embodiment, the method includes transforming a plant with at least one copy of a gene encoding a binding protein capable of binding to a DNA regulatory sequence which regulates one or more environmental stress tolerance genes in the plant; expressing the binding protein encoded by the gene; and stimulating expression of at least one environmental stress tolerance gene through binding of the binding protein to the DNA regulatory sequence. In another embodiment, the method includes transforming a plant with a promoter which regulates expression of at least one copy of a gene encoding a binding protein capable of binding to a DNA regulatory sequence which regulates one or more environmental stress tolerance genes in the plant; expressing the binding protein encoded by the gene; and stimulating expression of at least one environmental stress tolerance gene through binding of the binding protein to the DNA regulatory sequence.

[0024] In another embodiment, the method includes transforming a plant with one or more environmental stress tolerance genes whose expression is regulated by a DNA regulatory sequence; and expressing a binding protein capable of binding to the DNA regulatory sequence and activating expression of the one or more environmental stress tolerance genes.

[0025] According to any one of the above embodiments of the present invention, the binding protein may optionally be selected such that it selectively binds to a member of a class of DNA regulatory sequences which includes the subsequence CCG or more particularly one of the following subsequences: CCGM, CCGAT, CCGAC, CCGAG, CCGTA, CCGTT, CCGTC, CCGTG, CCGCA, CCGCT, CCGCG, CCGCC, CCGGA, CCGGT, CCGGC, CCGGG, AACCG, ATCCG, ACCCG, AGCCG, TACCG, TTCCG, TCCCG, TGCCG, CACCG CCCG, GACCG, GTCCG, GCCCG, GGCCG, ACCGA, ACCGT, ACCGC, ACCGG, TCCGA, TCCGT, TCCGC, TCCGG, CCCGA, CCCGT, CCCGC, CCCGG, GCCGA, GCCGT, GCCGC, and GCCGG. The binding protein may also be selected such that the binding protein includes an AP2 domain.

[0026] In each of the above embodiments, the level of expression of the binding protein may be the same or different than the level of expression of the binding protein in its native state. Expression of the binding protein in the transformed cell may be regulated by a recombinant promoter which may have the effect of increasing the level at which the binding protein is expressed, expressing the binding protein without being induced by an environmental stress and/or expressing the binding protein in response to a different form or degree of environmental stress than is otherwise needed to induce expression of the binding protein. Expression may also be induced by an exogenous agent. Expression may also be limited to selected types of plant tissues or selected periods in the plant's life based on which promoter is used. By selecting in what tissues and when in a plant's life the binding protein is expressed, in combination with the selecting how the binding protein is expressed (level of expression and/or type of environmental or chemical induction), an incredible range of control over the environmental stress responses of a plant can be achieved by the present invention.

[0027] In each of the above embodiments, the binding protein comprises an amino acid sequence which is capable of binding to a DNA regulatory sequence which regulates one or more environmental stress tolerance genes. In a preferred embodiment, the binding protein further comprises a transcription activation region which acts in concert with the binding sequence to regulate expression of one or more environmental stress tolerance genes in the plant by regulating expression of one or more environmental stress tolerance genes. The environmental stress tolerance gene, DNA regulatory sequence, sequence encoding the binding sequence, and the sequence encoding the transcription activation region may each independently be native or non-native to the plant and may each independently be homologous or heterologous relative to each other.

[0028] Optionally, the binding protein satisfies one or more of the following requirements:

[0029] the binding protein comprises an AP2 domain which comprises a consensus sequence sufficiently homologous to any one of the consensus sequences shown in FIGS. 19A, 19B, or 19C that the binding protein is capable of binding to a CCG regulatory sequence, preferably a CCGAC regulatory sequence;

[0030] the binding protein comprises an AP2 domain which comprises a consensus sequence shown in FIGS. 19A, 19B or 19C;

[0031] the binding protein comprises an AP2 domain which comprises the amino acid residues shown in FIGS. 19D or 19E;

[0032] the binding protein comprises an AP2 domain which is sufficiently homologous to at least one of the AP2 domains shown in the application such that it is capable of binding to a CCG regulatory sequence, preferably a CCGAC regulatory sequence;

[0033] the binding protein comprises one of the AP2 domain sequences shown in this application, including, but not limited to SEQ. I.D. Nos. 2, 13, 15, 39, 41, 43, 45, 47, 49, 51, 53, 55, 57, 59, 61, 63, 65, 67, 69, 71, 73, 75, 77, 79, 81, 83, 85, 87, 89, 91, 93, and 95;

[0034] the binding protein comprises a sequence which comprises one of the amino terminus domains shown in FIG. 20 (it is noted that the sequence need not be at the amino terminus of the binding protein);

[0035] the binding protein comprises the consensus sequence for the amino terminus domains shown in FIG. 20, (it is noted that the sequence need not be at the amino terminus of the binding protein);

[0036] the binding protein comprises a sequence which comprises one of the carboxy terminus domains shown in FIG. 21A (it is noted that the sequence need not be at the carboxy terminus of the binding protein);

[0037] the binding protein comprises the consensus sequence for the carboxy terminus domains shown in FIG. 21A (it is noted that the sequence need not be at the carboxy terminus of the binding protein); and

[0038] the binding protein comprises the consensus sequence for the carboxy terminus domains shown in FIG. 21B (it is noted that the sequence need not be at the carboxy terminus of the binding protein).

[0039] The amino acid sequence encoding the binding protein may be a naturally occurring sequence such as the ones shown in SEQ. ID. Nos. 2, 13, 15, 39, 41, 43, 45, 47, 49, 51, 53, 55, 57, 59, 61, 63, 65, 67, 69, 71, 73, 75, 77, 79, 81, 83, 85, 87, 89, 91, 93, and 95 or may be a non-naturally occurring sequence. It is noted, however, that binding proteins according to the present invention are intended to encompass non-naturally occurring sequences which are derivatives of the classes of binding proteins taught herein. For example, additional binding proteins may be constructed using one of the AP2 domains taught herein or the consensus sequence of these AP2 domains. It may be desirable to include with the AP2 domain a transcription activation region. The transcription activation region may be native to the plant or non-native to the plant in which the binding protein will be used. For example, the sequence may include a subsequence which encodes a binding domain for the DNA regulatory sequence fused to a transcription activating region, such as the transcription activating region of VP16 or GAL4.

[0040] Optionally, one can include in the binding protein one of the amino terminus domains, the consensus sequence for the amino terminus domain, one of the carboxy terminus domains and/or the consensus sequence for the carboxy terminus domains. It is noted that the amino terminus domain may be positioned away from the amino terminus of the new binding protein and the carboxy terminus domain may be positioned away from the carboxy terminus of the new binding protein.

[0041] Optionally, the binding protein can be viewed as comprising one of the amino terminus domains, the consensus sequence for the amino terminus domain, one of the carboxy terminus domains and/or the consensus sequence for the carboxy terminus domains. It is noted that the amino terminus domain may be positioned away from the amino terminus of the new binding protein and the carboxy terminus domain may be positioned away from the carboxy terminus of the new binding protein.

[0042] A method is also provided for identifying from a cDNA library of at least a portion of a plant genome a gene sequence encoding a protein capable of binding to a target DNA regulatory sequence. In one embodiment, the method comprises

[0043] taking a microorganism which includes a target DNA regulatory sequence for one or more environmental stress tolerance genes, a transcription activator for activating expression of a reporter gene, and a reporter gene whose expression is activated by a protein which includes a binding domain capable of binding to the target DNA regulatory sequence and an activation domain capable of activating the transcription activator;

[0044] fusing sequences from a cDNA library of at least a portion of a plant genome to a sequence which encodes a functional activation domain in the microorganism;

[0045] introducing the fused sequences into the microorganism; and

[0046] selecting microorganisms which express the reporter gene, expression of the reporter gene indicating expression of a fusion protein which includes a binding domain for the target DNA regulatory sequence and the activation domain; and

[0047] identifying the gene sequence from the cDNA library introduced into the microorganism. The target DNA regulatory sequence may optionally include the subsequence CCG or the subsequence CCGAC. This embodiment of the invention also relates to DNA in substantially isolated form, nucleic acid constructs capable of transforming a plant, cells, and transformed plants which include a gene sequence identified by this method.

[0048] While the present invention is described with regard to the use of binding proteins which can bind to a DNA regulatory sequence that regulates environmental stress tolerance genes in a plant, it is noted that these same binding proteins can also be used to regulate genes other than environmental stress tolerance genes by placing these other genes under the regulatory control of the DNA regulatory sequence. For example, protein kinases that induce cold and drought inducible genes can be regulated by placing a protein kinase gene under the control of a promoter whose expression is regulated by the DNA regulatory sequence. PCT/US97/23019 (Intl Publication Number WO 98/26045) describes protein kinases that when constitutively expressed, induce cold and drought inducible genes. The ATCDPK1a and the ATCDPK1 constitutive protein kinase coding regions (PCT/US97/23019) can be isolated by PCR and inserted into the drought and cold inducible promoters described in Example 8 by one skilled in the art. The expression of these ATCDPK1 constitutive protein kinase coding regions (PCT/US97/23019) from the drought and cold inducible promoters will increase the drought and cold tolerance of plants and should be synergistic with the the drought and cold tolerance induced by CBF expression under inducible promoters.

BRIEF DESCRIPTION OF THE DRAWINGS

[0049]
FIGS. 1A and 1B show how the yeast reporter strains were constructed.

[0050]
FIG. 1A is a schematic diagram showing the screening strategy.

[0051]
FIG. 1B is a chart showing activity of the “positive” cDNA clones in yeast reporter strains.

[0052]
FIGS. 2A, 2B, 2C and 2D provide an analysis of the pACT-11 cDNA clone.

[0053]
FIG. 2A is a schematic drawing of the pACT-11 cDNA insert indicating the location and 5′ to 3′ orientation of the 24 kDa polypeptide and 25s rRNA sequences.

[0054]
FIG. 2B is a DNA and amino acid sequence of the 24 kDa polypeptide (SEQ ID NO:1 and SEQ ID NO:2).

[0055]
FIG. 2C is a schematic drawing indicating the relative positions of the potential nuclear localization signal (NLS), the AP2 domain and the acidic region of the 24 kDa polypeptide.

[0056]
FIG. 2D is a chart showing comparison of the AP2 domain of the 24 kDa polypeptide with that of the tobacco DNA binding protein EREBP2.

[0057]
FIG. 3 is a chart showing activation of reporter genes by the 24 kDa polypeptide.

[0058]
FIG. 4 is a photograph of an electrophoresis gel showing expression of the recombinant 24 kDa polypeptide in E. coli.

[0059]
FIG. 5 is a photograph of a gel for shift assays indicating that CBF1 binds to the C-repeat/DRE.

[0060]
FIG. 6 is a photograph of a southern blot analysis indicating CBF1 is a unique or low copy number gene.

[0061]
FIGS. 7A, 7B and 7C relate to CBF1 transcripts in control and cold-treated Arabidopsis.

[0062]
FIG. 7A is a photograph of a membrane RNA isolated from Arabidopsis plants that were grown at 22 C or grown at 22 C and transferred to 2.5 C for the indicated times.

[0063]
FIG. 7B is a graph showing relative transcript levels of CBF1 in control and cold-treated plants.

[0064]
FIG. 7C is a graph showing relative transcript levels of COR15a in control and cold-treated plants.

[0065]
FIG. 8 is a Northern blot showing CBF1 and COR transcript levels in RLD and transgenic Arabidopsis plants.

[0066]
FIG. 9 is an immunoblot showing COR15am protein levels in RLD and transgenic Arabidopsis plants.

[0067]
FIGS. 10A and 10B are graphs showing freezing tolerance of leaves from RLD and transgenic Arabidopsis plants.

[0068]
FIG. 11 is a photograph showing freezing survival of RLD and A6 Arabidopsis plants.

[0069]
FIG. 12 shows the DNA sequence for CBF2 encoding CBF2.

[0070]
FIG. 13 shows the DNA sequence for CBF3 encoding CBF3.

[0071]
FIG. 14 shows the amino acid alignment of proteins CBF1, CBF2 and CBF3.

[0072]
FIG. 15 is a graph showing transcription regulation of COR genes by CBF1, CBF2 and CBF3 genes in yeast.

[0073]
FIG. 16 shows the amino acid sequence of a canola homolog and its alignment to the amino acid sequence of CBF1.

[0074]
FIGS. 17A, 17B, 17C, 17D, 17E, 17F and 17G show restriction maps of plasmids pMB12008, pMB12009, pMB12010, pMB12011, pMB12012, pMB12013, and pMB12014, respectively.

[0075]
FIG. 18A shows the DNA sequences for the CBF homologs from Brassica juncea, Brassica napus, Brassica oleracea, Brassica rapa, Glycine max, Raphanus sativus and Zea Maize.

[0076]
FIG. 18B shows the amino acid sequences (one-letter abbreviations) encoded by the DNA sequences (shown in FIG. 18A) for CBF homologs from Brassica juncea, Brassica napus, Brassica oleracea, Brassica rapa, Glycine max, Raphanus sativus and Zea Maize.

[0077]
FIG. 19A shows an amino acid alignment of the AP2 domains of several CBF proteins with the consensus sequence between the proteins highlighted as well as a comparison of the AP2 domains with that of the tobacco DNA binding protein EREBp2.

[0078]
FIG. 19B shows an amino acid alignment of the AP2 domains of several CBF proteins including dreb2a and dreb2b with the consensus sequence between the proteins highlighted.

[0079]
FIG. 19C shows an amino acid alignment of the AP2 domains of several CBF proteins including dreb2a, dreb2b, and tiny with the consensus sequence between the proteins highlighted.

[0080]
FIG. 19D shows a difference between the consensus sequence shown in FIG. 19A and tiny.

[0081]
FIG. 19E shows a difference between the consensus sequence shown in FIG. 19B and tiny.

[0082]
FIG. 20 shows an amino acid alignment of the amino terminus of several CBF proteins with their consensus sequence highlighted.

[0083]
FIGS. 21A and 21B show an amino acid alignment of the carboxy terminus of several CBF proteins, with their consensus sequences highlighted.

DETAILED DESCRIPTION

[0084] The present invention relates to DNA encoding binding proteins capable of binding to a DNA regulatory sequence which regulates expression of one or more environmental stress tolerance genes in a plant. The present invention also relates to the binding proteins encoded by the DNA. The DNA and binding proteins may be native or non-native relative to the DNA regulatory sequence of the plant. The DNA and binding proteins may also be native or non-native relative to environmental stress tolerance genes of the plant which are regulated by the DNA regulatory sequence.

[0085] The present invention also relates to methods for using the DNA and binding proteins to regulate expression of one or more native or non-native environmental stress tolerance genes in a plant. These methods may include introducing DNA encoding a binding protein capable of binding to a DNA regulatory sequence into a plant, introducing a promoter into a plant which regulates expression of the binding protein, introducing a DNA regulatory sequence into a plant to which a binding protein can bind, and/or introducing one or more environmental stress tolerance genes into a plant whose expression is regulated by a DNA regulatory sequence.

[0086] The present invention also relates to recombinant cells, plants and plant materials (e.g., plant tissue, seeds) into which one or more gene sequences encoding a binding protein have been introduced as well as cells, plants and plant materials within which recombinant binding proteins encoded by these gene sequences are expressed. By introducing a gene sequence encoding a binding protein into a plant, a binding protein can be expressed within the plant which regulates expression of one or more stress tolerance genes in the plant. Regulation of expression can include causing one or more stress tolerance genes to be expressed under different conditions than those genes would be in the plant's native state, increasing a level of expression of one or more stress tolerance genes, and/or causing the expression of one or more stress tolerance genes to be inducible by an exogenous agent. Expression of the binding protein can be under the control of a variety of promoters. For example, promoters can be used to overexpress the binding protein, change the environment conditions under which the binding protein is expressed, or enable the expression of the binding protein to be induced, for example by the addition of an exogenous inducing agent.

[0087] The present invention also relates to cells, recombinant plants and plant materials into which a recombinant promoter is introduced which controls a level of expression of one or more gene sequences encoding a binding protein. The one or more gene sequences may be recombinant native or non-native sequences or may be native, non-recombinant gene sequences whose expression is altered by the introduction of the recombinant promoter.

[0088] The present invention also relates to cells, recombinant plants and plant materials into which a recombinant native or non-native DNA regulatory sequence is introduced which regulates expression of one or more native or non-native environmental stress tolerance genes.

[0089] Examples of environmental stresses for which stress tolerance genes are known to exist include, but are not limited to, cold tolerance, dehydration tolerance, and salinity tolerance. As used herein, environmental stress tolerance genes refer to genes which function to acclimate a plant to an environment stress. For example, cold tolerance genes, also referred to as COR genes (COld Regulated), refer to genes which function to acclimate a plant to a cold temperature environment. These genes typically are activated when a plant is exposed to cold temperatures. Dehydration tolerance genes refer to genes which function to acclimate a plant to dehydration stress. These genes typically are activated in response to dehydration conditions which can be associated with drought or cold temperatures which cause water in the plant to freeze and thereby dehydrate the plant tissue. It is noted that some cold tolerance genes may function to provide a plant with a degree of dehydration tolerance and visa versa. For example, COR genes are known to also be activated by dehydration stress. This application is intended to encompass genes which regulate one or more environmental stress tolerance genes such as cold tolerance genes, dehydration tolerance genes, and genes which perform a dual function of cold and dehydration tolerance.

[0090] One embodiment of the invention relates to a DNA sequence in isolated form which includes a sequence encoding a binding protein capable of selectively binding to a DNA regulatory sequence which regulates expression of one or more environmental stress tolerance genes in a plant. The binding protein is preferably capable of regulating expression of one or more environmental stress tolerance genes in a plant by selectively binding to a DNA regulatory sequence which regulates the one or more environmental stress tolerance genes. In one variation, the binding protein is a non-naturally occurring protein formed by combining an amino acid sequence capable of binding to a CCG regulatory sequence, preferably a CCGAC regulatory sequence with an amino acid sequence which forms a transcription activation region which regulates expression of one or more environmental stress tolerance genes in a plant by regulating expression of one or more environmental stress tolerance genes when the binding protein binds to the regulatory region.

[0091] The DNA sequence may exist in a variety of forms including a plasmid or vector and can include sequences unrelated to the gene sequence encoding the binding protein. For example, the DNA sequence can include a promoter which regulates expression of the regulatory gene.

[0092] In one variation of this embodiment, the DNA regulatory sequence is a C-repeat cold and drought regulation element (C-repeat/DRE). As will be explained and demonstrated herein, C-repeat/DRE regulatory sequences appear to be conserved in plants with some degree of variability plant to plant. Using the teachings of the present invention, C-repeat/DRE regulatory sequences native to different plants can be identified as well as the native stress tolerance regulatory genes which encode for proteins which bind to the C-repeat/DRE DNA regulatory sequences. Hence, although the examples provided herein to describe the present invention are described with regard to the Arabadopsis C-repeat/DRE DNA regulatory sequence, the present invention is not intended to be limited to the Arabadopsis C-repeat/DRE DNA regulatory sequence. Rather, the Arabadopsis C-repeat/DRE DNA regulatory sequence is believed to be a member of a class of environmental stress response regulatory elements which includes the subsequence CCGAC which in turn is believed to be a member of a class of environmental stress response regulatory elements which includes the subsequence CCG. Other different classes of environmental stress response regulatory elements may also exist. The teachings of the present invention may be used to identify sequences which bind to these and other classes of environmental stress response regulatory elements once they are identified.

[0093] In one variation of this embodiment, the gene sequence encodes a binding protein which selectively binds to a member of a class of DNA regulatory sequences which includes the subsequence CCG. In another variation, the gene sequence encodes a binding protein which selectively binds to a member of a class of DNA regulatory sequences which includes the subsequence CCGAC. The CCGAC subsequence has been found to present in the C-repeat/DRE DNA regulatory sequences of Arabadopsis and Brassica and to function in Tobacco based on the ability of the C-repeat/DRE to direct cold and tolerance regulated gene expression.

[0094] In yet another variation, the stress tolerance regulatory gene sequence encodes a binding protein which includes an AP2 domain. It is believed that a significant class of environmental stress tolerance regulatory genes encode for binding proteins with an AP2 domain capable of binding to the DNA regulatory sequence. The AP2 domain of the binding protein is preferably a homolog of the AP2 domain of one of the CBF binding proteins described herein. The subsequence encoding the AP2 domain is preferably a homolog of a subsequence of one of the CBF genes described herein which encodes an AP2 domain.

[0095] In another variation, the DNA sequence encoding the binding protein satisfies one or more of the following requirements:

[0096] the binding protein comprises an AP2 domain which comprises a consensus sequence sufficiently homologous to any one of the consensus sequences shown in FIGS. 19A, 19B, or 19C that the binding protein is capable of binding to a CCG regulatory sequence, preferably a CCGAC regulatory sequence;

[0097] the binding protein comprises an AP2 domain which comprises a consensus sequence shown in FIGS. 19A, 19B or 19C;

[0098] the binding protein comprises an AP2 domain which comprises the amino acid residues shown in FIGS. 19D or 19E;

[0099] the binding protein comprises an AP2 domain which is sufficiently homologous to at least one of the AP2 domains shown in the application such that it is capable of binding to a CCG regulatory sequence, preferably a CCGAC regulatory sequence; the binding protein comprises one of the AP2 domain sequences shown in this application, including, but not limited to SEQ. I.D. Nos. 2, 13, 15, 39, 41, 43, 45, 47, 49, 51, 53, 55, 57, 59, 61, 63, 65, 67, 69, 71, 73, 75, 77, 79, 81, 83, 85, 87, 89, 91, 93, and 95;

[0100] the binding protein comprises a sequence which comprises one of the amino terminus domains shown in FIG. 20 (it is noted that the sequence need not be at the amino terminus of the binding protein);

[0101] the binding protein comprises the consensus sequence for the amino terminus domains shown in FIG. 20, (it is noted that the sequence need not be at the amino terminus of the binding protein);

[0102] the binding protein comprises a sequence which comprises one of the carboxy terminus domains shown in FIG. 21A (it is noted that the sequence need not be at the carboxy terminus of the binding protein);

[0103] the binding protein comprises the consensus sequence for the carboxy terminus domains shown in FIG. 21A (it is noted that the sequence need not be at the carboxy terminus of the binding protein);

[0104] the binding protein comprises the consensus sequence for the carboxy terminus domains shown in FIG. 21B (it is noted that the sequence need not be at the carboxy terminus of the binding protein);

[0105] one of SEQ. I.D. Nos. 1, 12, 14, 40, 42, 44, 46, 48, 50, 52, 54, 56, 58, 60, 62, 64, 66, 68, 70, 72, 74, 76, 78, 80, 82, 84, 86, 88, 90, 92, and 94; or

[0106] a sequence which has substantially the same degree of homology to SEQ. I.D. Nos. 1, 12, 14, 40, 42, 44, 46, 48, 50, 52, 54, 56, 58, 60, 62, 64, 66, 68, 70, 72, 74, 76, 78, 80, 82, 84, 86, 88, 90, 92, and 94 as these sequences have with each other.

