Expression Profile Matrix of Arabidopsis Transcription Factor Genes Suggests Their Putative Functions in Response to Environmental Stresses[W]

Abstract

Numerous studies have shown that transcription factors are important in regulating plant responses to environmental stress. However, specific functions for most of the genes encoding transcription factors are unclear. In this study, we used mRNA profiles generated from microarray experiments to deduce the functions of genes encoding known and putative Arabidopsis transcription factors. The mRNA levels of 402 distinct transcription factor genes were examined at different developmental stages and under various stress conditions. Transcription factors potentially controlling downstream gene expression in stress signal transduction pathways were identified by observed activation and repression of the genes after certain stress treatments. The mRNA levels of a number of previously characterized transcription factor genes were changed significantly in connection with other regulatory pathways, suggesting their multifunctional nature. The expression of 74 transcription factor genes responsive to bacterial pathogen infection was reduced or abolished in mutants that have defects in salicylic acid, jasmonic acid, or ethylene signaling. This observation indicates that the regulation of these genes is mediated at least partly by these plant hormones and suggests that the transcription factor genes are involved in the regulation of additional downstream responses mediated by these hormones. Among the 43 transcription factor genes that are induced during senescence, 28 of them also are induced by stress treatment, suggesting extensive overlap responses to these stresses. Statistical analysis of the promoter regions of the genes responsive to cold stress indicated unambiguous enrichment of known conserved transcription factor binding sites for the responses. A highly conserved novel promoter motif was identified in genes responding to a broad set of pathogen infection treatments. This observation strongly suggests that the corresponding transcription factors play general and crucial roles in the coordinated regulation of these specific regulons. Although further validation is needed, these correlative results provide a vast amount of information that can guide hypothesis-driven research to elucidate the molecular mechanisms involved in transcriptional regulation and signaling networks in plants.

Disease-Specific Expression of Host Genes During Downy Mildew Infection of Arabidopsis

“…Separate promoter analysis of the seven CS genes that are responsive to a broad range of abiotic stresses (Table 2) showed that these genes are enriched for more elements. A more significant enrichment was found of the EveningElement (P < 10 -6 ) and DREB1A/CBF3 (P < 10 -4 ) and several other elements, such as the DRE core motif (P < 10 -4 ) (consensus sequence RCCGAC) (Chen et al 2002), which is a relaxed form of DREB1A/CBF3, the CBF1 binding site (BS) (P < 10 -3 ) (consensus sequence TGGCCGAC) (Hao et al 2002) and the Zbox motif (P < 10 -3 ) (consensus sequence ATACGTGT) (Ha and An 1988). Although many CS genes show responsiveness toward ABA, the ABA responsive element ABRE (consensus sequence YACGTGGC) (Choi et al 2000) was not overrepresented and only found once in the promoter of CS-20/AtERF#109.…”

WRKY transcription factors: from DNA binding towards biological function

“…Since the WRKY transcription factors were last reviewed [2], a substantial number of WRKY-related publications have appeared. Furthermore, the availability of microarray data (http://ssbdjc2.nottingham.ac.uk/narrays/ experimentbrowse.pl; http://www.Arabidopsis.org/tools/ bulk/microarray/analysis/index.jsp) describing gene expression on a global basis is providing valuable information concerning the altered expression patterns of WRKY genes under defined experimental conditions [6,7].…”

Stress‐induced changes in the Arabidopsis thaliana transcriptome analyzed using whole‐genome tiling arrays

“…The products encoded by stress-responsive genes can directly protect the plant from stress, as in the case of late embryogenesis abundant (LEA) proteins, or play downstream roles in stress signaling, such as many transcription factors (Chen et al, 2002;Kilian et al, 2007). These studies have also led to the identification of cis-regulatory elements in the promoters of stress-responsive genes (reviewed in Yamaguchi- Shinozaki and Shinozaki, 2005).…”

“…Several reports have described the effects of abiotic stresses on the plant transcriptome (Seki et al, 2001;Chen et al, 2002;Fowler and Thomashow, 2002;Kreps et al, 2002;Provart et al, 2003;Rabbani et al, 2003;Kilian et al, 2007). The products encoded by stress-responsive genes can directly protect the plant from stress, as in the case of late embryogenesis abundant (LEA) proteins, or play downstream roles in stress signaling, such as many transcription factors (Chen et al, 2002;Kilian et al, 2007).…”