Roles of the CBF2 and ZAT12 transcription factors in configuring the low temperature transcriptome of Arabidopsis

Abstract

Summary The CBF cold response pathway has a prominent role in cold acclimation. The pathway includes action of three transcription factors, CBF1, 2 and 3 (also known as DREB1b, c and a, respectively), that are rapidly induced in response to low temperature followed by expression of the CBF-targeted genes (the CBF regulon) that act in concert to increase plant-freezing tolerance. The results of transcriptome profiling and mutagenesis experiments, however, indicate that additional cold response pathways exist and may have important roles in life at low temperature. To further understand the roles that the CBF proteins play in configuring the low temperature transcriptome and to identify additional transcription factors with roles in cold acclimation, we used the Affymetrix GeneChip containing probe sets for approximately 24,000 Arabidopsis genes to define a core set of cold-responsive genes and to determine which genes were targets of CBF2 and 6 other transcription factors that appeared to be coordinately regulated with CBF2. A total of 514 genes were placed in the core set of cold-responsive genes, 302 of which were upregulated and 212 downregulated. Hierarchical clustering and bioinformatic analysis indicated that the 514 cold-responsive transcripts could be assigned to one of seven distinct expression classes and identified multiple potential novel cis-acting cold-regulatory elements. Eighty-five cold-induced genes and eight cold-repressed genes were assigned to the CBF2 regulon. An additional nine cold-induced genes and 15 cold-repressed genes were assigned to a regulon controlled by ZAT12. Of the 25 core cold-induced genes that were most highly upregulated (induced over 15-fold), 19 genes (84%) were induced by CBF2 and another two genes (8%) were regulated by both CBF2 and ZAT12. Thus, the large majority (92%) of the most highly induced genes belong to the CBF and ZAT12 regulons. Constitutive expression of ZAT12 in Arabidopsis caused a small, but reproducible, increase in freezing tolerance, indicating a role for the ZAT12 regulon in cold acclimation. In addition, ZAT12 downregulated the expression of the CBF genes indicating a role for ZAT12 in a negative regulatory circuit that dampens expression of the CBF cold response pathway.

Functionality of soybean CBF/DREB1 transcription factors

“…AtADH1 was reported to be a cold, dehydration, hypoxia, and ABA-inducible gene [52,53]. Regulation of the ADH1 gene in Arabidopsis by AtCBF2 is suggested by experiments, which alter accumulation of CBF2 [54][55][56] and overexpression of CBF2 [57]. Maruyama et al [17] suggested that the specific promoter elements regulated by DREB2 are ACCGAC, GTCGGT and CCGACT, while DREB1A/CBF3 regulated primarily ACCGAC.…”

Cold responsive EARLI1 type HyPRPs improve freezing survival of yeast cells and form higher order complexes in plants

“…1, four members (including EARLI1) of this group are closely related and form a separate branch in the HyPRP phylogenetic tree (Josè-Estanyol et al 2004). Interestingly, each of the four members, At4g12470, At4g12480 (EARLI1), At4g12490, and At4g12500, is cold responsive (Vogel et al 2005). Biochemical and genetic approaches were used here to further investigate the potential role EARLI1 and perhaps its closely related paralogs play in plant cell protection.…”

“…4). Interestingly, it was shown in Arabidopsis that EARLI1, At4g12490, and At4g12500 had the same co-expression profile in response to cold, while At4g12470 belonged to a different class of cold responsive genes (Vogel et al 2005). Thus, it may be that EARLI1, At4g12490, and At4g12500 have a more significant role in protecting plant and yeast cells from freezing damage than At4g12470, which can be tested in future experiments using transgenic plants.…”

Opposing control by transcription factors MYB61 and MYB3 Increases Freezing Tolerance by relieving C-repeat Binding Factor suppression

“…AtCBF1 to AtCBF3 TFs bind DRE cis-elements and induce cold-responsive (COR) gene expression (Gilmour et al, 1998;Shinwari et al, 1998;Maruyama et al, 2004;Vogel et al, 2005) and, consequently, improve freezing tolerance (Gilmour et al, 2004). In addition, CBF gene expression is tightly regulated by calcium.…”