[0107] The present invention also relates to a method for identifying gene sequences from at least a portion of a plant genome which encode binding proteins capable of binding to a target DNA regulatory sequence which regulates expression of one or more stress tolerance genes in a plant.

[0108] In one embodiment, the method includes:

[0109] taking a microorganism which includes a target DNA regulatory sequence for one or more environmental stress tolerance genes, a transcription activator for activating expression of a reporter gene, and a reporter gene whose expression is activated by a protein which includes a binding domain capable of binding to the target DNA regulatory sequence and an activation domain capable of activating the transcription activator;

[0110] fusing sequences from a cDNA library of at least a portion of a plant genome to a sequence which encodes a functional activation domain in the microorganism;

[0111] introducing the fused sequences into the microorganism; and

[0112] selecting microorganisms which express the reporter gene, expression of the reporter gene indicating expression of a fusion protein which includes a binding domain for the target DNA regulatory sequence and the activation domain; and

[0113] identifying the gene sequence from the cDNA library introduced into the microorganism.

[0114] In one variation of the method, the target DNA regulatory sequence includes the subsequence CCG and in another embodiment includes the subsequence CCGAC. In yet another variation, the target DNA regulatory sequence is the C-repeat/DRE for Arabadopsis. According to the above method, the target DNA regulatory sequence is preferably native to the plant family and more preferably to the plant species from which the cDNA library is derived.

[0115] In another variation of this embodiment, the cDNA library used in the method consists of sequences which encode for a protein having an AP2 domain since it is believed that a significant class of genes encoding binding proteins for stress tolerance genes encode an AP2 domain. As will be explained herein, screening for DNA sequences from a plant genome which exhibit this functional feature has been shown to be effective for isolating gene sequences encoding binding proteins of the present invention.

[0116] In another variation of this method, the sequences from the cDNA library are fused to a sequence which includes a selectable marker, the method further including the step of selecting for microorganisms expressing the selectable marker.

[0117] While the above methodology of the present invention is described herein with regard to identifying binding protein gene sequences from Arabidopsis cDNA using the C-repeat/DRE regulatory sequence for Arabidopsis, it is noted that this methodology can be readily used to identify regulatory binding protein gene sequences for other plants by using a DNA regulatory sequence native to those plants. Alternatively, different permutations of the CCG subsequence can be used as the target DNA regulatory sequence.

[0118] An example of a microorganism which may be used in the above method is yeast. cDNA can be introduced into the microorganism by a variety of mechanisms including plasmids and vectors. In one particular embodiment, the reporter gene is beta-galactosidase.

[0119] The present invention also relates to any DNA sequences and binding proteins encoded by those DNA sequences which are identified by the above screening method.

[0120] The present invention also relates to a protein expressed by an environmental stress tolerance regulatory gene according to the present invention which can function in vivo in a plant to regulate expression of one or more environmental stress tolerance genes.

[0121] According to one embodiment, the protein is a recombinant binding protein expressed by a copy of a recombinant gene which is either not native to the plant or is native to the plant but introduced into the plant by recombinant methodology. For example, one might wish to introduce one or more copies of a regulatory gene which is native to the plant but is under the control of a promoter which overexpresses the binding protein, expresses the binding protein independent of an environmental stress, expresses the binding protein at a higher level in response to the same environmental stress than would a plant in its native state, expresses the binding protein in response to different environmental stress conditions, and/or be induced to express the binding protein by an exogenous agent to which the plant can be exposed. Alternatively, one might wish to introduce one or more copies of a regulatory gene which is not native to the plant. For example, the non-native regulatory gene may be used to alter the way in which native environmental stress tolerance genes are regulated. Alternatively, the non-native regulatory gene may be used to regulate environmental stress tolerance genes which are also not native to the plant. The non-native regulatory gene may be used to bind to a DNA regulatory region which is not native to the plant.

[0122] In another embodiment, the proteins have been isolated from a recombinant organism. The organism may be a microorganism (e.g., bacteria, yeast) or a multicellular organism such as a plant. In one variation, the protein is in substantially isolated form.

[0123] In yet another embodiment, the protein is a native, non-recombinant binding protein whose expression is regulated within a plant by a recombinant native or non-native promoter. For example, one might wish to replace a native promoter with a recombinant promoter which overexpresses the binding protein, expresses the binding protein independent of an environmental stress, expresses the binding protein at a higher level in response to the same environmental stress than would a plant in its native state, expresses the binding protein in response to different environmental stress conditions, and/or be induced to express the binding protein by an exogenous agent to which the plant can be exposed.

[0124] In one variation of the above embodiments, the protein is capable of selectively binding to a DNA regulatory sequence for one or more environmental stress tolerance genes in a plant. In another variation, the protein includes an AP2 domain which is capable of selectively binding to a DNA regulatory sequence for one or more environmental stress tolerance genes in a plant. One method which may be used to determine whether the protein binds selectively to the DNA regulatory sequence is a gel shift assay. The DNA regulatory sequence may optionally include a CCG subsequence, a CCGAC subsequence and optionally the C-repeat/DRE sequence of Arabadopsis.

[0125] In another variation of the above embodiments, the binding protein satisfies one or more of the following requirements:

[0126] the binding protein comprises an AP2 domain which comprises a consensus sequence sufficiently homologous to any one of the consensus sequences shown in FIGS. 19A, 19B, or 19C that the binding protein is capable of binding to a CCG regulatory sequence, preferably a CCGAC regulatory sequence;

[0127] the binding protein comprises an AP2 domain which comprises a consensus sequence shown in FIGS. 19A, 19B or 19C;

[0128] the binding protein comprises an AP2 domain which comprises the amino acid residues shown in FIGS. 19D or 19E;

[0129] the binding protein comprises an AP2 domain which is sufficiently homologous to at least one of the AP2 domains shown in the application such that it is capable of binding to a CCG regulatory sequence, preferably a CCGAC regulatory sequence;

[0130] the binding protein comprises one of the AP2 domain sequences shown in this application, including, but not limited to SEQ. I.D. Nos. 2, 13, 15, 39, 41, 43, 45, 47, 49, 51, 53, 55, 57, 59, 61, 63, 65, 67, 69, 71, 73, 75, 77, 79, 81, 83, 85, 87, 89, 91, 93, and 95;

[0131] the binding protein comprises a sequence which comprises one of the amino terminus domains shown in FIG. 20 (it is noted that the sequence need not be at the amino terminus of the binding protein);

[0132] the binding protein comprises the consensus sequence for the amino terminus domains shown in FIG. 20, (it is noted that the sequence need not be at the amino terminus of the binding protein);

[0133] the binding protein comprises a sequence which comprises one of the carboxy terminus domains shown in FIG. 21A (it is noted that the sequence need not be at the carboxy terminus of the binding protein);

[0134] the binding protein comprises the consensus sequence for the carboxy terminus domains shown in FIG. 21A (it is noted that the sequence need not be at the carboxy terminus of the binding protein); and

[0135] the binding protein comprises the consensus sequence for the carboxy terminus domains shown in FIG. 21B (it is noted that the sequence need not be at the carboxy terminus of the binding protein).

[0136] The sequence of the binding protein may be a naturally occurring sequence such as the ones shown in SEQ. ID. Nos. 2, 13, 15, 39, 41, 43, 45, 47, 49, 51, 53, 55, 57, 59, 61, 63, 65, 67, 69, 71, 73, 75, 77, 79, 81, 83, 85, 87, 89, 91, 93, and 95 or may be a non-naturally occurring sequence. It is noted, however, that binding proteins according to the present invention are intended to encompass non-naturally occurring sequences which are derivatives of the classes of binding proteins taught herein. For example, additional binding proteins may be constructed using one of the AP2 domains taught herein or the consensus sequence of these AP2 domains. It may be desirable to include with the AP2 domain a transcription activation region. The transcription activation region may be native to the plant or non-native to the plant in which the binding protein will be used. For example, the sequence may include a subsequence which encodes a binding domain for the DNA regulatory sequence fused to a transcription activating region, such as the transcription activating region of VP16 or GAL4. Optionally, one can include in the binding protein one of the amino terminus domains, the consensus sequence for the amino terminus domain, one of the carboxy terminus domains and/or the consensus sequence for the carboxy terminus domains. It is noted that the amino terminus domain may be positioned away from the amino terminus of the new binding protein and the carboxy terminus domain may be positioned away from the carboxy terminus of the new binding protein.

[0137] Optionally, the binding protein can be viewed as comprising one of the amino terminus domains, the consensus sequence for the amino terminus domain, one of the carboxy terminus domains and/or the consensus sequence for the carboxy terminus domains. It is noted that the amino terminus domain may be positioned away from the amino terminus of the new binding protein and the carboxy terminus domain may be positioned away from the carboxy terminus of the new binding protein.

[0138] In another embodiment, the binding protein is an isolated protein or a recombinantly produced protein which has a molecular weight of about 26 kDa as measured in an electrophoresis gel and binds to a DNA regulatory sequence which regulates a cold or dehydration regulated gene of Arabidopsis thaliana.

[0139] The present invention also relates to DNA and RNA constructs, such as plasmids, vectors, and the like, which are capable of transforming a plant. The constructs include a sequence which encodes a binding protein capable of selectively binding to a DNA regulatory sequence which regulates the one or more environmental stress tolerance genes. The binding protein is preferably able to regulate expression of one or more environmental stress tolerance genes in a plant by selectively binding to the DNA regulatory sequence. More preferably, when transformed into a plant, the sequence regulates expression of one or more environmental stress tolerance genes in the plant by expressing the binding protein. In one embodiment, the DNA construct includes a promoter and a regulatory gene sequence whose expression is under the control of the promoter. Different promoters may be used to select the degree of expression or conditions under which the regulatory gene is expressed. For example, the promoter can be used to cause overexpression of the regulatory gene, expression of the regulatory gene independent of an environmental stress, expression of the regulatory gene at a higher level in response to the same environmental stress than would a plant in its native state, expression of the regulatory gene in response to different environmental stress conditions, and/or induction of expression of the regulatory gene by an exogenous agent to which the plant can be exposed.

[0140] In another embodiment, the DNA construct comprises a sequence which encodes:

[0141] a binding protein comprising an AP2 domain which comprises a consensus sequence sufficiently homologous to any one of the consensus sequences shown in FIGS. 19A, 19B, or 19C that the binding protein is capable of binding to a CCG regulatory sequence, preferably a CCGAC regulatory sequence;

[0142] a binding protein comprising an AP2 domain which comprises a consensus sequence shown in FIGS. 19A, 19B or 19C;

[0143] a binding protein comprising an AP2 domain which comprises the amino acid residues shown in FIGS. 19D or 19E;

[0144] a binding protein comprising an AP2 domain which is sufficiently homologous to at least one of the AP2 domains shown in the application such that it is capable of binding to a CCG regulatory sequence, preferably a CCGAC regulatory sequence;

[0145] a binding protein comprising one of the AP2 domain sequences shown in this application, including, but not limited to SEQ. I.D. Nos. 2, 13, 15, 39, 41, 43, 45, 47, 49, 51, 53, 55, 57, 59, 61, 63, 65, 67, 69, 71, 73, 75, 77, 79, 81, 83, 85, 87, 89, 91, 93, and 95;

[0146] a binding protein comprising a sequence which comprises one of the amino terminus domains shown in FIG. 20 (it is noted that the sequence need not be at the amino terminus of the binding protein);

[0147] a binding protein comprising the consensus sequence for the amino terminus domains shown in FIG. 20, (it is noted that the sequence need not be at the amino terminus of the binding protein);

[0148] a binding protein comprising a sequence which comprises one of the carboxy terminus domains shown in FIG. 21A (it is noted that the sequence need not be at the carboxy terminus of the binding protein);

[0149] a binding protein comprising the consensus sequence for the carboxy terminus domains shown in FIG. 21A (it is noted that the sequence need not be at the carboxy terminus of the binding protein);

[0150] a binding protein comprising the consensus sequence for the carboxy terminus domains shown in FIG. 21B (it is noted that the sequence need not be at the carboxy terminus of the binding protein);

[0151] one of SEQ. I.D. Nos. 1, 12, 14, 40, 42, 44, 46, 48, 50, 52, 54, 56, 58, 60, 62, 64, 66, 68, 70, 72, 74, 76, 78, 80, 82, 84, 86, 88, 90, 92, and 94; or

[0152] a sequence which has substantially the same degree of homology to SEQ. I.D. Nos. 1, 12, 14, 40, 42, 44, 46, 48, 50, 52, 54, 56, 58, 60, 62, 64, 66, 68, 70, 72, 74, 76, 78, 80, 82, 84, 86, 88, 90, 92, and 94 as these sequences have with each other.

[0153] The present invention also relates to plasmids pCBF1 (ATCC 98063), pCBF2, and pCBF3.

[0154] The present invention also relates to a recombinant microorganism, such as a bacterium, yeast, fungus, virus, into which at least one copy of a regulatory gene encoding a binding protein of the present invention has been introduced by a recombinant methodology.

[0155] The present invention also relates to recombinant plants into which at least one copy of a regulatory gene encoding a binding protein of the present invention has been introduced by a recombinant methodology. The recombinant copy of the regulatory gene may be native or non-native to the plant and express a binding protein which is either native or non-native to the plant.

[0156] Expression of the recombinant copy of the regulatory gene may be under the control of the promoter. The promoter may increase the level at which the regulatory gene is expressed, express the regulatory gene without being induced by an environmental stress and/or express the regulatory gene in response to a different form or degree of environmental stress than would otherwise be needed to induce expression of the regulatory gene. For example, a promoter can be used which turns on at a temperature that is warmer than the temperature at which the plant normally exhibits cold tolerance. This would enable the cold tolerance thermostat of a plant to be altered. Similarly, a promoter can be used which turns on at a dehydration condition that is wetter than the dehydration condition at which the plant normally exhibits dehydration tolerance.

[0157] This would enable the level at which a plant responds to dehydration to be altered. A promoter can also be used which causes a higher level of expression to occur at a given environmental condition (e.g. temperature and/or dryness) than the plant would express in its native state. The promoter may also be inducible by an exogenous agent, i.e., express the regulatory gene in response to the presence of an agent to which the promoter is exposed. This would enable stress tolerance to be induced by applying an inducing agent to the plant.

[0158] Selection of the promoter can also be used to determine what tissues in the plant express the binding protein as well as when expression occurs in the plant's lifecycle. By selecting a promoter which regulates in what tissues and when in a plant's life the promoter functions to regulate expression of the binding protein, in combination with the selecting how that promoter regulates expression (level of expression and/or type of environmental or chemical induction), an incredible range of control over the environmental stress responses of a plant can be achieved according to the present invention. The environmental stress tolerance gene regulated by the recombinantly expressed regulatory gene may be native or non-native to the plant. Hence, in one embodiment, the plant includes a recombinant copy of a regulatory gene which is native to the plant and expresses a native protein which functions within the plant to regulate expression of a native environmental stress tolerance gene. In this embodiment, the recombinant plant expresses a higher level of the native regulatory gene than the plant would otherwise.

[0159] In another embodiment, at least one of the regulatory genes and the environmental stress tolerance genes is not native to the plant. For example, the regulatory gene can be native and the environmental stress tolerance gene is non-native, or the regulatory gene is non-native and the environmental stress tolerance gene is native to the plant.

[0160] In yet another embodiment, the plant can include a recombinant copy of a regulatory gene which is not native to the plant as well as a recombinant copy of one or more environmental stress tolerance genes which also is not native to the plant. According to this embodiment, the non-native regulatory gene expresses a non-native binding protein which functions within the plant to regulate expression of the one or more non-native environmental stress tolerance genes. In this regard, it is envisioned that the present invention can be used to introduce, change and/or augment the environmental stress tolerance of a plant by introducing and causing the expression of environmental stress tolerance which the plant does not have in its native form. Accordingly, plants from warmer climates can be engineered to include one or more cold tolerance genes along with a regulatory gene needed to cause expression of the cold tolerance genes in the plant so that the engineered plant can survive better in a colder climate. Similarly, a plant can be engineered to include one or more dehydration tolerance genes along with a regulatory gene needed to cause expression of the dehydration tolerance gene so that the engineered plant can grow better in a dryer climate. In this regard, it should be possible to take a plant which grows well in a first climate and engineer it to include stress tolerance genes and regulatory genes native to a second climate so that the plant can grow well in the second climate.

[0161] The present invention also relates to a method for changing or enhancing the environmental stress tolerance of a plant.

[0162] In one embodiment, the method includes introducing at least one copy of a regulatory gene encoding a binding protein of the present invention into a plant; expressing the binding protein encoded by the regulatory gene; and using the expressed binding protein to stimulate expression of at least one environmental stress tolerance gene through binding to a DNA regulatory sequence. According to this embodiment, the regulatory gene may be non-recombinant or recombinant native or non-native to the plant. Similarly, the DNA regulatory sequence and the environmental stress tolerance gene may each independently be native or non-native to the plant. In one variation of this embodiment, the method further includes recombinantly introducing an environmental stress tolerance gene into the plant which is regulated by the recombinant regulatory gene.

[0163] In another embodiment, the method includes introducing a recombinant promoter which regulates expression of a regulatory gene encoding a binding protein of the present invention into a plant; expressing the binding protein under the control of the recombinant promoter; and using the expressed binding protein to stimulate expression of at least one environmental stress tolerance gene through binding to a DNA regulatory sequence. According to this embodiment, the regulatory gene, the DNA regulatory sequence and the environmental stress tolerance gene may each independently be non-recombinant or recombinant native or non-native to the plant.

[0164] In yet another embodiment, the method includes introducing at least one recombinant environmental stress tolerance gene into a plant; expressing a binding protein; and using the expressed binding protein to stimulate expression of the recombinant environmental stress tolerance gene through binding to a DNA regulatory sequence. According to this embodiment, the gene encoding the regulatory protein, and the DNA regulatory sequence may each independently be non-recombinant or recombinant native or non-native to the plant. The recombinant environmental stress tolerance gene may be either native or non-native to the plant.

[0165] 1. Definitions

[0166] The term “C-repeat cold and drought regulation element” or “C-repeat/DRE” refers to a sequence which includes CCG and functions as a binding domain in a plant to regulate expression of one or more environmental stress tolerance genes, such as cold or dehydration stress tolerance genes.

[0167] The term “cold stress” refers to a decrease in ambient temperature, including a decrease to freezing temperatures, which causes a plant to attempt to acclimate itself to the decreased ambient temperature.

[0168] The term “dehydration stress” refers to drought, high salinity and other conditions which cause a decrease in cellular water potential in a plant.

[0169] Transformation means the process for changing the genotype of a recipient organism by the stable introduction of DNA by whatever means.

[0170] A transgenic plant is a plant containing DNA sequences which were introduced by transformation. Horticultural and crop plants particularly benefit from the present invention.

[0171] Translation means the process whereby the genetic information in an mRNA molecule directs the order of specific amino acids during protein synthesis.

[0172] The term “essentially homologous” means that the DNA or protein is sufficiently duplicative of that set forth in FIG. 2B to produce the same result. Such DNA can be used as a probe to isolate DNA's in other plants.

[0173] A promoter is a DNA fragment which causes transcription of genetic material. For the purposes described herein, promoter is used to denote DNA fragments that permit transcription in plant cells.

[0174] A poly-A addition site is a nucleotide sequence which causes certain enzymes to cleave mRNA at a specific site and to add a sequence of adenylic acid residues to the 3′-end of the mRNA.

[0175] The phrase “DNA in isolated form” refers to DNA sequence which has been at least partially separated from other DNA present in its native state in an organism. A cDNA library of genomic DNA is not “DNA in isolated form” whereas DNA which has been at least partially purified by gel electrophoresis corresponds to “DNA in isolated form”.

[0176] 2. C-Repeat/DRE Regulatory Elements In Plants

[0177] C-repeat cold and drought regulation elements (C-repeat/DRE) are sequences which function as a cis-acting regulatory element that stimulates transcription in response to an environmental stress, such as low temperature (Yamaguchi-Shinozaki, K., et al., The Plant Cell 6:251-264 (1994); and Baker, S. S., et al., Plant Mol. Biol. 24:701-713 (1994); Jiang, C., et al., Plant Mol. Biol. 30:679-684 (1996)) or dehydration stress and high salinity (Yamaguchi-Shinozaki, K., et al., The Plant Cell 6:251-264 (1994)). An object of the research leading to the present invention was the determination of how a C-repeat/DRE stimulates gene expression in response to these environmental factors, and whether cold, dehydration and high salinity affect independent or overlapping regulatory systems.

[0178] The first step toward determining how a C-repeat/DRE regulation element stimulates gene expression was the identification of the C-repeat cold and drought regulation element itself. The 5 base pair core sequence, CCGAC, has been found to be present once to multiple times in a variety of plant cold-regulated promoters in Arabidopsis and Brassica including the COR15a (Baker, S. S., et al, Plant. Mol. Biol. 24:701-713 (1994)); COR78/RD29A (Horvath, D. P., et al, Plant Physiol. 103:1047-1053 (1993) and Yamaguchi-Shinozaki, K., et al., The Plant Cell 6:251-264 (1994)); COR6.6 (Wang, H., et al., Plant Mol. biol. 28:605-617 (1995)); and KINI (Wang, H., et al, Plant Mol. Biol. 28:605-617 (1995)) genes of Arabidopsis and the BN115 gene of Brassica napus (White, T. C., et al, Plant Physiol. 106:917-928 (1994)). As shown in the examples herein, core sequence CCGAC was used to identify proteins encoded by genes within the Arabidopsis genome which bind to this core sequence.

