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The Thomashow Lab
MSU-DOE Plant Research Lab
Michigan State University |
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Molecular Genetics of Environmental Stress Tolerance
Our long range goal is to gain a systems level understanding of plant responses to abiotic stress and to use the first principles gained to develop novel strategies to improve the stress tolerance of agriculturally important crops. These objectives are important as abiotic stresses limit the geographical locations where crops can be grown and account for the majority of losses in yield on an annual basis. Improving the abiotic stress tolerance of crops is crucial to meeting future demands for food and fiber. It is also a key component of an emerging national vision to produce sufficient biomass per year in the U.S. to replace about 30% of petroleum-based transportation fuels with "biofuels" produced from renewable resources.
Our current research largely focuses on determining the low temperature transcriptional networks that plants have evolved to survive freezing. As there is a direct link between freezing and dehydration injury, the results should also provide further insights into the nature of gene modules that impart tolerance to drought and other dehydration stresses. Much of our work is with Arabidopsis, a plant that increases in freezing tolerance in response to low temperature, a process known as cold acclimation (Figure 1). Our specific aims include a systematic analysis of the cis-acting DNA regulatory elements and trans-acting factors that participate in cold-regulated gene expression; iterative computational analysis and empirical testing to reconstruct the low temperature regulatory network and identify the gene modules that it controls; and to identify which gene modules contribute to freezing tolerance and potentially tolerance to other abiotic stresses. In addition, we want to determine whether the low temperature transcriptional networks and gene modules that impart freezing tolerance in Arabidopsis are conserved in plants that cold acclimate and whether deficiencies in these networks contribute to the freezing sensitivity of plants that do not cold acclimate. We are addressing this objective through comparative genomic analysis of barley and three closely related Solanum species which differ in cold tolerance: tomato (S. lycopersicum), which is chilling and freezing sensitive; the common potato (S. tuberosum), which is chilling tolerant, but freezing sensitive; and the "wild" tuber-bearing diploid relative of potato, S. commersonii, which is chilling and freezing tolerant.
The CBF Cold Response Pathway
We have established that the Arabidopsis CBF cold response pathway has a major role in cold acclimation (Figures 2 and 3). Within 15 min of exposing plants to low temperature (4 C), genes are induced that encode a small family of transcription factors known as CBF1, CBF2, and CBF3 (alternatively known as DREB1B, DREB1C and DREB1A, respectively). Low temperature induction of CBF1-3 is quickly followed by expression of the "CBF regulon", a set of about 100 genes that is regulated by the CBF proteins. The immediate target genes of CBF1-3 have CRT (C-repeat)/DRE (dehydration responsive element) elements in their promoters, the DNA regulatory sequence to which the CBF1-3 proteins bind. Expression of the CBF regulon increases both plant freezing tolerance and drought tolerance. The mechanistic basis for this cross-protection lies in the fact that the injury caused by freezing is largely due to the cellular dehydration that occurs upon ice formation.
The Low Temperature Transcriptome
Gene expression profiling experiments have revealed that within 30 min of transferring plants to low temperature, waves of changes in transcriptome composition occur involving hundreds of genes and multiple cold-regulatory pathways (Figure 4). A set of 514 reproducibly cold-responsive genes, designated COS ("cold standard"), has been defined for use in deciphering the low temperature regulatory network. Of these COS genes, 302 are up-regulated and 212 down-regulated at least 2.5-fold (p ≤ 0.05) in response to low temperature.
We have found that the CBF cold response pathway has a major role in configuring the low temperature transcriptome. Of the 514 COS genes, 86 cold-induced and 8 cold-repressed have been assigned to the CBF regulon. We have also found that the CBF cold response has a major role in determining the low temperature metabolome. Of 325 polar metabolites found to increase in the cold, 256 (79%) increased in response to CBF3 overexpression.
While the CBF regulon has a major role in configuring the low temperature transcriptome, the large majority of cold-regulated genes are not a part of the CBF cold response pathway. A central goal is to identify the transcription factors that control these genes. One which we have identified is ZAT12 which controls a regulon of 24 genes (9 up- and 15 down-regulated) of which 7 members are also members of the CBF regulon. Through computational analysis and other approaches, we have identified a large set of additional candidate transcription factors which are currently being tested for their roles in cold-regulated gene expression and abiotic stress tolerance.
Conservation of the CBF Cold Response Pathway
Components of the CBF cold-response pathway are conserved in plants that cold acclimate. We have shown that the oilseed crop canola (Brassica napus) and the cereals wheat, barley and rye encode CBF orthologs that are induced in response to low temperature. Moreover, we have found that constitutive overexpression of the Arabidopsis CBF genes in canola increases the freezing and drought tolerance of the transgenic plants.
We have also found that tomato, which is freezing and chilling sensitive and does not cold acclimate, also has a complete CBF cold response pathway; i.e., tomato plants can sense low temperature, activate expression of a functional CBF ortholog which, in turn, can activate expression of target genes. However, expression of the tomato CBF regulon does not increase freezing tolerance. Our working hypothesis that that this is due to the fact that the tomato CBF regulon is composed of very few genes (it appears that it consists of about 10 genes). We are currently determining whether the small tomato CBF regulon is due to a defect in the CBF cold response pathway or is due to tomato having few genes with functional CRT/DRE cis-acting regulatory elements.
Key Publications in Cold Acclimation
Jaglo-Ottosen, K. R., S. J. Gilmour, D. G. Zarka, O. Schabenberger and M. F. Thomashow. 1998. Arabidopsis CBF1 overexpression induces COR genes and enhances freezing tolerance. Science 280: 104-106.
Jaglo K.R., S. Kleff, K. Amundsen, X. Zhang, V. Haake, J. Zhang, T. Deits and M.F. Thomashow. 2001. Components of the Arabidopsis CBF cold-response pathway are conserved in Brassica napus and other plant species. Plant Physiol 127: 910-917.
Fowler S., and M.F. Thomashow. 2002. Arabidopsis transcriptome profiling indicates multiple regulatory pathways are activated during cold acclimation in addition to the CBF cold-response pathway. Plant Cell 14: 1675-1690.
Zhang X., S. Fowler, H. Cheng, Y. Lou, S.Y. Rhee, E.J. Stockinger and M.F. Thomashow. 2004. Freezing sensitive tomato has a functional CBF cold response pathway, but a CBF regulon that differs from that of freezing tolerant Arabidopsis. Plant J 39: 905-919.
Cook D., S. Fowler, O. Fiehn and M.F. Thomashow. 2004. A prominent role of the CBF cold response pathway in configuring the low temperature metabolome of Arabidopsis. Proc Natl Acad Sci USA 101: 15243-15248.
Vogel, J.T., D.G. Zarka, H.A. Van Buskirk, S.G. Fowler, and M.F. Thomashow. 2005. Roles of the CBF2 and ZAT12 transcription factors in configuring the low temperature transcriptome of Arabidopsis. Plant J 41: 195-211.
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MSU Plant Research Laboratory |
US Department of Energy |
The Arabidopsis Information Resource |
National Science Foundation |
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Copyright
2006-2007© Thomashow Lab,MSU. All rights reserved.
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