[0179] Applicants believe that the CCGAC core sequence is a member of family of core sequences having the common subsequence CCG. The binding of CBF1 to the C-repeat/DRE involves the AP2 domain. In this regard, it is germane to note that the tobacco ethylene response element, AGCCGCC, closely resembles the C-repeat/DRE sequences present in the promoters of the Arabidopsis genes COR15a, GGCCGAC, and COR781RD29A, TACCGAC.

[0180] While the specific teachings in the present invention used only a DNA regulatory sequence which includes a CCGAC subsequence as the C-repeat/DRE core regulatory sequence, Applicants believe that other C-repeat/DRE regulatory sequences exist which belong to a broader CCG family of regulatory sequences. By screening plant genomes according to the methodology taught herein using other members of the CCG family, additional regulatory sequences as well as the binding proteins which bind to these regulatory sequences can be identified. For example, plants which are known to exhibit a form of environmental stress tolerance can be screened according to the blue colony assay and other screening methodologies used in the present invention with other members of the CCG family in order to identify other binding proteins and their gene sequences. Examples of other members of the CCG family include, but are not limited to, environmental stress response regulatory elements which include one of the following sequences: CCGAA, CCGAT, CCGAC, CCGAG, CCGTA, CCGTT, CCGTC, CCGTG, CCGCA, CCGCT, CCGCG, CCGCC, CCGGA, CCGGT,CCGGC, CCGGG, AACCG, ATCCG, ACCCG, AGCCG, TACCG, TTCCG, TCCCG, TGCCG, CACCG, CTCCG, CGCCG, CCCCG, GACCG, GTCCG, GCCCG, GGCCG, ACCGA, PCCGT, ACCGC, ACCGG, TCCGA, TCCGT, TCCGC, TCCGG, CCCGA, CCCGT, CCCGC, CCCGG, GCCGA, GCCGT, GCCGC, and GCCGG.

[0181] Applicants also believe that other families of environmental stress tolerance DNA regulatory sequences, other than the CCG family may exist. The methodologies of the present invention may be used once such other families are identified in order to identify specific environmental stress tolerance DNA regulatory sequences and associated binding proteins.

[0182] 3. Identification of Environmental Stress Tolerance Regulatory Gene Sequences Using Target Regulatory Sequence

[0183] It is possible to take a cDNA library of at least a portion of a plant genome and screen the cDNA library for the presence of regulatory gene sequences which encode binding proteins capable of binding to a target regulatory sequence. As used here, a target DNA regulatory sequence refers to a sequence to which a binding protein for one or more environmental stress tolerance genes binds. Permutations of the CCG and CCGAC families of DNA regulatory sequences represent examples of target DNA regulatory sequences. As detailed in Example 1 herein, this was the approach was used to identify CBF1, a sequence which encodes a binding protein for the Arabadopsis DNA regulatory sequence, from an Arabadopsis cDNA library.

[0184] First a target regulatory sequence is selected. The target regulatory sequence is preferably native to the plant from which the cDNA library being screened is derived.

[0185] Once a target regulatory sequence is selected, the target regulatory sequence is fused to a reporter gene and introduced into a microorganism. Expression of the reporter gene can be activated by a protein which includes a binding domain capable of binding to the target DNA regulatory sequence and an activation domain capable of activating transcription.

[0186] Sequences from a cDNA library of at least a portion of a plant genome are then fused to a sequence which encodes a functional activation domain in the microorganism. The fused sequences are then introduced into the microorganism. It is possible that the sequence from the cDNA library may already encode a functional activation domain, for example as described herein in Example 1.

[0187] Microorganisms which express the reporter gene are then selected. Since only those microorganisms which express a fusion protein which includes a binding domain for the target DNA regulatory sequence and an activation domain will stimulate expression of the reporter gene, expression of the reporter gene indicates expression of such a fusion protein.

[0188] The gene sequence from the cDNA library introduced into the microorganism which stimulates expression of the reporter gene is then identifed.

[0189] According to the above method, the target DNA regulatory sequence preferably includes the subsequence CCG and more preferably includes the subsequence CCGAC.

[0190] The “one-hybrid” strategy described in Li, J. J. and I. Herskowitz, Science 262:1870-1874 (1993) and used in Example 1 to screen Arabidopsis cDNA is an example of this method. This method can be used to screen any plant species for cDNAs that encode a target regulatory sequence, such as a C-repeat/DRE regulatory sequence. According to the “one hybrid” strategy, yeast strains are constructed that contain a lacZ reporter gene with either wild-type or mutant versions of target regulatory sequences in place of the normal UAS (upstream activator sequence) of the GALL promoter. Yeast strains carrying these reporter constructs produce low levels of βbeta-galactosidase and form white colonies on filters containing X-gal. Reporter strains carrying wild-type target regulatory sequences are transformed with a cDNA expression library that contains random cDNA inserts fused to the acidic activator domain of the yeast GAL4 transcription factor “GAL4-ACT”. Recombinant plasmids in the expression library that contain a cDNA insert encoding a C-repeat/DRE binding domain fused to GAL4-ACT will express fusion proteins which bind upstream of the lacZ reporter genes carrying the wild-type target regulatory sequence, activate transcription of the lacZ gene, and result in yeast forming blue colonies on X-gal-treated filters. Alternatively, the sequence from the cDNA library introduced into the microorganism may, as was observed in Example 1, include a sequence encoding an activator domain and thus not utilize the acidic activator domain of the yeast GAL4 transcription factor “GAL4-ACT”.

[0191] Recombinant plasmids from such “blue yeast” are then isolated and transformed back into reporter strains that contain either a wild-type or mutant version of target regulatory sequence fused to the lacZ gene. The plasmids that are desired are those that turn the former strains blue, but not the later, indicating that the cloned DNA binding domain is specific for the target regulatory sequence.

[0192] Based on presence of an AP2 binding domain in CBF1, CBF2 and CBF3, Applicants believe that an AP2 binding domain is present in a significant number of the environmental stress tolerance regulatory binding proteins. Accordingly, it is believed that the specificity of the above method for screening for gene sequences encoding a regulatory binding protein can optionally be improved by first selecting cDNA from a plant genome library which includes a potential AP2 domain site. This can be routinely done by selecting probes for selecting sequences in the library which include potential AP2 domain sequences.

[0193] 4. Screening for Expression Of Environmental Stress Tolerance Regulatory Protein

[0194] Once one or more microorganisms are selected which are believed to express a protein capable of binding to the target regulatory element and activate expression of the reporter gene, further analysis can be performed to identify and isolate full length cDNAs; i.e. cDNAs that encode the entire protein that binds to the target regulatory sequence. The coding sequence for the protein can then cloned into an expression vector, such as the pET bacterial expression vectors (Novagen), and used to produce the protein at high levels. The protein can then be analyzed by gel retardation experiments (See Example 1F) to confirm that it binds specifically to the target regulatory sequence.

[0195] Potential sequences can be further screened using known regulatory gene sequences, such as CBF1, CB2, and CBF3, or the presence of an AP2 domain which is believed to be common to a significant class of this genes. Once identified, particular sequences can be transformed into yeast to test for activation of expression of a reporter gene, for example as described in Example 1E.

[0196] 5. Screening for Binding to Target Regulatory Sequence

[0197] Once a regulatory gene sequence is identified, the sequence can be introduced into a microorganism in order to express the protein encoded by the sequence. A gel shift assay, such as the one described in Example 1F, can then be used to test for in vitro binding of the expressed protein to the target DNA regulatory sequence.

[0198] Mutagenesis of the target DNA regulatory sequence can also be performed in order to evaluate the binding selectivity of the expressed protein. It is preferred that the expressed protein selectively bind to the target DNA regulatory sequence over related sequences with one or more base differences from the target DNA regulatory sequence. For example, FIG. 5 is a photograph of a gel from a shift assay in which CBF1 was shown to selectively bind to the wild-type C-repeat/DRE CCGAC.

[0199] 6. Altering the Environmental Stress Tolerance of a Plant.

[0200] The present invention also provides a method for recombinant engineered plants with a new or altered response to one or more environmental stresses.

[0201] According to one embodiment, a copy of a gene native to a plant which encodes a binding protein according to the present invention is recombinantly introduced into the plant such that the plant expresses a recombinant binding protein encoded by the recombinant copy of the gene.

[0202] According to another embodiment, a non-native gene which encodes a binding protein according to the present invention is recombinantly introduced into a plant such that the plant expresses a recombinant binding protein encoded by the recombinant non-native gene.

[0203] According to yet another embodiment, a native or non-native DNA regulatory sequence is recombinantly introduced into a plant such that the recombinant DNA regulatory sequence regulates the expression of one or more environmental stress tolerance genes in the plant. The plant includes a gene which encodes a binding protein capable of binding to the recombinant DNA regulatory sequence.

[0204] In yet another embodiment, a native or non-native promoter is recombinantly introduced into a plant such that the recombinant promoter regulates the expression of a binding protein which binds to a DNA regulatory sequence.

[0205] According to each of the above embodiments, unless otherwise specified, the gene encoding the binding protein, the promoter promoting the expression of the binding protein, the DNA regulatory sequence, and the environmental stress tolerance genes may be non-recombinant or recombinant sequences. The recombinant sequences may be native to the plant or may be non-native to the plant. All the above permutations are intended to fall within the scope of the present invention.

[0206] As an example, many plants increase in freezing tolerance in response to low non-freezing temperatures, a process known as cold acclimation. A large number of biochemical changes occur during cold acclimation including the activation of COR (COld Regulated) genes. These genes, which are also expressed in response to dehydration (e.g., drought and high salinity), are thought to help protect plant cells against the potentially deleterious effects of dehydration associated with freezing, drought and high salinity stress. Indeed, expression of the COR15a gene in plants grown at normal temperatures (22° C.) enhances the freezing tolerance of chloroplasts.

[0207] By manipulating the expression of COR genes, the stress tolerance of crop and horticultural plants could be improved, e.g., engineer broader climate ranges; target stress resistance to stress-sensitive parts of plants; render plants stress-resistant when a stress condition (frost and drought) is imminent. To bring about these effects, however, the expression of the COR genes must be manipulated. The gene, CBF1, that encodes the transcription factor that binds to the C-repeat/DRE regulatory element present in the promoters of all COR genes described to date has been isolated. CBF1 in yeast activates expression of reporter genes that have been fused to the C-repeat/DRE element. Further, expression of CBF1 in plants has been shown to activate the expression of COR genes.

[0208] By introducing modified versions of sequences encoding regulatory binding proteins, such as CBF1, into plants, the expression of COR genes can be modified, and thereby enhance the freezing and dehydration tolerance of plants.

[0209] In each of the above embodiments, expression of the recombinant copy of the regulatory gene may be under the control of a promoter. The promoter may be recombinant or non-recombinant. In the case of recombinant promoters, the promoter may be native or non-native to the plant.

[0210] When a recombinant promoter is used, the promoter can be selected to cause expression of the binding protein in a manner which is different than how the binding protein is expressed by the plant in its native state. For example, the promoter may increase the level at which the binding protein is expressed, express the binding protein without being induced by an environmental stress and/or express the binding protein in response to a different form or degree of environmental stress than would otherwise be needed to induce expression of the binding protein. The promoter may also be inducible by an exogenous agent. For example, a strong constitutive promoter could be used to cause increased levels of COR gene expression in both non-stress and stressed plants which in turn, results in enhanced freezing and dehydration tolerance. A tissue specific promoter could be used to alter COR gene expression in tissues that are highly sensitive to stress (and thereby enhance the stress tolerance of these tissues). Examples of such strong constitutive promoters include but are not limited to the nopaline synthase (NOS) and octopine synthase (OCS) promoters, the cauliflower mosaic virus (CaMV) 19S and 35S (Odell et al., Nature 313: 810-812 (1985)) promoters or the enhanced CaMV 35S promoters (Kay et al., Science 236: 1299-1302 (1987)).

[0211] A tissue-specific promoter could also be used to alter COR gene expression in tissues that are highly sensitive to stress, thereby enhancing the stress tolerance of these tissues. Examples tissue-specific promoters include, but are not limited to, seed-specific promoters for the B. napus napin gene (U.S. Pat. No. 5,420,034), the soybean 7S promoter, the Arabidopsis 12S globulin (cruiferin) promoter (Pang, et al. Plant Molecular Biology 11: 805-820 (1988)), the maize 27 kd zein promoter, the rice glutelin 1 promoter and the phytohemaglutinin gene, fruit active promoters such as the E8 promoter from tomatoes, tuber-specific promoters such as the patatin promoter, and the promoter for the small subunit of ribuloe-1,5-bis-phosphate carboxylase (ssRUBISCO) whose expression is activated in photosynthetic tissues such as leaves.

[0212] Alternatively, an inducible promoter may be used to control the expression of the regulatory binding protein, such as CBF1, in plants. Because, in some cases, constitutive expression of higher levels of CBF proteins may have some detrimental effects on plant growth and development, the controlled expression of CBF genes is especially advantageous. For example, a promoter could be used to induce the expression of CBF proteins only at a proper time, such as prior to a frost that may occur earlier or later in the growing season of a plant, thereby prolonging the growing season of a crop and increasing the productivity of the land. This may be accomplished by applying an exogenous inducer by a grower whenever desired. Alternatively, a promoter could be used which turns on at a temperature that is warmer than the temperature at which the plant normally exhibits cold tolerance. This would enable the cold tolerance thermostat of a plant to be altered. Similarly, a promoter can be used which turns on at a dehydration condition that is wetter than the dehydration condition at which the plant normally exhibits dehydration tolerance. This would enable the level at which a plant responds to dehydration to be altered.

[0213] Promoters which are known or are found to cause inducible transcription of the DNA into mRNA in plant cells can be used in the present invention. Such promoters may be obtained from a variety of sources such as plant and inducible microbial sources, and may be activated by a variety of exogenous stimuli, such as cold, heat, dehydration, pathogenesis and chemical treatment. The particular promoter selected is preferably capable of causing sufficient expression of the regulatory binding protein, such as CBF1, to enhance plant tolerance to environmental stresses. Examples of promoters which may be used include, but are not limited to, the promoter for the DRE (C-repeat) binding protein gene dreb2a (Liu, et al. Plant Cell 10: 1391-1406 (1998)) that is activated by dehydration and high-salt stress, the promoter for delta 1-pyrroline-5-carboxylate synthetase (P5CS) whose expression is induced by dehydration, high salt and treatment with plant hormone abscisic acid (ABA) (Yoshiba, et al., Plant J. 7 751-760 (1987)), the promoters for the rd22 gene from Arabidopsis whose transcription is induced under by salt stress, water deficit and endogenous ABA (Yamaguchi-Shinozaki and Shinozaki, Mol Gen Genet 238 17-25 (1993)), the promoter for the rd29b gene (Yamaguchi-Shinizaki and Shinozaki, Plant Physiol., 101 1119-1120 (1993)) whose expression is induced by desiccation, salt stress and exogenous ABA treatment (Ishitani et al., Plant Cell 10 1151-1161 (1998)), the promoter for the rab18 gene from Arabidopsis whose transcripts accumulate in plants exposed to water deficit or exogenous ABA treatment, and the promoter for the pathogenesis-related protein 1a (PR-1a) gene whose expression is induced by pathogenesis organisms or by chemicals such as salicylic acid and polyacrylic acid.

[0214] It should be noted that the promoters described above may be further modified to alter their expression characteristics. For example, the drought/ABA inducible promoter for the rab18 gene may be incorporated into seed-specific promoters such that the rab18 promoter is drought/ABA inducible only when developing seeds. Similarly, any number of chimeric promoters can be created by ligating a DNA fragment sufficient to confer environmental stress inducibility from the promoters described above to constitute promoters with other specificities such as tissue-specific promoters, developmentally regulated promoters, light-regulated promoters, hormone-responsive promoters, etc. This should result in the creation of chimeric promoters capable of being used to cause expression of the regulatory binding proteins in any plant tissue or combination of plant tissues. Expression can also be made to occur either at a specific time during a plant's life cycle or throughout the plant's life cycle.

[0215] According to the present invention, an expression vector can be constructed to express the regulatory binding protein in the transformed plants to enhance their tolerance to environmental stresses. In one embodiment, the DNA construct may contain (1) an inducible promoter that activates expression of the regulatory binding protein in response to environmental stimuli; (2) a sequence encoding the regulatory binding protein; and (3) a 3′ non-translated region which enables 3′ transcriptional termination and polyadenylation of the mRNA transcript. The inducible promoter may be any one of the natural or recombinant promoters described above. The gene encoding the regulatory binding protein can be any one disclosed in the present invention. The 3′ region downstream from this gene should be capable of providing a polyadenylation signal and other regulatory sequences that may be required for the proper expression and processing of a mRNA may be operably linked to the 3′end of a structural gene to accomplish the invention. This may include the native 3′ end of the homologous gene form which the regulatory binding protein and/or the inducible promoter is derived, the 3′ end from a heterologous gene encoding the same protein from other species, the 3′ end from viral genes such as the 3′ end of the 35S or the 19S cauliflower mosaic virus transcripts, the 3′ end of the opine synthesis genes of Agrobacterium tumefaciens, or the 3′ end sequences from any source such that the sequence employed provides the necessary regulatory information within its nucleic acid sequence to result in the proper expression of the promoter/coding region combination to which the 3′ end sequence is operably linked.

[0216] A variety of expression vectors can be used to transfer the gene encoding the regulatory binding protein as well as the desired promoter into the plant. Examples include but not limited to those derived from a Ti plasmid of Agrobacterium tumefaciens, as well as those disclosed by Herrera-Estrella, L., et al., Nature 303: 209(1983), Bevan, M., Nucl. Acids Res. 12: 8711-8721 (1984), Klee, H. J., Bio/Technology 3: 637-642 (1985), and EPO Publication 120,516 (Schilperoort et al.) for dicotyledonous plants. Alternatively, non-Ti vectors can be used to transfer the DNA constructs of this invention into monotyledonous plants and plant cells by using free DNA delivery techniques. Such methods may involve, for example, the use of liposomes, electroporation, microprojectile bombardment, silicon carbide wiskers, viruses and pollen. By using these methods transgenic plants such as wheat, rice (Christou, P., Bio/Technology 9: 957-962 (1991)) and corn (Gordon-Kamm, W., Plant Cell 2: 603-618 (1990)) are produced. An immature embryo can also be a good target tissue for monocots for direct DNA delivery techniques by using the particle gun (Weeks, T. et al., Plant Physiol. 102: 1077-1084 (1993); Vasil, V., Bio/Technology 10: 667-674 (1993); Wan, Y. and Lemeaux, P., Plant Physiol. 104: 37-48 (1994), and for Agrobacterium-mediated DNA transfer (Hiei et al., Plant J. 6: 271-282 (1994); Rashid et al., Plant Cell Rep. 15: 727-730 (1996); Dong, J., et al., Mol. Breeding 2: 267-276 (1996); Aldemita, R. and Hodges, T., Planta 199: 612-617 (1996); Ishida et al., Nature Biotech. 14: 745-750 (1996)).

[0217] In one embodiment, the plasmid vector pMEN020 is preferred, which is derived from a Ti plasmid pMON10098 which is the type of binary vector described in U.S. Pat. Nos. 5,773,701 and 5,773,696. PMEN20 differs from pMON10098 by the substitution of a KpnI, SalI, SacI, SacI, NotI, and XbaI restriction sites between the ECaMV 35S promoter and the E9 3′ region.

[0218] Plasmid pMON10098 contains the following DNA segments. Starting at the bottom of the plasmid map is the origin of bacterial replication for maintenance in E. coli (ori-322). Moving in a counter-clockwise direction on the map, next is ori-V, which is the vegetative origin of replication (Stalker et al. Mol. Gen. Genet. 181:8-12 (1981)). Next is the left border of the T-DNA. Next is the chimeric gene used as the selectable marker. The chimera includes the 0.35 kilobase (kb) of the cauliflower mosaic virus 35S promoter (P-35S) (Odell et al. (1985) Nature 313:810-812). , a 0.84 kb neomycin phosphotransferase type 11 gene (KAN) and a 0.25 kb 3′ non-translated region of the nopaline synthase gene (NOS 3′) (Fraley et al. (1983) Proc. Natl. Acad. Sci. USA 80:1803-1807). The next sequence contains the enhanced CaMV 35S promoter and E9 3′ region gene cassette and restriction sites for inserting genes such as the coding region of CBF genes. This chimeric gene cassette ends with the 0.65 kb of the E9 3′ region from the pea small subunit of RUBISCO gene (U.S. Pat. No. 5,773,701). Next is the right border of the T-DNA. Next is the 0.93 kb fragment isolated from transposon Tn7 that encodes the bacterial spectinomycin/streptomycin resistance (Spc/Str), which is a determinant for selection in E. coli and Agrobacterium tumefaciens (Fling et al., Nucl. Acids Res. 13:7095-7106 (1985)).

[0219] The pMEN020 plasmid construct is a binary cloning vector that contains both E. coli and Agrobacterium tumefaciens origins of DNA replication but no vir genes encoding proteins essential for the transfer and integration of the target gene inserted in the T-DNA region. PMEN020 requires the trfA gene product to replicate in Agrobacterium. The strain of Agrobacterium containing this trfA gene is called the ABI strain and is described below and in U.S. Pat. Nos. 5,773,701 and 5,773,696. This cloning vector serves as an E. coli-Agrobacterium tumefaciens shuttle vector. All of the cloning steps are carried out in E. coli before the vector is introduced into ABI strain of Agribacterium tumefaciens.

[0220] The recipient ABI strain of Agribacterium carries a modified defective Ti plasmid that serves as a helper plasmid containing a complete set of vir genes but lacks portions or all of the T-DNA region. ABI is the A208 Agrobacterium tumefaciens strain carrying the disarmed pTiC58 plasmid pMP9ORK (Koncz et al. Mol. Gen. Genet. 204:383-396 (1986)). The disarmed Ti plasmid provides the trfA gene functions that are required for autonomous replication of the binary vectors after transfer into the ABI strain. When plant tissue is incubated with the ABI:binary vector strains, the vectors are transferred to the plant cells by the vir functions encoded by the disarmed pMP9ORK Ti plasmid. After the introduction of the binary vector into the recipient Agribacterium, the vir gene products mobilize the T-DNA region of the pMEN020 plasmid to insert the target gene, e.g. the gene encoding the regulatory binding protein, into the plant chromosomal DNA, thus transforming the cell.

[0221] After transformation of cells or protoplasts, the choice of methods for regenerating fertile plants is not particularly important. Suitable protocols are available for Leguminosae (alfalfa, soybean, clover, etc.), Umbelliferae (Carrot, celery, parsnip), Cruciferae (cabbage, radish, rapeseed, broccoli, etc.), Curcurbitaceae (melons and cucumber), Gramineae (wheat, corn, rice, barley, millet, etc.), Solanaceae (potato, tomato, tobacco, peppers, etc.), and various other crops See protocols described in Ammirato et al. (1984) Handbook of Plant Cell Culture—Crop Species. Macmillan Publ. Co. Shimamoto et al. Nature 338:274-276 (1989); Fromm et al., Bio/Technology 8:833-839 (1990); Vasil et al. Bio/Technology 8:429-434 (1990).

[0222] It is envisioned that the present invention can be used to introduce, change and/or augment the environmental stress tolerance of a plant by introducing and causing the expression of environmental stress tolerance in a manner which the plant does not exhibit in its native form. For example, by using different promoters in combination with recombinant regulatory genes, native environmental stress tolerance genes can be expressed independent of environmental stress, made responsive to different levels or types of environmental stress, or rendered inducible independent of an environmental stress. Further, selection of the promoter can also be used to determine what tissues in the plant express the binding protein as well as when the expression occurs in the plant's lifecycle. By selecting a promoter which regulates in what tissues and when in a plant's life the promoter functions to regulate expression of the binding protein, in combination with the selecting how that promoter regulates expression (level of expression and/or type of environmental or chemical induction), an incredible range of control over the environmental stress responses of a plant can be achieved using the present invention.

[0223] By recombinantly introducing a native environmental stress tolerance gene into a plant in combination with a recombinant regulatory gene under the control of an inducible promoter, a plant can be engineered which includes its native environmental stress tolerance as well as inducible environmental stress tolerance. This might be useful for inducing a cold stress tolerance reaction in anticipation of a frost.

[0224] By recombinantly introducing a non-native environmental stress tolerance gene into a plant in combination with a recombinant regulatory gene, a plant can be engineered which includes environmental stress tolerance properties that the plant would not otherwise have. In this regard, plants from warmer climates can be engineered to include one or more cold tolerance genes along with a regulatory gene needed to cause expression of the cold tolerance genes in the plant so that the engineered plant can survive better in a colder climate. Similarly, a plant can be engineered to include one or more dehydration tolerance genes along with a regulatory gene needed to cause expression of the dehydration tolerance gene so that the engineered plant can grow better in a dryer climate. In this regard, it should be possible to take a plant which grows well in a first climate and engineer it to include stress tolerance genes and regulatory genes native to a second climate so that the plant can grow well in the second climate.

[0225] By modifying the promoter controlling the expression of the gene encoding a binding protein which regulates the expression of environmental stress tolerance genes, the operation of native, non-recombinant environmental stress tolerance genes and regulatory genes can be changed. For example, the conditions under which the stress tolerance genes are expressed can be changed. Expression can also be rendered inducible by an exogenous agent.

[0226] 7. Methods for Detecting Stress Tolerance Regulatory Gene Homologs.

[0227] Once one DNA sequence encoding an environmental stress tolerance regulatory binding protein has been identified, several methods are available for using that sequence and knowledge about the protein it encodes to identify homologs of that sequence from the same plant or different plant species. For example, let us assume that a cDNA encoding a first target binding domain has been isolated from plant species “A.” The DNA sequence encoding the first target DNA regulatory sequence could be radiolabeled and used to screen cDNA libraries of plant species “A,” or any other plant species, for DNA inserts that encode proteins related to the first target DNA regulatory sequence. This could be done by screening colony or phage “lifts” using either high (Tm of about −10° C.) or low (Tm of about −30° C. or lower) stringency DNA hybridization conditions (Sambrook, J. et al, Molecular Cloning. A Laboratory Manual Cold Spring Harbor Laboratory Press, Cold Spring Harbor, N.Y., 2nd Ed. (1989)). cDNA inserts that hybridize with the first target DNA regulatory sequence could be sequenced and compared to the original first target DNA regulatory sequence. If the insert is confirmed to encode a polypeptide similar to the first target DNA regulatory sequence, the insert could be cloned into an expression vector to produce the encoded protein. The protein would then be analyzed by gel retardation experiments to confirm that it binds specifically to the first target DNA regulatory sequence.

[0228] It is recognized that not all proteins that bind to a first target DNA regulatory sequence will be transcriptional activators. However, a number of routine tests may be performed in order to determine whether a particular protein is in fact a transcriptional activator. One test involves expressing the protein in yeast strains which contain the target DNA regulatory sequence fused to the lacZ reporter gene, as described above. If the protein is a transcriptional activator, it should activate expression of the reporter gene and result in blue colonies.

[0229] Another test is a plant transient assay. In this case, a reporter gene, such as GUS, carrying the target DNA regulatory sequence as an upstream activator is introduced into plant cells (e.g. by particle bombardment) with or without a the putative transcriptional activator under control of a constitutive promoter. If the protein is an activator, it will stimulate expression of the reporter (this may be further enhanced if the plant material is placed at low temperature or is subjected to water stress as the C-repeat/DRE is responsive to low temperature and dehydration).

[0230] Significantly, once a target DNA regulatory sequence is identified, the sequence can be fused to any potential activator or repressor sequence to modify expression of plant genes that carry the target regulatory sequence as a control element. That is, the DNA regulatory sequence can be used to target “managed” expression of the battery of environmental stress tolerance related genes in a given plant species.

[0231] It is possible that the target DNA regulatory sequence of the regulatory element that imparts environmental stress tolerance related gene expression in plant species “A” might be slightly different from the analogous target DNA regulatory element that imparts environmental stress tolerance in species “B.” Thus, optimal regulation of the battery of environmental stress tolerance related genes in a given species may require the use of the regulatory binding proteins from that or a closely related plant species. Knowledge of gene sequences which encode for proteins which bind to the DNA regulatory sequence of the regulatory element, in combination with knowledge of the DNA regulatory sequence, greatly simplify the identification of sequences encoding binding proteins native to the plant species.

[0232] With the advent of fast and efficient DNA sequencing technologies, the number of plant genomes recorded on computer databases is growing rapidly. These computer databases can be used to search for homologs to CBF sequences identified in this application as well as other sequences which encode binding proteins which regulate cold tolerance genes. As more and more binding protein sequences are identified and the number of computerized plant genome databases increase, searching computer databases for additional sequences encoding binding proteins which regulate cold tolerance genes will become increasingly simplified.

[0233] 8. Preparation of Binding Proteins Derivatives Using Sequences Identified in this Application.

[0234] According to the present invention, the binding protein is a protein which is capable of binding to a DNA regulatory sequence which regulates expression of one or more environmental stress tolerance genes in a plant. These DNA regulatory sequences are preferably a member of the CCG family of regulatory sequences and more preferably a member of the CCGAC family of regulatory sequences.

[0235] Numerous amino acid sequences for CBF binding protein homologs are disclosed in this application including those shown in FIGS. 2B, 14, and 18B and listed in SEQ. I.D. Nos. 2, 13, 15, 39, 41, 43, 45, 47, 49, 51, 53, 55, 57, 59, 61, 63, 65, 67, 69, 71, 73, 75, 77, 79, 81, 83, 85, 87, 89, 91, 93, and 95. Nucleic acid sequences encoding these CBF binding protein homologs are disclosed in this application in FIGS. 2B, 12, 13, and 18A and listed in SEQ. I.D. Nos. 1, 12, 14, 40, 42, 44, 46, 48, 50, 52, 54, 56, 58, 60, 62, 64, 66, 68, 70, 72, 74, 76, 78, 80, 82, 84, 86, 88, 90, 92, and 94. These sequences were derived from a variety of different plant species including Arabidopsis, Brassica juncea, Brassica napus, Brassica oleracea, Brassica rapa, Glycine max, Raphanus sativus and Zea Maize.

[0236] The sequences identified in these figures may generally be divided into three regions: AP2 domain, amino terminus domain, and carboxy terminus domain. FIGS. 19A-19E show different AP2 domains from these homologs and consensus sequences between the different AP2 domains shown. FIG. 19A shows an amino acid alignment of the AP2 domains of several CBF proteins with the consensus sequence between the proteins highlighted as well as a comparison of the AP2 domains with that of the tobacco DNA binding protein EREBp2. FIG. 19B shows an amino acid alignment of the AP2 domains of several CBF proteins including dreb2a and dreb2b with the consensus sequence between the proteins highlighted. FIG. 19C shows an amino acid alignment of the AP2 domains of several CBF proteins including dreb2a, dreb2b, and tiny with the consensus sequence between the proteins highlighted. FIG. 19D shows a consensus sequence corresponding to the difference between the consensus sequence shown in FIGS. 19A and tiny. FIG. 19E shows a consensus sequence corresponding to the difference between the consensus sequence shown in FIGS. 19B and tiny.

[0237]
FIGS. 21A and 21B show different carboxy terminus domains from these homologs and consensus sequences between the different carboxy terminus domains shown.

[0238] The binding proteins utilized in the present invention include classes of binding proteins which satisfy one or more of the following requirements:

[0239] the binding protein comprises an AP2 domain which comprises a consensus sequence sufficiently homologous to any one of the consensus sequences shown in FIGS. 19A, 19B, or 19C that the binding protein is capable of binding to a CCG regulatory sequence, preferably a CCGAC regulatory sequence;

[0240] the binding protein comprises an AP2 domain which comprises a consensus sequence shown in FIG. 19A, 19B or 19C;

[0241] the binding protein comprises an AP2 domain which comprises the amino acid residues shown in FIG. 19D or 19E;

[0242] the binding protein comprises an AP2 domain which is sufficiently homologous to at least one of the AP2 domains shown in the application such that it is capable of binding to a CCG regulatory sequence, preferably a CCGAC regulatory sequence;

[0243] the binding protein comprises one of the AP2 domain sequences shown in this application, including, but not limited to SEQ. I.D. Nos. 2, 13, 15, 39, 41, 43, 45, 47, 49, 51, 53, 55, 57, 59, 61, 63, 65, 67, 69, 71, 73, 75, 77, 79, 81, 83, 85, 87, 89, 91, 93, and 95;

[0244] the binding protein comprises a sequence which comprises one of the amino terminus domains shown in FIG. 20 (it is noted that the sequence need not be at the amino terminus of the binding protein);

[0245] the binding protein comprises the consensus sequence for the amino terminus domains shown in FIG. 20, (it is noted that the sequence need not be at the amino terminus of the binding protein);

[0246] the binding protein comprises a sequence which comprises one of the carboxy terminus domains shown in FIG. 21A (it is noted that the sequence need not be at the carboxy terminus of the binding protein);

[0247] the binding protein comprises the consensus sequence for the carboxy terminus domains shown in FIG. 21A (it is noted that the sequence need not be at the carboxy terminus of the binding protein); and

[0248] the binding protein comprises the consensus sequence for the carboxy terminus domains shown in FIG. 21B (it is noted that the sequence need not be at the carboxy terminus of the binding protein).

[0249] The sequence of the binding protein may be a naturally occurring sequence such as the ones shown in SEQ. ID. Nos. 2, 13, 15, 39, 41, 43, 45, 47, 49, 51, 53, 55, 57, 59, 61, 63, 65, 67, 69, 71, 73, 75, 77, 79, 81, 83, 85, 87, 89, 91, 93, and 95 or may be a non-naturally occurring sequence. It is noted, however, that binding proteins according to the present invention are intended to encompass non-naturally occurring sequences which are derivatives of the classes of binding proteins taught herein.

[0250] Additional binding proteins may be constructed using one of the AP2 domains taught herein or the consensus sequence of these AP2 domains. It may be desirable to include with the AP2 domain a transcription activation region. The transcription activation region may be native to the plant or non-native to the plant in which the binding protein will be used. For example, the sequence may include a subsequence which encodes a binding domain for the DNA regulatory sequence fused to a transcription activating region, such as the transcription activating region of VP16 or GAL4. Optionally, one can include in the binding protein one of the amino terminus domains, the consensus sequence for the amino terminus domain, one of the carboxy terminus domains and/or the consensus sequence for the carboxy terminus domains. It is noted that the amino terminus domain may be positioned away from the amino terminus of the new binding protein and the carboxy terminus domain may be positioned away from the carboxy terminus of the new binding protein.

[0251] Optionally, the binding protein can be viewed as comprising one of the amino terminus domains, the consensus sequence for the amino terminus domain, one of the carboxy terminus domains and/or the consensus sequence for the carboxy terminus domains. It is noted that the amino terminus domain may be positioned away from the amino terminus of the new binding protein and the carboxy terminus domain may be positioned away from the carboxy terminus of the new binding protein.

EXAMPLES

[0252] 1. Isolation and Analysis of Arabidopsis thaliana cDNA Clone (CBF1) Encoding C-repeat/DRE Binding Factor

[0253] The following example describes the isolation of an Arabidopsis thaliana cDNA clone that encodes a C-repeat/DRE binding factor, CBF1 (C-repeat/DRE Binding Factor 1). Expression of CBF1 in yeast was found to activate transcription of reporter genes containing the C-repeat/DRE (CCGAC) as an upstream activator sequence. Meanwhile, CBF1 did not activate transcription of mutant versions of the CCGAC binding element, indicating that CBF1 is a transcription factor that binds to the C-repeat/DRE. Binding of CBF1 to the C-repeat/DRE was also demonstrated in gel shift assays using recombinant CBF1 protein expressed in Escherichia coli. Analysis of the deduced CBF1 amino acid sequence indicated that the protein has a potential nuclear localization sequence, a possible acidic activation domain and an AP2 domain, a DNA-binding motif of about 60 amino acids that is similar to those present in Arabidopsis proteins APETALA2, AINTEGUMENTA and TINY, the tobacco ethylene response element binding proteins, and numerous other plant proteins of unknown function.

[0254] A. Materials

[0255] Plant Material and Cold Treatment.

[0256] A thaliana (L.) Heyn. ecotype RLD plants were grown in pots in controlled environment chambers at 22° C. under constant illumination with cool-white fluorescent lamps (100 μmol m−2s−1) essentially as described (Gilmour, S. J., Plant Physiol. 87:745-750 (1988)). Plants were cold-treated by placing pots in a cold room at 2.5° C. under constant illumination with cool-white florescent lamps (25 μmol m−2s−1) for the indicated times.

[0257] Arabidopsis cDNA Expression Library.

[0258] The Arabidopsis pACT cDNA expression library was constructed by John Walker and colleagues (NSF/DOE/USDA Collaborative Research in Plant Biology Program grant USDA 92-37105-7675) and deposited in the Arabidopsis Biological Resource Center (stock #CD4-10).

[0259] Yeast Reporter Strains.

[0260] Oligonucleotides (Table 1) (synthesized at the MSU Macromolecular Structure Facility) encoding either wild-type or mutant versions of the C-repeat/DRE were ligated into the BglII site of the lacZ reporter vector pBgl-lacZ (Li, J. J. and I. Herskowitz, Science 262:1870-1874 (1993); kindly provided by Joachim Li). The resulting reported constructs were integrated into the ura3 locus of Saccharomyces cerevisiae strain GGY1 (MAT gal4 gal80 ura3 leu2 his3 ade2 tyr) (Li, J. J. and I. Herskowitz, Science 262:1870-1874 (1993); provided by Joachim Li) by transformation and selection for uracil prototrophy.

[0261]

E. coli
Strains.

[0262]

Escherichia coli
strain GM2163 containing plasmid pEJS251 was deposited under the Budapest Treaty on May 17, 1996 with the American Type Culture Collection, Rockville, Md. as ATCC 98063. It is available by name and number pursuant to the provisions of the Budapest Treaty.

1TABLE IOligonucleotides encoding wild type and mutant versionsof the C-repeat/DREOligonucleotideC-repeat/DRE*SequenceSEQ ID NO:MT50COR15aGatcATTTCATGGCCGACCTGCTTTTT3MT52M1COR15aCACAATTTCAaGaattcaCTGCTTTTTT4MT80M2COR15aGatcATTTCATGGtatgtCTGCTTTTT5MT125M3COR15aGatcATTTCATGGaatcaCTGCTTTTT6MT68COR15bGatcACTTGATGGCCGACCTCTTTTTT7MT66COR78-1GatcAATATACTACCGACATGAGTTCT8MT86COR78-2ACTACCGACATGAGTTCCAAAAAGC9*The C-repeat/DRE sequences tested are either wild-type found in the promoters of COR15a (Baker, S. S., et al., Plant. mol. Biol. 24: 701-713 (1994)), COR15b or COR78/RD29A (Horvath, D. P., et al., Plant Physiol. 103: 1047-1053 (1993); Yamaguchi-shinozaki, K., et al., The Plant Cell 6: 251-264 (1994)) or are mutant versions of the COR15a C-repeat/DRE (M1 COR15a, M2COR15a and M3COR15a). #Uppercase letters designate bases in wild type C-repeat/DRE sequences. The core CCGAC sequence common to the above sequences is indicated in bold type. Lowercase letters at the beginning of a sequence indicate bases added to facilitate cloning. The lowercase letters that are underlined indicated the mutations in the C-repeat/DRE sequence of COR15a.

[0263] #Uppercase letters designate bases in wild type C-repeat/DRE sequences. The core CCGAC sequence common to the above sequences is indicated in bold type. Lowercase letters at the beginning of a sequence indicate bases added to facilitate cloning. The lowercase letters that are underlined indicate the mutations in the C-repeat/DRE sequence of COR15a.

[0264] B. Methods

[0265] Screen of Arabidopsis cDNA Library.

[0266] The Arabidopsis pACT cDNA expression library was screened for clones encoding C-repeat/DRE environmental stress response regulatory elements by the following method. The cDNA library, harbored in Escherichia coli BNN132, was amplified by inoculating 0.5 ml of the provided glycerol stock into 1 L of M9 minimal glucose medium (Sambrook, J. et al, Molecular Cloning. A Laboratory Manual (Cold Spring Harbor Laboratory Press, Cold Spring Harbor, N.Y., 2nd Ed. (1989)) and shaking the bacteria for 20 h at 37° C. Plasmid DNA was isolated and purified by cesium chloride density gradient centrifugation (Sambrook et al (1989)) and transformed into the yeast GGY1 reporter strains selecting for leucine prototrophy. Yeast transformants that had been grown for 2 or 3 days at 30° C. were overlaid with either a nitrocellulose membrane filter (Schleicher and Schuell, Keene, N.H.) or Whatman #50 filter paper (Hillsboro, Oreg.) and incubated overnight at 30° C. The yeast impregnated filters were then lifted from the plate and treated with X-gal (5-bromo-4-chloro-3-indolyl-D-galactosidase) to assay colonies for beta-galactosidase activity (Li, J. J. and I. Herskowitz, Science 262:1870-1874 (1993)). Plasmid DNA from “positive” transformants (those forming blue colonies on the X-gal-treated filters) was recovered (Strathern, J. N., and D. R. Higgens, Methods Enzymol. 194:319-329 (1991)), propagated in E. coli DH5α and transformed back into the yeast reporter strains to confirm activity.

[0267] Yeast Transformation and Quantitative Beta-Galactosidase Assays.

[0268] Yeast were transformed by either electroporation (Becker, D. M., et al., Methods Enzymol. 194:182-187 (1991)) or the lithium acetate/carrier DNA method (Schiestl, R. H., et al., Current Genetics 16:339-346 (1989)). Quantitative in vitro beta-galactosidase assays were done as described (Rose, M., et al., Methods Enzymol. 101:167-180 (1983)).

[0269] Expression of CBF1 Protein in E. coli and Yeast.

[0270] CBF1 was expressed in E. coli using the pET-28a(+) vector (Novagen, Madison, Wis.). The BglII-BclI restriction fragment of pACT-11 encoding CBF1 was ligated into the BamHI site of the vector bringing CBF1 under control of the T7 phage promoter. The construct resulted in a “histidine tag,” a thrombin recognition sequence and a “T7 epitope tag” being fused to the amino terminus of CBF1. The construct was transformed into E. coli BL21 (DE3) and the recombinant CBF1 protein was expressed as recommended by the supplier (Novagen). Expression of CBF1 in yeast was accomplished by ligating restriction fragments encoding CBF1 (the BclI-BglII and BglII-BglII fragments from pACT-11) into the BglII site of pDB20.1 (Berger, S. L., et al., Cell 70:251-265 (1992); kindly provided by Steve Triezenberg) bringing CBF1 under control of the constitutive ADC1 (alcohol dehydrogenase constitutive 1) promoter.

[0271] Gel Shift Assays.

[0272] The presence of expressed protein which binds to a C-repeat/DRE binding domain was evaluated using the following gel shift assay. Total soluble E. coli protein (40 ng) was incubated at room temperature in 10 μl of 1× binding buffer [15 mM HEPES (pH 7.9), 1 mM EDTA, 30 mM KCl, 5% glycerol, 5% BSA, 1 mM DTT) plus 50 ng poly(dl-dC):poly(dl-dC) (Pharmacia, Piscataway, N.J.) with or without 100 ng competitor DNA. After 10 min, probe DNA (1 ng) that was 32P-labeled by end-filling (Sambrook et al, 1989) was added and the mixture incubated for an additional 10 min. Samples were loaded onto polyacrylamide gels (4% w/v) and fractionated by electrophoresis at 150V for 2h (Sambrook et al). Probes and competitor DNAs were prepared from oligonucleotide inserts ligated into the BamHI site of pUC118 (Vieira, J., et al., Methods Enzymol. 153:3-11 (1987)). Orientation and concatenation number of the inserts were determined by dideoxy DNA sequence analysis (Sambrook, et al, (1989)). Inserts were recovered after restriction digestion with EcoRI and HindIII and fractionation on polyacrylamide gels (12% w/v) (Sambrook et al, 1989).

[0273] Northern and Southern Analysis.

[0274] Northern and southern analysis was performed as follows. Total RNA was isolated from Arabidopsis (Gilmour, S. J., et al., Plant Physiol. 87:745-750 (1988)) and the poly(A) fraction purified using oligo dT cellulose (Sambrook, et al (1989)). Northern transfers were prepared and hybridized as described (Hajela, R. K., et al., Plant Physiol. 93:1246-1252 (1990)) except that high stringency wash conditions were at 50 C in 0.1× SSPE [× SSPE is 3.6 M NaCl, 20 mM EDTA, 0.2 M Na2—HPO4 (pH7.7)], 0.5% SDS. Membranes were stripped in 0.1× SSPE, 0.5% SDS at 95° C. for 15 min prior to re-probing. Total Arabidopsis genomic DNA was isolated (Stockinger, E. J., et al., J. Heredity, 87:214-218 (1996)) and southern transfers prepared (Sambrook et al 1989) using nylon membranes (MSI, Westborough, Mass.). High stringency hybridization and wash conditions were as described by Walling et al (Walling, L. L., et al., Nucleic Acids Res. 16:10477-10492 (1988)). Low stringency hybridization was in 6× SSPE, 0.5% SDS, 0.25% low fat dried milk at 60° C. Low stringency washes were in 1× SSPE, 0.5% SDS at 50° C. Probes used for the entire CBF1 coding sequence and 3′ end of CBF1 were the BclI/BglII and EcoRV/BglII restriction fragments from pACT-11, respectively, that had been gel purified (Sambrook et al (1989)). DNA probes were radiolabeled with 32P-nucleotides by random priming (Sambrook). Autoradiography was performed using hyperfilm-MP (Amersham, Arlington Heights, Ill.). Radioactivity was quantified using a Betascope 603 blot analyzer (Betagen Corp., Waltham, Mass.).

[0275] C. Screen of Arabidopsis cDNA library for Sequence Encoding a C-repeat/DRE Binding Domain.

[0276] The “one-hybrid” strategy (Li, J. J. and 1. Herskowitz, Science 262:1870-1874 (1993)) was used to screen for Arabidopsis cDNA clones encoding a C-repeat/DRE binding domain. In brief, yeast strains were constructed that contained a lacZ reporter gene with either wild-type or mutant C-repeat/DRE sequences in place of the normal UAS (upstream activator sequence) of the GALL promoter.

[0277]
FIGS. 1A and 1B show how the yeast reporter strains were constructed. FIG. 1A is a schematic diagram showing the screening strategy. Yeast reporter strains were constructed that carried C-repeat/DRE sequences as UAS elements fused upstream of a lacZ reporter gene with a minimal GAL1 promoter. The strains were transformed with an Arabidopsis expression library that contained random cDNA inserts fused to the GAL4 activation domain (GAL4-ACT) and screened for blue colony formation on X-gal-treated filters. FIG. 1B is a chart showing activity of the “positive” cDNA clones in yeast reporter strains. The oligonucleotides (oligos) used to make the UAS elements, and their number and direction of insertion, are indicated by the arrows.

[0278] Yeast strains carrying these reporter constructs produced low levels of beta-galactosidase and formed white colonies on filters containing X-gal. The reporter strains carrying the wild-type C-repeat/DRE sequences were transformed with a DNA expression library that contained random Arabidopsis cDNA inserts fused to the acidic activator domain of the yeast GAL4 transcription factor, “GAL4-ACT” (FIG. 1A). The notion was that some of the clones might contain a cDNA insert encoding a C-repeat/DRE binding domain fused to GLA4-ACT and that such a hybrid protein could potentially bind upstream of the lacZ reporter genes carrying the wild type C-repeat/DRE sequence, activate transcription of the lacZ gene and result in yeast forming blue colonies on X-gal-treated filters.

[0279] Upon screening about 2×106 yeast transformants, three “positive” cDNA clones were isolated; i.e., clones that caused yeast strains carrying lacZ reporters fused to wild-type C-repeat/DRE inserts to form blue colonies on X-gal-treated filters (FIG. 1B). The three cDNA clones did not cause a yeast strain carrying a mutant C-repeat/DRE fused to LacZ to turn blue (FIG. 1B). Thus, activation of the reporter genes by the cDNA clones appeared to be dependent on the C-repeat/DRE sequence. Restriction enzyme analysis and DNA sequencing indicated that the three cDNA clones had an identical 1.8 kb insert (FIG. 2A). One of the clones, designated pACT-11, was chosen for further study.

[0280] D. Identification of 24 kDa Polypeptide With an AP2 Domain Encoded by pACT-11.

[0281]
FIGS. 2A, 2B, 2C and 2D provide an analysis of the pACT-11 cDNA clone. FIG. 2A is a schematic drawing of the pACT-11 cDNA insert indicating the location and 5′ to 3′ orientation of the 24 kDa polypeptide and 25s rRNA sequences. The cDNA insert was cloned into the Xhol site of the pACT vector. FIG. 2B is a DNA and amino acid sequence of the 24 kDa polypeptide (SEQ ID NO:1 and SEQ ID NO:2). The AP2 domain is indicated by a double underline. The basic amino acids that potentially act as a nuclear localization signal are indicated with asterisks. The BclI site immediately upstream of the 24 kDa polypeptide used in subcloning the 24 kDa polypeptide and the EcoRV site used in subcloning the 3′ end of CBF1 are indicated by single underlines. FIG. 2C is a schematic drawing indicating the relative positions of the potential nuclear localization signal (NLS), the AP2 domain and the acidic region of the 24 kDa polypeptide. Numbers indicate amino acid residues. FIG. 2D is a chart showing comparison of the AP2 domain of the 24 kDa polypeptide with that of the tobacco DNA binding protein EREBP2 (Okme-Takagi, M., et al., The Plant Cell 7:173-182 (1995) SEQ ID NOS: 10 and 11). Identical amino acids are indicated with single lines; similar amino acids are indicated by double dots; amino acids that are invariant in AP2 domains are indicated with asterisks (Klucher, K. M., et al., The Plant Cell 8:137-153 (1996)); and the histidine residues present in CBF1 and TINY (Wilson, K., et al., The Plant Cell 8:659-671 (1996)) that are tyrosine residues in all other described AP2 domains are indicated with a caret. A single amino acid gap in the CBF1 sequence is indicated by a single dot.

[0282] Our expectation was that the cDNA insert in pACT-11 would have a C-repeat/DRE binding domain fused to the yeast GAL4-ACT sequence. However, DNA sequence analysis indicated that an open reading frame of only nine amino acids had been added to the C-terminus of GAL4-ACT. It seemed highly unlikely that such a short amino acid sequence could comprise a DNA binding domain. Also surprising was the fact that about half of the cDNA insert in pACT-11 corresponded to 25s rRNA sequences (FIG. 2A). Further analysis, however, indicated that the insert had an open reading frame, in opposite orientation to the GAL4-ACT sequence, deduced to encode a 24 kDa polypeptide (FIGS. 2A-C). The polypeptide has a basic region that could potentially serve as a nuclear localization signal (Raikhel, N., Plant Physiol. 100:1627-1632 (1992)) and an acidic C-terminal half (pl of 3.6) that could potentially act as an acidic transcription activator domain (Hahn, S., Cell 72:481-483 (1993)). A search of the nucleic acid and protein sequence databases indicated that there was no previously described homology of the 24 kDa polypeptide. However, the polypeptide did have an AP2 domain (Jofuku, K. D., et al., The Plant Cell 6:1211-1225 (1994)) (FIGS. 2B, D), a DNA binding motif of about 60 amino acids (Ohme-Takagi, M., et al., The Plant Cell 7:173-182 (1994)) that is present in numerous plant proteins including the APETALA2 (Jofuku, K. D., et al., The Plant Cell 6:1211-1225 (1994)), AINTEGUMENTA (Klucher, K. M., et al., The Plant Cell 8:137-153 (1996); Elliot, R. C., et al., The Plant Cell 8:155-168 (1996)) and TINY (Wilson, K., et al., The Plant Cell 8:659-671 (1996)) proteins of Arabidopsis and the EREBPs (ethylene response element binding proteins) of tobacco (Ohme-Takagi, M., et al., The Plant Cell 7:173-182 (1995)).

[0283] E. 24 kDa Polypeptide Binds to the C-repeat/DRE and Activates Transcription in Yeast.

[0284] We hypothesized that the 24 kDa polypeptide was responsible for activating the lacZ reporter genes in yeast. To test this, the BclI-BglII fragment of pACT-11 containing the 24 kDa polypeptide, and the BglII-BglII fragment containing the 24 kDa polypeptide plus a small portion of the 25s rRNA sequence, was inserted into the yeast expression vector pDB20.1 FIG. 3 is a chart showing activation of reporter genes by the 24 kDa polypeptide. Restriction fragments of pACT-11 carrying the 24 kDa polypeptide (BclI-BglII) or the 24 kDa polypeptide plus a small amount of 25s RNA sequence (BglII-BglII) were inserted in both orientations into the yeast expression vector pDB20.1 (see FIGS. 2A and 2B for location of BclI and BglII restriction sites). These “expression constructs” were transformed into yeast strains carrying the lacZ reporter gene fused to direct repeat dimers of either the wild-type COR15a C-repeat/DRE (oligonucleotide MT50) or the mutant M2COR15a C-repeat/DRE (oligonucleotide MT80). The specific activity of beta-galactosidase (nmoles o-nitrophenol produced/min×mg protein−1) was determined from cultures grown in triplicate. Standard deviations are indicated. Abbreviations: pADC1, ADC1 promoter; tADC1, ADC1 terminator.

[0285] Plasmids containing either insert in the same orientation as the ADC1 promoter stimulated synthesis of beta-galactosidase when transformed into yeast strains carrying the lacZ reporter gene fused to a wild-type COR15a C-repeat/DRE (FIG. 3). The plasmids did not, however, stimulate synthesis of beta-galactosidase when transformed into yeast strains carrying lacZ fused to a mutant version of the COR15a C-repeat/DRE (FIG. 3). These data indicated that the 24 kDa polypeptide could bind to the wild-type C-repeat/DRE and activate expression for the lacZ reporter gene in yeast. Additional experiments indicated that the 24 kDa polypeptide could activate expression of the lacZ reporter gene fused to either a wild-type COR78 C-repeat/DRE (dimer of MT66) or a wild-type COR15b C-repeat/DRE (dimer of MT 68) (not shown). A plasmid containing the BclI-BglII fragment (which encodes only the 24 kDa polypeptide) cloned in opposite orientation to the ADC1 promoter did not stimulate synthesis of beta-galactosidase in reporter strains carrying the wild-type COR15a C-repeat/DRE fused to lacZ (FIG. 3). In contrast, a plasmid carrying the BglII-BglII fragment (containing the 24 kDa polypeptide plus some 25s rRNA sequences) cloned in opposite orientation to the ADC1 promoter produced significant levels of beta-galactosidase in reporter strains carrying the wild-type COR15a C-repeat/DRE (FIG. 3). Thus, a sequence located closely upstream of the 24 kDa polypeptide was able to serve as a cryptic promoter in yeast, a result that offered an explanation for how the 24 kDa polypeptide was expressed in the original pACT-11 clone.

[0286] F. Gel Shift Analysis Indicates that the 24 kDa Polypeptide Binds to the C-repeat/DRE.

[0287] Gel shift experiments were conducted to demonstrate further that the 24 kDa polypeptide bound to the C-repeat/DRE. Specifically, the open reading frame for the 24 kDa polypeptide was inserted into the pET-28a(+) bacterial expression vector (see Materials and Methods) and the resulting 28 kDa fusion protein was expressed at high levels in E. coli. (FIG. 4).

[0288]
FIG. 4 is a photograph of an electrophoresis gel showing expression of the recombinant 24 kDa polypeptide in E. coli. Shown are the results of SDS-PAGE analysis of protein extracts prepared from E. coli harboring either the expression vector alone (vector) or the vector plus an insert encoding the 24 kDa polypeptide in sense (sense insert) or antisense (antisense insert) orientation. The 28 kDa fusion protein (see Materials and Methods) is indicated by an arrow.

[0289]
FIG. 5 is a photograph of a gel for shift assays indicating that CBF1 binds to the C-repeat/DRE. The C-repeat/DRE probe (1 ng) used in all reactions was a 32P-labeled dimer of the oligonucleotide MT50 (wild type C-repeat/DRE from COR15a). The protein extracts used in the first four lanes were either bovine serum albumin (BSA) or the indicated CBF1 sense, antisense and vector extracts described in FIG. 4. The eight lanes on the right side of the figure used the CBF1 sense protein extract plus the indicated competitor C-repeat/DRE sequences (100 ng). The numbers 1×, 2× and 3× indicate whether the oligonucleotides were monomers, dimers or trimers, respectively, of the indicated C-repeat/DRE sequences.

[0290] Protein extracts prepared from E. coli expressing the recombinant protein produced a gel shift when a wild-type COR15a C-repeat/DRE was used as probe (FIG. 5). No shift was detected with BSA or E. coli extracts prepared from strains harboring the vector alone, or the vector with an antisense insert for the 24 kDa polypeptide. Oligonucleotides encoding wild-type C-repeat/DRE sequences from COR15a or COR78 competed effectively for binding to the COR15a C-repeat/DRE probe, but mutant version of the COR15a C-repeat/DRE did not (FIG. 5). These in vitro results corroborated the in vivo yeast expression studies indicating that the 24 kDa polypeptide binds to the C-repeat/DRE sequence. The 24 kDa polypeptide was thus designated CBF1 (C-repeat/DRE binding factor 1) and the gene encoding it named CBF1.

[0291] G. CBF1 is a Unique or Low Copy Number Gene.

[0292]
FIG. 6 is a photograph of a southern blot analysis indicating CBF1 is a unique or low copy number gene. Arabidopsis DNA (1 μg) was digested with the indicated restriction endonucleases and southern transfers were prepared and hybridized with a 32P-labeled probe encoding the entire CBF1 polypeptide.

[0293] The hybridization patterns observed in southern analysis of Arabidopsis DNA using the entire CBF1 gene as probe were relatively simple indicating that CBF1 is either a unique or low copy number gene (FIG. 6). The hybridization patterns obtained were not altered if only the 3′ end of the gene was used as the probe (the EcoRV/BglII restriction fragment from pACT-11 encoding the acidic region of CBF1, but not the AP2 domain) or if hybridization was carried out at low stringency (not shown).

[0294] H. CBF1 Transcript Level Response to Low Temperature.

[0295]
FIGS. 7A, 7B and 7C relate to CBF1 transcripts in control and cold-treated Arabidopsis. FIG. 7A is a photograph of a membrane RNA isolated from Arabidopsis plants that were grown at 22° C. or grown at 22° C. and transferred to 2.5° C. for the indicated times. FIGS. 7B and 7C are graphs showing relative transcript levels of CBF1 and COR15a in control and cold-treated plants. The radioactivity present in the samples described in FIG. 7A were quantified using a Betascope 603 blot analyzer and plotted as relative transcript levels (the values for the 22° C. grown plants being arbitrarily set as 1) after adjusting for differences in loading using the values obtained with the pHH25 probe.

[0296] Based on FIGS. 7A-7C, northern analysis indicated that the level of CBF1 transcripts increased about 2 to 3 fold in response to low temperature (FIG. 7B). In contrast, the transcript levels for COR15a increased approximately 35 fold in cold-treated plants (FIG. 7C). Only a singly hybridizing band was observed for CBF1 at either high or low stringency with probes for either the entire CBF1 coding sequence or the 3′ end of the gene (the EcoRV/BglII fragment of pACT-1 1) (not shown). The size of the CBF1 transcripts was about 1.0 kb.

[0297] I. Discussion of Experimental Results.

[0298] The above example regarding CBF1 represents the first identification of a gene sequence which encodes a protein capable of binding to the C-repeat/DRE sequence CCGAC. The experimental results presented evidence that CBF1 binds to the C-repeat/DRE both in vitro via gel shift assays and in vivo via yeast expression assays. Further, the results demonstrate that CBF1 can activate transcription of reporter genes in yeast that contain the C-repeat/DRE.

[0299] The results of the southern analysis indicate that CBF1 is a unique or low copy number gene in Arabidopsis. However, the CBF1 protein contains a 60 amino acid motif, the AP2 domain, that is evolutionary conserved in plants (Weigel, D., The plant Cell 7:388-389 (1995)). It is present in the APETALA2 (Jofuku, K. D., et al., The Plant Cell 6:1211-1225 (1994)), AINTEGUMENTA (Klucher, K. M., et al., the Plant Cell 8:137-153 (1996; and Elliot, R. C., et al., The Plant Cell 8:155-168 (1996)), TINY (Wilson, K., et al., The Plant Cell 8:659-671 (1996)) and cadmium-induced (Choi, S. -Y., et al., Plant Physiol. 108:849 (1995)) proteins of Arabidopsis and the EREBPs of tobacco (Ohme-Takagi, M. et al., The Plant Cell 7:173-182 (1995)). In addition, a search of the GenBank expressed sequence tagged cDNA database indicates that there is one cDNA from B. napus, two from Ricinus communes, and more than 25 from Arabidopsis and from rice, that are deduced to encode proteins with AP2 domains. The results of Ohme-Takagi and Shinshi (Ohme-Takagi, M., et al., The Plant Cell 7:173-182 (1995)) indicate that the function of the AP2 domain is DNA-binding; this region of the putative tobacco transcription factor EREBP2 is responsible for its binding to the cis-acting ethylene response element referred to as the GCC-repeat. As discussed by Ohme-Takagi and Shinshi (Ohme-Takagi, M., et al., the Plant Cell 7:173-182 (1995)), the DNA-binding domain of EREBP2 (the AP2 domain) contains no significant amino acid sequence similarities or obvious structural similarities with other known transcription factors or DNA binding motifs. Thus, the domain appears to be a novel DNA-binding motif that to date, has only been found in plant proteins.

[0300] It is believed that the binding of CBF1 to the C-repeat/DRE involves the AP2 domain. In this regard, it is germane to note that the tobacco ethylene response element, AGCCGCC, closely resembles the C-repeat/DRE sequences present in the promoters of the Arabidopsis genes COR15a, GGCCGAC, and COR781RD29A, TACCGAC. Applicants believe that CBF1, the EREBPs and other AP2 domain proteins are members of a superfamily of DNA binding proteins that recognize a family of cis-acting regulatory elements having CCG as a common core sequence. Differences in the sequence surrounding the CCG core element could result in recruitment of different AP2 domain proteins which, in turn, could be integrated into signal transduction pathways activated by different environmental, hormonal and developmental cues. Such a scenario is akin to the situation that exists for the ACGT-family of cis-acting elements (Foster et al., FASEB J. 8:192-200 (1994)). In this case, differences in the sequence surrounding the ACGT core element result in the recruitment of different bZIP transcription factors involved in activating transcription in response to a variety of environmental and developmental signals.

[0301] The results of the yeast transformation experiments indicate that CBF1 has a domain that can serve as a transcriptional activator. The most likely candidate for this domain is the acidic C-terminal half of the polypeptide. Indeed, random acidic amino acid peptides from E. coli have been shown to substitute for the GAL4 acidic activator domain of GAL4 in yeast (Ma, J. and M. Ptashne, Cell 51:113-199 (1987)). Moreover, acidic activator domains have been found to function across kingdoms (Hahn, S., Cell 72:481-483 (1993)); the yeast GAL4 acidic activator, for instance, can activate transcription in tobacco (Ma, J., et al., Nature 334:631-633 (1988)). It has also been shown that certain plant transcription factors, such as Vp1 (McCarty, D. R., et al., Cell 66:895-905 (1991)), have acidic domains that function as transcriptional activators in plants. Significantly, the acidic activation domains of the yeast transcription factors VP16 and GCN4 require the “adaptor” proteins ADA2, ADA3, and GCN5 for full activity (see Guarente, L., Trends Biochem. Sci. 20:517-521 (1995)). These proteins form a heteromeric complex (Horiuchi, J., et al., Mol. Cell Biol. 15:1203-1209 (1995)) that bind to the relevant activation domains. The precise mechanism of transcriptional activation is not known, but appears to involve histone acetylation: there is a wealth of evidence showing a positive correlation between histone acetylation and the transcriptional activity of chromatin (Wolffe, A. P., Trends Biochem. Sci. 19:240-244 (1994)) and recently, the GCN5 protein has been shown to have histone acetyltransferase activity (Brownell, J. E., et al., Cell 84:843-851 (1996)). Genetic studies indicate that CBF1, like VP16 and GCN4, requires ADA2, ADA3 and GCN5 to function optimally in yeast. The fundamental question thus raised is whether plants have homologs of ADA2, ADA3 and GCN5 and whether these adaptors are required for CBF1 function (and function of other transcription factors with acidic activator regions) in Arabidopsis.

[0302] A final point regards regulation of CBF1 activity. The results of the northern analysis indicate that CBF1 transcript levels increase only slightly in response to low temperature, while those for COR15a increase dramatically (FIG. 7). Thus, unlike in yeast, it would appear that transcription of CBF1 in Arabidopsis at warm temperatures is not sufficient to cause appreciable activation of promoters containing the C-repeat/DRE. The molecular basis for this apparent low temperature activation of CBF1 in Arabidopsis is not known. One intriguing possibility, however is that CBF1 might be modified at low temperature in Arabidopsis resulting in either stabilization of the protein, translocation of the protein from the cytoplasm to the nucleus, or activation of either the DNA binding domain or activation domain of the protein. Such modification could involve a signal transduction pathway that is activated by low temperature. Indeed, as already discussed, cold-regulated expression of COR genes in Arabidopsis and alfalfa appears to involve a signal transduction pathway that is activated by low temperature-induced calcium flux (Knight, H., et al., The Plant Cell 8:489-503 (1996); Knight, M. R., et al., Nature 352:524-526 (1991); Monroy, A. F., et al, Plant Physiol. 102:1227-1235 (1993); Monroy, A. F., and R. S., The Plant Cell, 7:321-331 (1995)). It will, therefore, be of interest to determine whether CBF1 is modified at low temperature, perhaps by phosphorylation, and if so, whether this is dependent on calcium-activated signal transduction.

[0303] 2. Use of CBF1 to Induce Cold Regulated Gene Expression in Nonacclimated Arabidopsis Plants.

[0304] The following example demonstrates that increased expression of CBF1 induces COR gene expression in nonacclimated Arabidopsis plants. Transgenic Arabidopsis plants that overexpress CBF1 were created by placing a cDNA encoding CBF1 under the control of the strong cauliflower mosaic virus (CaMV) 35S promoter and transforming the chimeric gene into Arabidopsis ecotype RLD plants (Standard procedures were used for plasmid manipulations (J. Sambrook, et al., Molecular Cloning, A Laboratory Manual (Cold Spring Harbor Laboratory Press, Cold Spring Harbor, ed. 2, (1989)). The CBF1-containing AseI-BglII fragment from pACT-Bgl+(Stockinger, E. J., et al., Proc. Natl. Acad. Sci. U.S.A. 94:1035 (1997)) was gel-purified, BamHI linkers were ligated to both ends and the fragment was inserted into the BamHI site in pCIB710 (S. Rothstein, et al., Gene 53:153-161 (1987)) which contains the CaMV 35S promoter and terminator. The chimeric plasmid was linearized at the KpnI site and inserted into the KpnI site of the binary vector pCIB10g (Ciba-Geigy, Research Triangle Park, N.C.). The plasmid was transformed into Agrobacterium tumefaciens strain C58C1 (pMP90) by electroporation. Arabidopsis plants were transformed by the vacuum infiltration procedure (N. Bechtold, J. Ellis, and G. Pelletier, C. R. Acad. Sci. Paris, Life Sci. 316:1194-1199 (1993)) as modified (A. van Hoof, P. J. Green, Plant Journal 10:415-424 (1996)). Initial screening gave rise to two transgenic lines, A6 and B16, that accumulated CBF1 transcripts at elevated levels.

[0305]
FIG. 8 is a Northern blot showing CBF1 and COR transcript levels in RLD and transgenic Arabidopsis plants. Leaves from nonacclimated and three-day cold-acclimated plants (Arabidopsis thaliana ecotype RLD plants were grown in pots under continuous light (100 μE/m2/sec) at 22 C for 18-25 days as described (Gilmour, S. J., et al., Plant Physiol. 87:735 (1988)). In some cases, plants were then cold-acclimated by placing them at 2.5° C. under continuous light (50 μE/m2/sec) for varying amounts of time. Leaves were harvested and total RNA prepared and analyzed for CBF1 and COR transcripts by RNA blot analysis using 32P-radiolabeled probes (Total RNA was isolated from plant leaves and subjected to RNA blot analysis using high stringency hybridization and wash conditions as described (E. J. Stockinger, et al., Proc. Natl. Acad. Sci. USA 94:1035 (1997); and S. J. Gilmour, et al., Plant Physiol. 87:735 (1988)).

[0306]
FIG. 9 is an immunoblot showing COR15am protein levels in RLD and transgenic Arabidopsis plants. Total soluble protein (100 μg) was prepared from leaves of the nonacclimated RLD (RLDw), 4-day cold-acclimated RLD (RLDc4), 7-day cold-acclimated RLD (RLDc7) and nonacclimated A6 and B16 plants and the levels of COR15am determined by immunoblot analysis using antiserum raised against the COR15am polypeptide (Total soluble protein was isolated from plant leaves, fractionated by tricine SDS-PAGE and transferred to 0.2 micron nitrocellulose as previously described (N. N. Artus et al., Proc. Natl. Acad. Sci. U.S.A. 93:13404 (1996)). COR15am protein was detected using antiserum raised to purified COR15am and protein A conjugated alkaline phosphatase (Sigma, St. Louis, Mo.) (N. N. Artus et al., Proc. Natl. Acad. Sci. U.S.A. 93:13404 (1996)). No reacting bands were observed with preimmune serum (not shown).

[0307] Southern analysis indicated that the A6 line had a single DNA insert while the B16 line had multiple inserts (not shown). Examination of fourth generation homozygous A6 and B16 plants indicated that CBF1 transcript levels were higher in nonacclimated A6 and B16 plants than they were in nonacclimated RLD plants, the levels in A6 being about three fold higher than in B16 (FIG. 8).

[0308] CBF1 overexpression resulted in strong induction of COR gene expression (FIG. 8). Specifically, the transcript levels of COR6.6, COR15a, COR47 and COR78 were dramatically elevated in nonacclimated A6 and B16 plants as compared to nonacclimated RLD plants. The effect was greater in the A6 line, where COR transcript levels in nonacclimated plants approximated those found in cold-acclimated RLD plants. The finding that COR gene expression was greater in A6 plants than in B16 plants was consistent with CBF1 transcript levels being higher in the A6 plants (FIG. 7A). Immunoblot analysis indicated that the levels of the COR15am (FIG. 9) and COR6.6 (not shown) polypeptides were also elevated in the A6 and B16 lines, the level of expression again being higher in the A6 line. Attempts to identify the CBF1 protein in either RLD or transgenic plants were unsuccessful. Overexpression of CBF1 had no effect on the transcript levels for elF4A (eukaryotic initiation factor 4A) (Metz, A. M., et al., Gene 120:313 (1992)), a constitutively expressed gene that is not responsive to low temperature (FIG. 8) and had no obvious effects on plant growth and development.

[0309] The results from this example demonstrate that overexpression of the Arabidopsis transcriptional activator CBF1 induces expression of an Arabidopsis COR “regulon” composed of genes carrying the CRT/DRE DNA regulatory element. It appears that CBF1 binds to the CRT/DRE DNA regulatory elements present in the promoters of these genes and activates transcription which is consistent with the notion of CBF1 having a role in COR gene regulation. Significantly, there was a strong correlation between CBF1 transcript levels and the magnitude of COR gene induction in nonacclimated A6, B16, and RLD plants (FIG. 8). However, upon low temperature treatment the level of CBF1 transcripts remained relatively low in RLD plants, while COR gene expression was induced to about the same level as that in nonacclimated A6 plants (FIG. 8). Thus, it appears that CBF1 or an associated protein becomes “activated” in response to low temperature.

[0310] 3. CBF1 Overexpression Resulted in a Marked Increase in Plant Freezing Tolerance

[0311] The following example describes a comparison of the freezing tolerance of nonacclimated Arabidopsis plants which overexpress CBF1 to that of cold-acclimated wild-type plants. As described below, the freezing tolerance of nonacclimated Arabidopsis plants overexpressing CBF1 significantly exceeded that of non-acclimated wild-type Arabidopsis plants and approached that of cold-acclimated wild-type plants.

[0312] Freezing tolerance was determined using the electrolyte leakage test (Sukumaran, N. P., et al., HortScience 7:467 (1972)). Detached leaves were frozen to various subzero temperatures and, after thawing, cellular damage (due to freeze-induced membrane lesions) was estimated by measuring ion leakage from the tissues.

[0313]
FIGS. 10A and 10B are graphs showing freezing tolerance of leaves from RLD and transgenic Arabidopsis plants. Leaves from nonacclimated RLD (RLDw) plants, cold-acclimated RLD (RLDc) plants and nonacclimated A6, B16 and T8 plants were frozen at the indicated temperatures and the extent of cellular damage was estimated by measuring electrolyte leakage (Electrolyte leakage tests were conducted as described (N. P. Sukumaran, et al., HortScience 7, 467 (1972); and S. J. Gilmour, et al., Plant Physiol. 87:735 (1988)) with the following modifications. Detached leaves (2-4) from nonacclimated or cold-acclimated plants were placed in a test tube and submerged for 1 hour in a −2° C. water-ethylene glycol bath in a completely randomized design, after which ice crystals were added to nucleate freezing. After an additional hour of incubation at −2° C., the samples were cooled in decrements of 1° C. each hour until −8° C. was reached. Samples (five replicates for each data point) were thawed overnight on ice and incubated in 3 ml distilled water with shaking at room temperature for 3 hours. Electrolyte leakage from leaves was measured with a conductivity meter. The solution was then removed, the leaves frozen at −80° C. (for at least one hour), and the solution returned to each tube and incubated for 3 hours to obtain a value for 100% electrolyte leakage. In FIGS. 10A and 10B, the RLDc plants were cold-acclimated for 10 and 11 days, respectively. Error bars indicate standard deviations.

[0314] As can be seen from FIGS. 10A and 10B, CBF1 overexpression resulted in a marked increase in plant freezing tolerance. The experiment presented in FIG. 10A indicates that the leaves from both nonacclimated A6 and B16 plants were more freezing tolerant than those from nonacclimated RLD plants. Indeed, the freezing tolerance of leaves from nonacclimated A6 plants approached that of leaves from cold-acclimated RLD plants. The results also indicate that the leaves from nonacclimated A6 plants were more freezing tolerant than those from nonacclimated B16 plants, a result that is consistent with the greater level of CBF1 and COR gene expression in the A6 line.

[0315] The results presented in FIG. 10B further demonstrate that the freezing tolerance of leaves from nonacclimated A6 plants was greater than that of leaves from nonacclimated RLD plants and that it approached the freezing tolerance of leaves from cold-acclimated RLD plants. In addition, the results indicate that overexpression of CBF1 increases freezing tolerance to a much greater extent than overexpressing COR15a alone. This conclusion comes from comparing the freezing tolerance of leaves from nonacclimated A6 and T8 plants (FIG. 10B). T8 plants (Artus, N. N., et al., Proc. Natl. Acad. Sci. U.S.A. 93:13404 (1996)) are from a transgenic line that constitutively expresses COR15a (under control of the CaMV 35S promoter) at about the same level as in A6 plants (FIG. 1). However, unlike in A6 plants, other CRT/DRE-regulated COR genes are not constitutively expressed in T8 plants (FIG. 8).

[0316] A comparison of EL50 values (the freezing temperature that results in release of 50% of M tissue electrolytes) of leaves from RLD, A6, B16 and T8 plants is presented in Table 2.

[0317] EL50 values were calculated and compared by analysis of variance curves fitting up to third order linear polynomial trends were determined for each electrolyte leakage experiment. To insure unbiased predictions of electrolyte leakage, trends significantly improving the model fit at the 0.2 probability level were retained. EL50 values were calculated from the fitted models. In Table 2, an unbalanced one-way analysis of variance, adjusted for the different numbers of EL50 values for each plant type, was determined using SAS PROC GLM [SAS Institute, Inc. (1989), SASISTAT User's Guide, Version 6, Cory, NC)]. EL50 values±SE (n) are presented on the diagonal line for leaves from nonacclimated RLD (RLDw), cold-acclimated (7 to 10 days) RLD (RLDc) and nonacclimated A6, B16 and T8 plants. P values for comparisons of EL50 values are indicated in the intersecting cells.

2TABLE 2EL50 valuesRLDwRLDcA6B16T8RLDw−3.9 ±P <P < 0.0001P = 0.0014P = 0.74060.21 (8)0.0001RLDc−7.6 ±P = 0.3261P < 0.0001P < 0.00010.30 (4)A6−7.2 ± 0.25P < 0.0001P < 0.0001(6)B16−5.2 ± 0.27P = 0.0044(5)T8−3.8 ± 0.35(3)

[0318] The data confirm that: 1) the freezing tolerance of leaves from both nonacclimated A6 and B16 plants is greater than that of leaves from both nonacclimated RLD and T8 plants; and 2) that leaves from nonacclimated A6 plants are more freezing tolerant than leaves from nonacclimated B16 plants. No significant difference was detected in EL50 values for leaves from nonacclimated A6 and cold-acclimated RLD plants or from nonacclimated RLD and T8 plants.

[0319] The enhancement of freezing tolerance in the A6 line was also apparent at the whole plant level. FIG. 11 is a photograph showing freezing survival of RLD and A6 Arabidopsis plants. Nonacclimated (WARM) RLD and A6 plants and 5-day cold-acclimated (COLD) RLD plants were frozen at −5° C. for 2 days and then returned to a growth chamber at 22° C. (Pots (3.5 inch) containing about 40 nonacclimated Arabidopsis plants (20 day old) and 4 day cold-acclimated plants (25 days old) (Arabidopsis thaliana ecotype RLD plants were grown in pots under continuous light (100 μE/m2/sec) at 22° C. for 18-25 days as described (S. J. Gilmour, et al., Plant Physiol. 87:735 (1988)). In some cases, plants were then cold-acclimated by placing them at 2.5° C. under continuous light (50 μE/m2/sec) for varying amounts of time) were placed in a completely randomized design in a −5° C. cold chamber in the dark. After 1 hour, ice chips were added to each pot to nucleate freezing. Plants were removed after 2 days and returned to a growth chamber at 22° C.). A photograph of the plants after 7 days of regrowth is shown.

[0320] Although the magnitude of the difference varied from experiment to experiment, nonacclimated A6 plants consistently displayed greater freezing tolerance in whole plant freeze tests than did nonacclimated RLD plants (FIG. 11). No difference in whole plant freeze survival was detected between nonacclimated B16 and RLD plants or nonacclimated T8 and RLD plants (not shown).

[0321] The results of this experiment show that CBF1-induced expression of CRT/DRE-regulated COR genes result in a dramatic increase in freezing tolerance and confirms the belief that COR genes play a major role in plant cold acclimation. The increase in freezing tolerance brought about by expressing the battery of CRT/DRE-regulated COR genes was much greater than that brought about by overexpressing COR15a alone indicating that COR genes in addition to COR15a have roles in freezing tolerance.

[0322] Traditional plant breeding approaches have met with limited success in improving the freezing tolerance of agronomic plants (Thomashow, M. F., Adv. Genet 28:99 (1990)). For instance, the freezing tolerance of the best wheat varieties today is essentially the same as the most freezing-tolerance varieties developed in the early part of this century. Thus, in recent years there has been considerable interest that biotechnology might offer new strategies to improve the freezing tolerance of agronomic plants. By the results of the present invention, Applicants demonstrate the ability to enhance the freezing tolerance of nonacclimated Arabidopsis plants by increasing the expressing of the Arabidopsis regulatory gene CBF1. As described throughout this application, the ability of the present invention to modify the expression of environmental stress tolerance genes such as core genes has wide ranging implications since the CRT/DRE DNA regulatory element is not limited to Arabidopsis (Jiang C., et al., Plant Mol. Biol. 30:679 (1996)). Rather, CBF1 and homologous genes can be used to manipulate expression of CRT/DRE-regulated COR genes in important crop species and thereby improve their freezing tolerance. By transforming modified versions of CBF1 (or homologs) into such plants, it will extend their safe growing season, increase yield and expand areas of production.

[0323] 4. Selection of Promoters to Control Expression of CBF1 in Plants

[0324] The following examples describe the isolation of different promoters from plant genomic DNA, construction of the plasmid vectors carrying the CBF1 gene and the inducible promoters, transformation of Arabidoposis cells/plants with these constructs, and regeneration of transgenic plants with increased tolerance to environmental stresses.

[0325] A. Isolation of Inducible Promoters from Plant Genomic DNAs

[0326] Inducible promoters from different plant genomic DNAs were identified and isolated by PCR amplification using primers designed to flank the promoter region and contain suitable restriction sites for cloning into the expression vector. The following genes were used to BLAST search Genbank to find the inducible promoters: Dreb2a; P5CS; Rd22; Rd29a; Rd29b; Rab18; Cor47. Table 3 lists the accession numbers and positions of these promoters. Table 4 lists the forward and reverse primers that were used to isolate the promoters.

3TABLE 3Gene NameAccession No.PositionLength (bps)Dreb2aAB01069251901-539552054P5CSAC00300045472-474601988Rd22D10703 17-10461029Rd29aD130443870-55111641Rd29bD13044 90-17851695Rab18AB0133898070-97571687Cor47AB004872 1-13701370

[0327]

4

TABLE 4

Promoter

name
Primer name
Cloning sites
SEQ. ID. No.

Dreb2a
Dreb2a-reverse
HindIII (AAGCTT)
19

Dreb2a-forward
BgIII (AGATCT)
20

P5CS
P5CS-reverse
HindIII (AAGCTT)
21

P5CS-forward
BgIII (AGATCT)
22

Rd22
Rd22-reverse
HindIII (AAGCTT)
23

Rd22-forward
KpnI (GGTACC)
24

Rd29a
Rd29a-reverse
HindIII (AAGCTT)
25

Rd29a-forward
KpnI (GGTACC)
26

Rd29b
Rd29b-reverse
HindIII (AAGCTT)
27

Rd29b-forward
KpnI (GGTACC)
28

Rab18
Rab18-reverse
HindIII (AAGCTT)
29

Rab18-forward
BgIII (AGATCT)
30

Cor47
Cor47-reverse
HindIII (AAGCTT)
31

Cor47-forward
BgIII (AGATCT)
32

[0328] (1) Dreb2a Promoter

[0329] A cDNA encoding DRE (C-repeat) binding protein (DREB2A) has been recently identified (Liu, et al. 1998 Plant Cell 10:1391-1406). The transcription of the DREB2A gene is activated by dehydration and high-salt stress, but not by cold stress. The upstream untranslated region (166 bps) of dreb2a was used to BLAST-search the public database. A region containing the DREB2A promoter was identified in chromosome 5 of Arabidopsis (Accession No. AB010692) between nucleotide positions 51901-53955 (Table 3).

[0330] Two PCR primers designed to amplify the promoter region from Arabidopsis thaliana genomic DNA are as follows: dreb2a-reverse: 5′-GCCCAAGCTTCAAGTTTAGTGAGCACTATGTGCTCG-3′ [SEQ ID No. 19]; and dreb2a-forward: 5′-GGAAGATCTCCTTCCCAGAAACAACACMTCTAC-3′ [SEQ. ID. No. 20]. The dre2ba-reverse primer includes a Hind III (AAGCTT) restriction site near the 5′-end of the primer and dreb2a-forward primer has a Bgl II (AGATCT) restriction site at near 5′-end of the primer. These restriction sites may be used to facilitate cloning of the fragment into an expression vector.

[0331] Total genomic DNA may be isolated from Arabidopsis thaliana (ecotype colombia) by using the CTAB method (Ausubel et al. (1992) Current Protocols in Molecular Biology (Greene & Wiley, New York)). Ten nanograms of the genomic DNA can be used as a template in a PCR reaction under conditions suggested by the manufacturer (Boehringer Mannheim). The reaction conditions that may be used in this PCR experiment are as follows: Segment 1: 94° C., 2 minutes; Segment 2: 94° C., 30 seconds; 60° C., 1 minute; 72° C., 3 minutes, for a total of 35 cycles; Segment 3: 72° C. for 10 minutes. A PCR product of 2054 bp is expected.

[0332] The PCR products can be subject to electrophoresis in a 0.8% agarose gel and visualized by ethidium bromide staining. The DNA fragments containing the inducible promoter will be excised and purified using a Qiaquick gel extraction kit (Qiagen, Calif.).

[0333] (2) P5CS Promoter

[0334] A cDNA for delta 1-pyrroline-5-carboxylate synthetase (P5CS) has been isolated and characterized (Yoshiba, et al., 1995, Plant J. 7:751-760). The cDNA encodes an enzyme involved in the biosynthesis of proline under osmotic stress (drought/high salinity). The transcription of the P5CS gene was found to be induced by dehydration, high salt and treatment with plant hormone ABA, while it did not respond to heat or cold treatment.

[0335] A genomic DNA containing a promoter region of P5CS was identified by a BLAST search of Genbank using the upstream untranslated region (106 bps) of the P5CS sequence (Accession No. D32138). The sequence for the P5CS promoter is located in the region between from nucleotide positions 45472 to 47460 (Accession No. AC003000; Table 3).

[0336] Reverse and forward PCR primers designed to amplify this promoter region from Arabidopsis thaliana genomic DNA are P5CS-reverse primer 5′-GCCCAAGCTTGTTTCATTTTCTCCATGAAGGAGAT-3′ [SEQ. ID. No. 21]; and P5CS-forward primer 5′-GGAAGATCTTATCGTCGTCGTCGTCTACCAAAACCACAC-3′ [SEQ. ID. No. 22].

[0337] Total genomic DNA may be isolated from Arabidopsis thaliana (ecotype colombia) by using the CTAB method (Ausubel et al. (1992) Current Protocols in Molecular Biology (Greene & Wiley, New York)). Ten nanograms of the genomic DNA can be used as a template in a PCR reaction under conditions suggested by the manufacturer (Boehringer Mannheim). The PCR product is expected to be 1988 bps and may be PCR amplified and gel purified following the same protocol described for the dreb2a promoter.

[0338] (3) rd22Promoter

[0339] A cDNA clone of rd22 was isolated from Arabidopsis under dehydration conditions (Yamaguchi-Shinozaki and Shinozaki, Mol. Gen. Genet. 238:17-25 (1993)). Transcripts of rd22 were found to be induced by salt stress, water deficit and endogenous abscisic acid (ABA) but not by cold or heat stress. A promoter region was identified from Genebank by using Nucleotide Search WWW Entrez at the NCBI with the rd22 as a search word. The sequence for the rd22 promoter is located in the region between nucleotide positions 17 to 1046 (Accession No. D10703; Table 3).

[0340] Reverse and forward PCR primers designed to amplify this promoter region from Arabidopsis thaliana genomic DNA are rd22-reverse primer 5′-GCTCTAAGCTTCACAAGGGGTTCGTTTGGTGC-3′ [SEQ. ID. No. 23]; and rd22-forward T primer 5′-GGGGTACCTTTTGGGAGTTGGMTAGAAATGGGTTTGATG-3′ [SEQ. ID. No. 24].

[0341] The rd22-reverse primer includes a Hind III (AAGCTT ) restriction site near the 5′-end of primer and rd22-forward primer has a Kpnl (GGTACC) restriction site at near 5′-end of primer.

[0342] Total genomic DNA may be isolated from Arabidopsis thaliana (ecotype colombia) by using the CTAB method (Ausubel et al. (1992) Current Protocols in Molecular Biology (Greene & Wiley, New York)). Ten nanograms of the genomic DNA can be used as a template in a PCR reaction under conditions suggested by the manufacturer (Boehringer Mannheim). The PCR product is expected to be 1029 bps and may be PCR amplified and gel purified following the same protocol described for the dreb2a promoter.

[0343] (4) rd29a Promoter

[0344] The rd29a and rb29b genes were isolated and characterized by Shinozaki's group in Japan (Yamaguchi-Shinizaki and Shinozaki, Plant Physiol. 101: 1119-1120 (1993)). Both rd29a and rb29b gene expressions were found to be induced by desiccation, salt stress and exogenous ABA treatment (Yamaguchi-Shinizaki and Shinozaki, Plant Physiol. 101: 1119-1120 (1993); Ishitani et al., Plant Cell 10: 1151-1161 (1998)). The rd29a gene expression was induced within 20 min after desiccation, but rd29b mRNA did not accumulate to a detectable level until 3 hours after desiccation. Expression of rd29a could also be induced by cold stress, whereas expression of rd29b could not be induced by low temperature.

[0345] A genomic clone carrying the rd29a promoter was identified by using Nucleotide Search WWW Entrez at the NCBI with the rd29a as a search word. The sequence for the rd29a promoter is located in the region between nucleotide positions 3870 to 5511 (Accession No. D13044, Table 3).

[0346] Reverse and forward primers designed to amplify this promoter region from Arabidopsis genomic DNA are: rd29a-reverse primer 5′-GCCCAAGCTTAATTTTACTCAAAATGTTTTGGTTGC-3′ [SEQ. ID. No. 25]; and rd29a-forward primer 5′-CCGGTACCTTTCCAAAGATTTTTTTCTTTCCAATAGMGTAATC-3′ [SEQ. ID. No.26]. The rd29a-reverse primer includes a Hind Ill (AAGCTT) restriction site near the 5′-end of primer and rd29a-forward primer has a Kpnl (GGTACC) restriction site near 5′-end of primer.

[0347] Total genomic DNA may be isolated from Arabidopsis thaliana (ecotype colombia) by using the CTAB method (Ausubel et al. (1992) Current Protocols in Molecular Biology (Greene & Wiley, New York)). Ten nanograms of the genomic DNA can be used as a template in a PCR reaction under conditions suggested by the manufacturer (Boehringer Mannheim). The PCR product is expected to be 1641 bps and may be PCR amplified and gel purified following the same protocol described for the dreb2a promoter.

[0348] (5) rd29b Promoter

[0349] A genomic clone carrying the rd29b promoter was identified by using Nucleotide Search WWW Entrez at the NCBI with the rd29b as a search word. The sequence for the rd29a promoter was located in the region between nucleotide positions 90 to 1785 for rd29b (Accession No. D13044; Table 3).

[0350] Reverse and forward PCR primers designed to amplify this promoter region from Arabidopsis thaliana genomic DNA are: rd29b-reverse primer 5′-GCGGAAGCTTCATTTTCTGCTACAGAAGTG-3′ [SEQ. ID. No. 27]; and rd29b-forward primer 5′-CCGGTACCTTTCCAAAGCTGTGTTTTCTCTTTTTCAAGTG-3′ [SEQ. ID. No. 28].

[0351] Total genomic DNA may be isolated from Arabidopsis thaliana (ecotype colombia) by using the CTAB method (Ausubel et al. (1992) Current Protocols in Molecular Biology (Greene & Wiley, New York)). Ten nanograms of the genomic DNA can be used as a template in a PCR reaction under conditions suggested by the manufacturer (Boehringer Mannheim). The PCR product is expected to be 1695 bps and may be PCR amplified and gel purified following the same protocol described for the dreb2a promoter.

[0352] (6) rab18 Promoter

[0353] A rab-related (responsive to ABA) gene, rab18 from arabidopsis has been isolated. The gene encodes a hydrophilic, glycine-rich protein with the conserved serine- and lysine-rich domains. The rab18 transcripts accumulate in plants exposed to water deficit or exogenous abscisic acid (ABA) treatment. A weak induction of rab18 mRNA by low temperature was also observed (Ishitani et al., Plant Cell 10: 1151-1161 (1998)).

[0354] A genomic DNA containing a promoter region of rab18 was identified by a BLAST search of Genbank using the upstream untranslated region (757 bps) of the rab18 sequence (Accession No. L04173). The sequence of the rab18 promoter is located in the region between nucleotide positions 8070 to 9757 (Accession No. AB013389).

[0355] Reverse and forward PCR primers designed and used to amplify this promoter region from Arabidopsis thaliana genomic DNA are: rab18-reverse primer 5′-GCCCAAGCTTCAAATTCTGMTATTCACATATCAAAAAGTG-3′ [SEQ. ID. No. 29]; and rab18-forward primer 5′-GGAAGATCTGTTCTTCTTGTCTTAAGCAAACACTTTGAGC-3′ [SEQ. ID. No. 30]. The rab18-reverse primer includes a Hind III (AAGCTT) restriction site near the 5′-end of the primer and rab18-forward primer has a Bgl II (AGATCT) restriction site near the 5′-end of the primer.

[0356] Total genomic DNA may be isolated from Arabidopsis thaliana (ecotype colombia) by using the CTAB method (Ausubel et al. (1992) Current Protocols in Molecular Biology (Greene & Wiley, New York)). Ten nanograms of the genomic DNA can be used as a template in a PCR reaction under conditions suggested by the manufacturer (Boehringer Mannheim). The PCR product is expected to be 1687 bps and may be PCR amplified and gel purified following the same protocol described for the dreb2a promoter.

[0357] (7) Cor47 Promoter

[0358] The DNA sequence of cDNA for cold-regulated (cor47) gene of Arabidopsis thaliana was determined. Gilmour et al., Plant Molecular Biology 18: 13-21 (1992)). Expression of cor47 gene was induced by cold stress, dehydration and high NaCl treatment (Ishitani et al., Plant Cell, 10: 1151-1161 (1998)). The promoter region of cor47 gene was identified in Genbank by using Nucleotide Search WWW Entrez at the NCBI with the cor47 as a search word. The sequence of the cor47 promoter is located in the region between nucleotide positions 1-1370 (Accession No. AB004872; Table 3).

[0359] Reverse and forward PCR primers designed to amplify this promoter region from Arabidopsis thaliana genomic DNA are: cor47-reverse primer 5′-GCCCAAGCTTTCGTCTGTTATCATACMGGCACAAAACGAC-3′ [SEQ. ID. No. 31]; and cor47-forward primer 5′-GGAAGATCTAGTTMTCTTGATTTGATTAAAAGTTTATATAG-3′ [SEQ. ID. No. 32]. The cor47-reverse primer includes a Hind III (AAGCTT) restriction site near the 5′-end of the primer and cor47-forward primer has a Bgl II (AGATCT) restriction site near the 5′-end of the primer.

[0360] Total genomic DNA may be isolated from Arabidopsis thaliana (ecotype Colombia) by using the CTAB method (Ausubel et al. (1992) Current Protocols in Molecular Biology (Greene & Wiley, New York)). Ten nanograms of the genomic DNA can be used as a template in a PCR reaction under conditions suggested by the manufacturer (Boehringer Mannheim). The PCR product is expected to be 1370 bps and may be PCR amplified and gel purified following the same protocol described for the dreb2a promoter.

[0361] B. Construction of the Plamids Containing CBF1 and Inducible Promoter

[0362] The expression binary vector pMEN020 contains a kanamycin resistance gene (neomycin phosphotransferase) for antibiotic selection of the transgenic plants and a Spc/Str gene used for bacterial or agrobacterial selections. The pMEN020 plasmid is digested with restriction enzymes such as HindIII and BgIII to remove the 35S promoter. The 35S promoter is then replaced with an inducible promoter.

[0363] (1) Cloning of the Inducible Promoter into pMEN020

[0364] The sequences of the inducible promoters that are PCR amplified and gel purified, as well as the plasmid pMEN020, are subject to restriction digestion with their respective restriction enzymes as listed in Table 4. Both DNA samples are purified by using the Qiaquick purification kit (Qiagen, Calif.) and ligated at a ratio of 3:1 (vector to insert). Ligation reactions using T4 DNA ligase (New England Biolabs, MA) are carried out at 16° C. for 16 hours. The ligated DNAs are transformed into competent cells of the E. coli strain DH5a by using the heat shock method. The transformed cells are plated on LB plates containing 100 μg/ml spectinomycin (Sigma). Individual colonies are grown overnight in five milliliters of LB broth containing 100 μg/ml spectinomycin at 37° C.

[0365] Plasmid DNAs from transformants are purified by using Qiaquick Mini Prep kits (Qiagen, Calif.) according to the manufacturer's instruction. The presence of the promoter insert is verified by restriction mapping with the respective restriction enzymes as listed in Table 4 to cut out the cloned insert. The plasmid DNA is also subject to double-strand DNA sequencing analysis using a vector primer (E9.1 primer 5′-CAAACTCAGTAGGATTCTGGTGTGT-3′ [SEQ. ID. No. 33].

[0366] (2) Cloning of the cbf1gene into the Plasmids Containing the Inducible Promoters

[0367] To clone the CBF1 gene into the plasmids, different PCR primers with suitable restriction sites for each plasmid are used to isolate cbf1 gene from Arabidopsis thaliana genomic DNA.

[0368] The primers that may be used are listed in Table 5.

5TABLE 5Promoter namePrimer nameCloning sitesDreb2aCbf1-reverse1BgIII (AGATCT)Cbf1-forward1BamHI (GGATCC)P5CSCbf1-reverse1BgIII (AGATCT)Cbf1-forward1BamHI (GGATCC)Rd22Cbf1-reverse2KpnI (GGTACCCbf1-forward1BamHI (GGATCC)Rd29aCbf1 -reverse2KpnI (GGTACCCbf1-forward1BamHI (GGATCC)Rd29bCbf1-reverse2KpnI (GGTACCCbf1-forward1BamHI (GGATCC)Rab18Cbf1-reverse1BgIII (AGATCT)Cbf1-forward2XbaI (TCTAGACor47Cbf1-reverse1BgIII (AGATCT)Cbf1-forward1BamHI (GGATCC)

[0369] Two of the four available PCR primers (Table 5) are used for cloning the at-cbf1 gene into the expression vectors containing each inducible promoter described above. The four primers have these sequences: cbf1-reverse 1 5′-GGAAGATCTTGAAACAGAGTACTCTGATCAATGAACTC-3′ [SEQ. ID. No. 34], cbf1-forward 1 5′-CGCGGATCCCTCGTTTCTACAACAATAAAATAAAATAAAATG-3′ [SEQ. ID. No. 35], cbf1-reverse 2 5′-GGGGTACCTGAAACAGAGTACTCTGATCAATGAACTC-3′ [SEQ. ID. No. 36], and cbf1-forward 2 5′-GCTCTAGACTCGTTTCTACAACAATAAAATAAAATAAAATG-3′ [SEQ. ID. No. 37]. For example, for the Dreb2a, P5CS, and COR47 promoters that are ligated to a BamHI and BgIII flanked insert, the cbf1-reverse 1 and cbf1-forward 1 primers [SEQ. ID. No. 34 and 35, respectively] are used to isolate cbf1 gene from Arabidopsis thaliana genomic DNA. The cbf1-reverse primer includes a BgIII (AGATCT) restriction site near the 5′-end of the primer and cbf1-forward primer has a BamHI (GGATCC) restriction site near the 5′-end of the primer. A PCR product of 764 bp is expected. The genomic DNA (10 ng) is used as a template in a PCR reaction under conditions suggested by the manufacturer (Boehringer Mannheim). The reaction conditions to be used in this PCR experiment are as follows: Segment 1: 94° C., 2 minutes; Segment 2: 94° C., 30 seconds; 55° C., 1 minute; 72° C., 1 minute, for a total of 35 cycles; Segment 3: 72° C. for 10 minutes.

[0370] The PCR products are subject to electrophoresis in a 0.8% agarose gel and visualized by ethidium bromide staining. The DNA fragment containing cbf1 is excised and purified by using a Qiaquick gel extraction kit (Qiagen, a; Calif.). The purified fragment and the vector pMBI2001 containing the inducible promoter (Table 5) are each digested with BgIII and BamHI restriction enzymes at 37° C. for 2 hours. Both DNA samples are purified by using the Qiaquick purification kit (Qiagen, Calif.) and ligated at a ratio of 3:1 (vector to insert). Ligation reactions using T4 DNA ligase (New England Biolabs, MA) are carried out at 16° C. for 16 hours. The ligated DNAs are transformed into competent cells of the E. coli strain DH5α by using the heat shock method. The transformation are plated on LB plates containing 100 (g/ml spectinomycin (Sigma).

[0371] Individual colonies are grown overnight in five milliliters of LB broth containing 100 g/ml spectinomycin at 37° C. Plasmid DNA are purified by using Qiaquick Mini Prep kits (Qiagen, Calif.). The presence of the cbf1 insert is verified by restriction mapping with BgIII and BamHI. The plasmid DNA is also subject to double-strand DNA sequencing analysis by using vector primer E9.1 (5′-CAAACTCAGTAGGATTCTGGTGTGT-3′) [SEQ. ID. No. 33]. The other primers shown in Table 5 and appropriate restriction enzymes are used in a similar way to clone the Cbf1 gene into plasmids containing the other inducible promoters. The resulting plasmids are listed in Table 6 and shown in FIGS. 17A-17G.

[0372] A similar cloning strategy may be used to clone other genes, such as cbf2, cbf3, and the other full length CBF genes listed in Table 9 and shown in FIG. 18 (new CBF gene table) into plasmids containing inducible promoters.

6TABLE 6Construct namePromoter nameFigure namePMBI2008Dreb2aPMBI2009P5CSPMBI2010Rd22PMBI2011Rd29aPMBI2012Rd29bPMBI2013Rab18PMBI2014Cor47FIG. 17G

[0373] C. Transformation of Agrobacterium with Plasmids Containing CBF1 Gene and Inducible Promoters

[0374] After the plasmid vectors containing cbf1 gene and inducible promoters are constructed, these vectors are used to transform Agrobacterium tumefaciens cells expressing the gene products. The stock of Agrobacterium tumefaciens cells for transformation are made as described by Nagel et al. FEMS Microbiol Letts 67: 325-328 (1990). Agrobacterium strain ABI is grown in 250 ml LB medium (Sigma) overnight at 28° C. with shaking until an absorbance (A600) of 0.5-1.0 is reached. Cells are harvested by centrifugation at 4,000× g for 15 min at 4 C. Cells are then resuspended in 250 μl chilled buffer (1 mM HEPES, pH adjusted to 7.0 with KOH). Cells are centrifuged again as described above and resuspended in 125 μl chilled buffer. Cells are then centrifuged and resuspended two more times in the same HEPES buffer as described above at a volume of 100 μl and 750 μl, respectively. Resuspended cells are then distributed into 40 pi aliquots, quickly frozen in liquid nitrogen, and stored at −80 C.

[0375] Agrobacterium cells are transformed with plasmids formed as described above in Section 4B(2) following the protocol described by Nagel et al. FEMS Microbiol Letts 67: 325-328 (1990). For each DNA construct to be transformed, 50-100 ng DNA (generally resuspended in 10 mM Tris-HCl, 1 mM EDTA, pH 8.0) is mixed with 40 μl of Agrobacterium cells. The DNA/cell mixture is then transferred to a chilled cuvette with a 2 mm electrode gap and subject to a 2.5 kV charge dissipated at 25 μF and 200 μF using a Gene Pulser II apparatus (Bio-Rad). After electroporation, cells are immediately resuspended in 1.0 ml LB and allowed to recover without antibiotic selection for 2-4 hours at 28° C. in a shaking incubator. After recovery, cells are plated onto selective medium of LB broth containing 100 μg/ml spectinomycin (Sigma) and incubated for 24-48 h at 28° C. Single colonies are then picked and inoculated in fresh medium. The presence of the plasmid construct are verified by PCR amplification and sequence analysis.

[0376] D. Transformation of Arabidopsis Plants With Agrobacterium tumefaciens Carrying Expression Vector for CBF1 Protein

[0377] After transformation of Agrobacterium tumefaciens with plasmid vectors containing cbf1 gene and inducible promoters, single Agrobacterium colonies containing each of pMBI2008-pMBI2014 are identified, propagated, and used to transform Arabidopsis Plants. Briefly, 500 ml cultures of LB medium containing 100 ug/ml spectinomycin are inoculated with the colonies and grown at 28 C with shaking for 2 days until an absorbance (A600) of >2.0 is reached. Cells are then harvested by centrifugation at 4,000× g for 10 min, and resuspended in infiltration medium (1/2× Murashige and Skoog salts (Sigma), 1× Gamborg's B-5 vitamins (Sigma), 5.0% (w/v) sucrose (Sigma), 0.044 μM benzylamino purine (Sigma), 200 μl/L Silwet L-77 (Lehle Seeds) until an absorbance (A600) of 0.8 is reached.

[0378] Prior to transformation, Arabidopsis thaliana seeds (ecotype Columbia) are sown at a density of ˜10 plants per 4″ pot onto Pro-Mix BX potting medium (Hummert International) covered with fiberglass mesh (18 mm×16 mm). Plants are grown under continuous illumination (50-75 μE/m2/sec) at 22-23 C with 65-70% relative humidity. After about 4 weeks, primary inflorescence stems (bolts) are cut off to encourage growth of multiple secondary bolts. After flowering of the mature secondary bolts, plants are prepared for transformation by removal of all siliques and opened flowers.

[0379] The pots are then immersed upside down in the mixture of Agrobacterium/infiltration medium as described above for 30 sec, and placed on their sides to allow draining into a 1′×2′ flat surface covered with plastic wrap. After 24 h, the plastic wrap is removed and pots are turned upright. The immersion procedure is repeated one week later, for a total of two immersions per pot. Seeds are then collected from each transformation pot and analyzed following the protocol described below.

[0380] E. Identification of Arabidopsis Primary Transformants

[0381] Seeds collected from the transformation pots are sterilized essentially as follows. Seeds are dispersed into in a solution containing 0.1% (v/v) Triton X-100 (Sigma) and sterile H2O and washed by shaking the suspension for 20 min. The wash solution is then drained and replaced with fresh wash solution to wash the seeds for 20 min with shaking. After removal of the second wash solution, a solution containing 0.1% (v/v) Triton X-100 and 70% EtOH (Equistar) is added to the seeds and the suspension is shaken for 5 min. After removal of the ethanol/detergent solution, a solution containing 0.1% (v/v) Triton X-100 and 30% (v/v) bleach (Chlorox) is added to the seeds, and the suspension is shaken for 10 min. After removal of the bleach/detergent solution, seeds are then washed five times in sterile distilled H2O. The seeds are stored in the last wash water at 4° C. for 2 days in the dark before being plated onto antibiotic selection medium (1× Murashige and Skoog salts (pH adjusted to 5.7 with 1 M KOH), 1× Gamborg's B-5 vitamins, 0.9% phytagar (Life Technologies), and 50 μg/L kanamycin). Seeds are germinated under continuous illumination (50-75 μE/m2/sec) at 22-23° C. After 7-10 days of growth under these conditions, kanamycin resistant primary transformants (T1 generation) are visible and are obtained for each of constructs pMBI2008-pMBI2014. These seedlings are transferred first to fresh selection plates where the seedlings continued to grow for 3-5 more days, and then to soil (Pro-Mix BX potting medium). Progeny seeds (T2) are collected; kanamycin resistant seedlings selected and analyzed as described above.

[0382] F. Transformation of Cereal Plants with Plasmid Vectors Containing cbf1 Gene and Inducible Promoters

[0383] Cereal plants, such as corn, wheat, rice, sorghum and barley, can also be transformed with the plasmid vectors containing the cbf genes and inducible promoters to increase their tolerance to environmental stresses. In these cases, the cloning vector, pMEN020, is modified to replace the Nptl I coding region with the BAR gene of Streptomyces hygroscopicus that confers resistance to phosphinothricin. The KpnI and BgIII sites of the Bar gene are removed by site-directed mutagenesis with silent codon changes. After cloning of the inducible promoters into the modified plasmid by the same procedures described above, the at-cbf coding region of cbf1gene is inserted into the plasmid following the same procedures as described above. The resulted plasmids are listed in Table 7.

7TABLE 7Promoter nameConstruct nameDreb2aPMBI2015P5CSPMBI2016Rd22PMBI2017Rd29aPMBI2018Rd29bPMBI2019Rab18PMBI2020Cor47PMBI2021

[0384] It is now routine to produce transgenic plants of most cereal crops (Vasil, I., Plant Molec. Biol. 25: 925-937 (1994)) such as corn, wheat, rice, sorghum (Cassas, A. et al., Proc. Natl. Acad Sci USA 90: 11212-11216 (1993) and barley (Wan, Y. and Lemeaux, P. Plant Physiol. 104:37-48 (1994) Other direct DNA transfer methods such as the microprojectile gun or Agrobacterium tumefaciens-mediated transformation can be used for corn (Fromm. et al. Bio/Technology 8: 833-839 (1990); Gordon-Kamm et al. Plant Cell 2: 603-618 (1990); Ishida, Y., Nature Biotechnology 14:745-750 (1990)), wheat (Vasil, et al. Bio/Technology 10:667-674 (1992); Vasil et al., Bio/Technology 11:1553-1558 (1993); Weeks et al., Plant Physiol. 102:1077-1084 (1993)), rice (Christou Bio/Technology 9:957-962 (1991); Hiei et al. Plant J. 6:271-282 (1994); Aldemita and Hodges, Planta 199:612-617; Hiei et al., Plant Mol Biol. 35:205-18 (1997)). For most cereal plants, embryogenic cells derived from immature scutellum tissues are the preferred cellular targets for transformation (Hiei et al., Plant Mol Biol. 35:205-18 (1997); Vasil, Plant Molec. Biol. 25: 925-937 (1994)).

[0385] Plasmids according to the present invention may be transformed into corn embryogenic cells derived from immature scutellar tissue by using microprojectile bombardment, with the A188XB73 genotype as the preferred genotype (Fromm, et al., Bio/Technology 8: 833-839 (1990); Gordon-Kamm et al., Plant Cell 2: 603-618 (1990)). After microprojectile bombardment the tissues are selected on phosphinothricin to identify the transgenic embryogenic cells (Gordon-Kamm et al., Plant Cell 2: 603-618 (1990)). Transgenic plants are regenerated by standard corn regeneration techniques (Fromm, et al., Bio/Technology 8: 833-839 (1990); Gordon-Kamm et al., Plant Cell 2: 603-618 (1990)).

[0386] The plasmids prepared as described above can also be used to produce transgenic wheat and rice plants (Christou, Bio/Technology 9:957-962 (1991); Hiei et al., Plant J. 6:271-282 (1994); Aldemita and Hodges, Planta 199:612-617 (1996); Hiei et al., Plant Mol Biol. 35:205-18 (1997)) by following standard transformation protocols known to those skilled in the art for rice and wheat Vasil, et al. Bio/Technology 10:667-674 (1992); Vasil et al., Bio/Technology 11:1553-1558 (1993); Weeks et al., Plant Physiol. 102:1077-1084 (1993)), where the BAR gene is used as the selectable marker.

[0387] 5. Identification of CBF1 Homologs CBF2 and CBF3 Using CBF1

[0388] This example describes two homologs of CBF1 from Arabidopsis thaliana and named them CBF2 and CBF3.

[0389] CBF2 and CBF3 have been cloned and sequenced as described below. The sequences of the DNA and encoded proteins are set forth in SEQ ID NOS: 12, 13, 14 and 15. FIG. 12 shows the DNA sequence for CBF2 encoding CBF2. FIG. 13 shows the DNA sequence for CBF3 encoding CBF3.

[0390] A lambda cDNA library prepared from RNA isolated from Arabidopsis thaliana ecotype Columbia (Lin and Thomashow, Plant Physiol. 99: 519-525 (1992)) was screened for recombinant clones that carried inserts related to the CBF1 gene (Stockinger, E. J., et al., Proc Natl Acad Sci USA 94:1035-1040 (1997)). CBF1 was 32P-radiolabeled by random priming (Sambrook et al., Molecular Cloning. A Laboratory Manual, Ed. 2, Cold Spring Harbor Laboratory Press, New York (1989)) and used to screen the library by the plaque-lift technique using standard stringent hybridization and wash conditions (Hajela, R. K., et al., Plant Physiol 93:1246-1252 (1990); Sambrook et al., Molecular Cloning. A Laboratory Manual, Ed 2. Cold Spring Harbor laboratory Press, New York (1989) 6× SSPE buffer, 60° C. for hybridization and 0.1× SSPE buffer and 60° C. for washes). Twelve positively hybridizing clones were obtained and the DNA sequences of the cDNA inserts were determined at the MSU-DOE Plant Research Laboratory sequencing facility. The results indicated that the clones fell into three classes. One class carried inserts corresponding to CBF1. The two other classes carried sequences corresponding to two different homologs of CBF1, designated CBF2 and CBF3. The nucleic acid sequences and predicted protein coding sequences for CBF1, CBF2 and CBF3 appear at FIG. 14.

[0391] A comparison of the nucleic acid sequences of CBF1, CBF2 and CBF3 indicate that they are 83 to 85% identical as shown in Table 8. FIG. 14 shows the amino acid alignment of proteins CBF1, CBF2 and CBF3.

8TABLE 8Percent identityaDNAbPolypeptidecbf1/cbf28586cbf1/cbf38384cbf2/cbf38485aPercent identity was determined using the Clustal algorithm from the Megalign program (DNASTAR, Inc.). bComparisons of the nucleic acid sequences of the open reading frames are shown.

[0392] Similarly, the amino acid sequences of the three CBF polypeptides range from 84 to 86% identity. An alignment of the three amino acidic sequences reveals that most of the differences in amino acid sequence occur in the acidic C-terminal half of the polypeptide. This region of CBF1 serves as an activation domain in both yeast and Arabidopsis (not shown).

[0393] Residues 47 to 106 of CBF1 correspond to the AP2 domain of the protein, a DNA binding motif that to date, has only been found in plant proteins. A comparison of the AP2 domains of CBF1, CBF2 and CBF3 indicates that there are a few differences in amino acid sequence. These differences in amino acid sequence might have an effect on DNA binding specificity.

[0394] 6. Activation of Transcription in Yeast Containing C-repeat/DRE Using CBF1, CBF2 and CBF3

[0395] This example shows that CBF1, CBF2 and CBF3 activate transcription in yeast containing CRT/DREs upstream of a reporter gene. The CBFs were expressed in yeast under control of the ADC1 promoter on a 2μ plasmid (pDB20.1; Berger, S. L., et al., Cell 70:251-265 (1992)). Constructs expressing the different CBFs were transformed into yeast reporter strains which had the indicated CRT/DRE upstream of the lacZ reporter gene. Copy number of the CRT/DREs and its orientation relative to the direction of transcription from each promoter is indicated by the direction of the arrow.

[0396]
FIG. 15 is a graph showing transcription regulation of CRT/DRE containing reporter genes by CBF1, CBF2 and CBF3 genes in yeast. In FIG. 15, the vertical lines across the arrows of the COR15a construct represent the m3cor15a mutant CRT/DRE construct. Each CRT/DRE-lacZ construct was integrated into the URA3 locus of yeast. Error bars represent the standard deviation derived from three replicate transformation events with the same CBF activator construct into the respective reporter strain. Quantitative B-gal assays were performed as described by Rose and Botstein (Rose, M., et al., Methods Enzymol. 101:167-180 (1983)).

[0397] 7. Homologous CBF Encoding Genes in Other Plants.

[0398] This example shows that homologous sequences to CBF1 are present in other plants. The presence of these homologous sequences suggest that the same or similar cold regulated environmental stress response regulatory elements such as the C-repeat/DRE of Arabidopsis (CCGAC) exist in other plants. This example serves to indicate that genes with significant homology to CBF1, CBF2 and CBF3 exist in a wide range of plant species.

[0399] Total plant DNAs from Arabadopsis thaliana, Nicotiana tabacum, Lycopersicon pimpinellifolium, Prunis avium, Prunus cerasus, Cucumis sativus, and Oryza saliva were isolated according to Stockinger al (Stockinger, E. J., et al., J. Heredity, 87:214-218 (1996)). Approximately 2 to 10 μg of each DNA sample was restriction digested, transferred to nylon membrane (Micron Separations, Westboro, Mass.) and hybridized according to Walling et al. (Walling, L. L., et al., Nucleic Acids Res. 16:10477-10492 (1988)). Hybridization conditions were: 42° C. in 50% formamide, 5× SSC, 20 mM phosphate buffer 1× Denhardt's, 10% dextran sulfate, and 100 μg/ml herring sperm DNA. Four low stringency washes at RT in 2× SSC, 0.05% Na sarcosyl and 0.02% Na4 pyrophosphate were performed prior to high stringency washes at 55° C. in 0.2× SSC, 0.05% Na sarcosyl and 0.01% Na4 pyrophosphate. High stringency washes were performed until no counts were detected in the washout. The BclI-BglII fragment of CBF1 (Stockinger et al., Proc Natl Acad Sci USA 94:1035-1040 (1997)) was gel isolated (Sambrook et al., Molecular Cloning. A Laboratory Manual, Ed 2. Cold Spring Harbor Laboratory Press, New York (1989)) and direct prime labelled (Feinberg and Vogelstein, Anal. Biochem 132: 6-13 (1982)) using the primer MT117 (TTGGCGGCTACGAATCCC; SEQ ID NO:16). Specific activity of the radiolabelled fragment was approximately 4×108 cpm/μg. Autoradiography was performed using HYPERFILM-MP (Amersham) at −80° C. with one intensifying screen for 15 hours.

[0400] Autoradiography of the gel showed that DNA sequences from Arabadopsis thaliana, Nicotiana tabacum, Lycopersicon pimpinellifolium, Prunis avium, Prunus cerasus, Cucumis sativus, and Oryza sativa hybridized to the labeled BclI, BglII fragment of CBF1. These results suggest that homologous CBF encoding genes are present in a variety of other plants.

[0401] 8. Identification of Homologous Sequence to CBF1 in Canola

[0402] This example describes the identification of homologous sequences to CBF1 in canola using PCR. Degenerate primers were designed for regions of AP2 binding domain and outside of the AP2 (carboxyl terminal domain). More specifically, the following degenerate PCR primers were used:

9Mol 368 (reverse)5′- CAY CCN ATH TAY MGN GGN GT -3′Mol 378 (forward)5′- GGN ARN ARC ATN CCY TCN GCC -3′

[0403] (Y: C/T, N: A/C/G/T, H: A/C/T, M: A/C, R: A/G)

[0404] Primer Mol 368 is in the AP2 binding domain of CBF1 (amino acid seq: H P I Y R G V) while primer Mol 378 is outside the AP2 domain (carboxyl terminal domain)(amino acid seq: M A E G M L L P).

[0405] The genomic DNA isolated from Brassica Napus was PCR amplified by using these primers following these conditions: an initial denaturation step of 2 min at 93° C.; 35 cycles of 93° C. for 1 min, 55° C. for 1 min, and 72° C. for 1 min; and a final incubation of 7 min at 72° C. at the end of cycling.

[0406] The PCR products were separated by electrophoresis on a 1.2% agarose gel and, transferred to nylon membrane and hybridized with the AT CBF1 probe prepared from Arabidopsis genomic DNA by PCR amplification. The hybridized products were visualized by colormetric detection system (Boehringer Mannheim) and the corresponding bands from a similar agarose gel were isolated (By Qiagen Extraction Kit). The DNA fragments were ligated into the TA clone vector from TOPO TA Cloning Kit (Invitrogen) and transformed into E. coli strain TOP10 (Invitrogen).

[0407] Seven colonies were picked and the inserts were sequenced on an ABI 377 machine from both strands of sense and antisense after plasmid DNA isolation. The DNA sequence was edited by sequencer and aligned with the AtCBF1 by GCG software and NCBI blast searching.

[0408]
FIG. 16 shows an amino acid sequence of a homolog [CAN1; SEQ. ID. No. 17] identified by this process and its alignment to the amino acid sequence of CBF1. The nucleic acid sequence for CAN1 is listed herein as SEQ. ID. No. 18.

[0409] As illustrated in FIG. 16, the DNA sequence alignment in four regions of BN-CBF1 shows 82% identity in the AP2 binding domain region and range from 75% to 83% with some alignment gaps due to regions of lesser homology or introns in the genomic sequence. The aligned amino acid sequences show that the BNCBF1 gene has 88% identity in the AP2 domain region and 85% identity outside the AP2 domain when aligned for two insertion sequences that are outside the AP2 domain. The extra amino acids in the 2 insertion regions are either due to the presence of introns in this region of the BNCBF1 gene, as it was derived from genomic DNA, or could be due to extra amino acids in these regions of the BNCBF1 gene. Isolation and sequencing of a cDNA of the BNCBF1 gene using the genomic DNA as a probe will resolve this.

[0410] 9. Identification of Homologous Sequence to CBF1 in Canola and Other Species

[0411] A PCR strategy similar to that described in Example 8 was used to isolate additional CBF homologues from Brassica juncea, Brassica napus, Brassica oleracea, Brassica rapa, Glycine max, Raphanus sativus and Zea Maize. The nucleotide (e.g. bjCBF1) and peptide sequences (e.g. BJCBF1-PEP) of these isolated CBF homologues are shown in FIGS. 18A and 18B, respectively. Table 9 lists the sequence names and sequence ID Nos. of these isolated CBF homologues. The PCR primers are internal to the gene so partial gene sequences are initially obtained. The full length sequences of some of these genes were further isolated by inverse PCR or ligated linker PCR. One skilled in the art can use the conserved regions in these genes to design PCR primers to isolate additional CBF genes.

10TABLE 9DNA Seq. NameSeq. ID No.Peptide Seq. NameSeq. ID No.bjCBF138BJCBF1-PEP39bJCBF240BJCBF2-PEP41bjCBF342BJCBF3-PEP43bjCBF444BJCBF4-PEP45bnCBF146BNCBF1-PEP47bnCBF248BNCBF2-PEP49bnCBF350BNCBF3-PEP51bnCBF452BNCBF4-PEP53bnCBF554BNCBF5-PEP55bnCBF656BNCBF6-PEP57bnCBF758BNCBF7-PEP59bnCBF860BNCBF8-PEP61bnCBF962BNCBF9-PEP63boCBF164BOCBF1-PEP65boCBF266BOCBF2-PEP67boCBF368BOCBF3-PEP69boCBF470BOCBF4-PEP71boCBF572BOCBF5-PEP73brCBF174BRCBF1-PEP75brCBF276BRCBF2-PEP77brCBF378BRCBF3-PEP79brCBF480BRCBF4-PEP81brCBF582BRCBF5-PEP83brCBF684BRCBF6-PEP85brCBF786BRCBF7-PEP87gmCBF188GMCBF1-PEP89rsCBF190RSCBF1-PEP91rsCBF292RSCBF2-PEP93zmCBF194ZMCBF1-PEP95

[0412]
FIG. 19A shows an amino acid alignment of the AP2 domains of the CBF proteins listed in Table 9 with their consensus sequences highlighted. FIG. 19A also provides a comparison of the consensus sequence with that of the tobacco DNA binding protein EREBP2 (Okme-Takagi, M., et al., The Plant Cell 7:173-182 (1995). The sequences of these CBF proteins are BRCBF3-PEP [SEQ. ID. No. 79], BRCBF6-PEP [SEQ. ID. No.85], BNCBF5-PEP [SEQ. ID. No. 55], ATCBF2-PEP [SEQ. ID. No. 13], ATCBF3-PEP [SEQ. ID. No. 15], ATCBF1-PEP [SEQ. ID. No. 2], BNCBF2-PEP [SEQ. ID. No. 49], BNCBF6-PEP [SEQ. ID. No. 57], BOCBF3-PEP [SEQ. ID. No. 69], BNCBF3-PEP [SEQ. ID. No. 51], BNCBF8-PEP [SEQ. ID. No. 61], BNCBF9-PEP [SEQ. ID. No. 63], BRCBF2-PEP [SEQ. ID. No. 77], BOCBF5-PEP [SEQ. ID. No. 73], BOCBF2-PEP [SEQ. ID. No. 67], RSCBF2-PEP [SEQ. ID. No. 93], BNCBF4-PEP [SEQ. ID. No. 53], BNCBF7-PEP [SEQ. ID. No. 59], BOCBF4-PEP [SEQ. ID. No. 71], BRCBF7-PEP [SEQ. ID. No. 87], BRCBF4-PEP [SEQ. ID. No. 81], BRCBF5-PEP [SEQ. ID. No. 83], RSCBF1-PEP [SEQ. ID. No. 91], BJCBF2-PEP [SEQ. ID. No. 41], BJCBF3-PEP [SEQ. ID. No. 43], BNCBF1-PEP [SEQ. ID. No.47], BOCBF1-PEP [SEQ. ID. No. 65], BRCBF1-PEP [SEQ. ID. No. 75], BJCBF4-PEP [SEQ. ID. No. 45], ZMCBF1-PEP [SEQ. ID. No. 95], and GMCBF1-PEP [SEQ. ID. No. 89].

[0413] As can be seen from the consensus sequence shown in FIG. 19A, a significant portion of the AP2 domain is conserved among the different CBF proteins. In view of this data, Applicants use the conserved sequence in the AP2 domain to define a class of AP2 domain proteins comprising this conserved sequence.

[0414]
FIG. 19B shows an amino acid alignment of the AP2 domains shown in FIG. 19A and dreb2a and dreb2b and a consensus sequence between the proteins highlighted. As can be seen, a very high degree of homology exists between AP2 domains shown in FIG. 19A and dreb2a and dreb2b. Applicants employ the conserved sequence in the AP2 domain shown in FIG. 19B to define a broader class of AP2 domain proteins which are capable of binding to CCG regulatory region.

[0415]
FIG. 19C shows an amino acid alignment of the AP2 domains shown in FIG. 19B and tiny and a consensus sequence between the proteins highlighted. As can be seen, a very high degree of homology exists between AP2 domains shown in FIG. 19A, dreb2a, dreb2b and tiny. Applicants employ the conserved sequence in the AP2 domain shown in FIG. 19C to define a yet broader class of AP2 domain proteins which are capable of binding to CCG regulatory region.

[0416]
FIG. 19D shows a consensus sequence corresponding to the difference between the consensus sequence shown in FIGS. 19A and tiny. Applicants employ the highlighted portion of the conserved sequence shown in FIG. 19D to define a group of amino acid residues which may be critical to binding to a CCG regulatory region.

[0417]
FIG. 19E shows a consensus sequence corresponding to the difference between the consensus sequence shown in FIGS. 19B and tiny. Applicants employ the highlighted portion of the conserved sequence shown in FIG. 19E to define another group of amino acid residues which may be critical to binding to a CCG regulatory region.

[0418]
FIG. 20 shows the amino acid alignment of the amino terminus of the CBF proteins with their consensus sequence highlighted. The sequences of these CBF proteins are: BRCBF3-PEP [SEQ. ID. No. 79], BRCBF6-PEP [SEQ. ID. No.85], BNCBF5-PEP [SEQ. ID. No. 55], ATCBF2-PEP [SEQ. ID. No. 13], ATCBF3-PEP [SEQ. ID. No. 15], ATCBF1-PEP [SEQ. ID. No. 2], BNCBF2-PEP [SEQ. ID. No. 49], BNCBF6-PEP [SEQ. ID. No. 57], BOCBF3-PEP [SEQ. ID. No. 69], BNCBF3-PEP [SEQ. ID. No. 51], BNCBF8-PEP [SEQ. ID. No. 61], BNCBF9-PEP [SEQ. ID. No. 63], BRCBF2-PEP [SEQ. ID. No. 77], BOCBF5-PEP [SEQ. ID. No. 73], BOCBF2-PEP [SEQ. ID. No. 67], RSCBF2-PEP [SEQ. ID. No. 93], BNCBF4-PEP [SEQ. ID. No. 53 ], BNCBF7-PEP [SEQ. ID. No. 59], BOCBF4-PEP [SEQ. ID. No. 71], BRCBF7-PEP [SEQ. ID. No. 87], BRCBF4-PEP [SEQ. ID. No. 81], BRCBF5-PEP [SEQ. ID. No. 83], and RSCBF1-PEP [SEQ. ID. No. 91].

[0419] As can be seen from the consensus sequence shown in FIG. 20, a significant portion of the amino terminus of CBF proteins is conserved among the different CBF proteins. In view of this data, Applicants employ the conserved sequence in the amino terminus domain to define a class of proteins comprising this conserved sequence.

[0420]
FIG. 21A shows the amino acid alignment of the carboxy terminus of 24 CBF proteins with their consensus sequences highlighted. The sequences of these CBF proteins are: BRCBF6-PEP [SEQ. ID. No.85], BNCBF5-PEP [SEQ. ID. No. 55], ATCBF2-PEP [SEQ. ID. No. 13], ATCBF3-PEP [SEQ. ID. No. 15], ATCBF1-PEP [SEQ. ID. No. 2], BNCBF2-PEP [SEQ. ID. No. 49], BNCBF6-PEP [SEQ. ID. No. 57], BOCBF3-PEP [SEQ. ID. No. 69], BNCBF3-PEP [SEQ. ID. No. 51], BNCBF8-PEP [SEQ. ID. No. 61], BNCBF9-PEP [SEQ. ID. No. 63], BRCBF2-PEP [SEQ. ID. No. 77], BOCBF5-PEP [SEQ. ID. No. 73], RSCBF2-PEP [SEQ. ID. No. 93], BNCBF4-PEP [SEQ. ID. No. 53], BNCBF7-PEP [SEQ. ID. No. 59], BOCBF4-PEP [SEQ. ID. No. 71], BRCBF7-PEP [SEQ. ID. No. 87], BRCBF5-PEP [SEQ. ID. No. 83], RSCBF1-PEP [SEQ. ID. No. 91], BJCBF2-PEP [SEQ. ID. No. 41], BJCBF3-PEP [SEQ. ID. No. 43], BNCBF1-PEP [SEQ. ID. No. 47], and BOCBF1-PEP [SEQ. ID. No. 65].

[0421] As can be seen from the consensus sequence shown in FIG. 21A, a significant portion of the carboxy terminus of CBF proteins is conserved among the different CBF proteins. In view of this data, Applicants employ the conserved sequence in the carboxy terminus domain to define a class of proteins comprising this conserved sequence.

[0422]
FIG. 21B shows the amino acid alignment of the carboxy terminus of 9 CBF proteins with their consensus sequences highlighted. The sequences of these CBF proteins are: BNCBF2-PEP [SEQ. ID. No. 49], BOCBF3-PEP [SEQ. ID. No. 69], BNCBF3-PEP [SEQ. ID. No. 51], BNCBF8-PEP [SEQ. ID. No. 61], BNCBF9-PEP [SEQ. ID. No. 63], BRCBF2-PEP [SEQ. ID. No. 77], BOCBF5-PEP [SEQ. ID. No. 73], BNCBF1-PEP [SEQ. ID. No. 47], and BNCBF6-PEP [SEQ. ID. No. 57].

[0423] As can be seen from the consensus sequence shown in FIG. 21B, a greater portion of the carboxy terminus is conserved when these 9 CBF proteins are used. In view of this data, Applicants employ the conserved sequence in the carboxy terminus domain to define another class of proteins comprising this conserved sequence.

[0424] While the present invention is disclosed by reference to the preferred embodiments and examples detailed above, it is to be understood that these examples are intended in an illustrative rather than limiting sense, as it is contemplated that modifications will readily occur to those skilled in the art, which modifications will be within the spirit of the invention and the scope of the appended claims.

	Number	Date	Country
Parent	09198119	Nov 1998	US
Child	09996140	Nov 2001	US

	Number	Date	Country
Parent	09018233	Feb 1998	US
Child	09198119	Nov 1998	US
Parent	09017816	Feb 1998	US
Child	09198119	Nov 1998	US
Parent	09018235	Feb 1998	US
Child	09198119	Nov 1998	US
Parent	09017575	Feb 1998	US
Child	09198119	Nov 1998	US
Parent	09018227	Feb 1998	US
Child	09198119	Nov 1998	US
Parent	09018234	Feb 1998	US
Child	09198119	Nov 1998	US
Parent	08706270	Sep 1996	US
Child	09198119	Nov 1998	US

Plant having altered environmental stress tolerance

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