An in silico strategy identified the target gene candidates regulated by dehydration responsive element binding proteins (DREBs) in Arabidopsis genome

Abstract

Identification of downstream target genes of stress-relating transcription factors (TFs) is desirable in understanding cellular responses to various environmental stimuli. However, this has long been a difficult work for both experimental and computational practices. In this research, we presented a novel computational strategy which combined the analysis of the transcription factor binding site (TFBS) contexts and machine learning approach. Using this strategy, we conducted a genome-wide investigation into novel direct target genes of dehydration responsive element binding proteins (DREBs), the members of AP2-EREBPs transcription factor super family which is reported to be responsive to various abiotic stresses in Arabidopsis. The genome-wide searching yielded in total 474 target gene candidates. With reference to the microarray data for abiotic stresses-inducible gene expression profile, 268 target gene candidates out of the total 474 genes predicted, were induced during the 24-h exposure to abiotic stresses. This takes about 57% of total predicted targets. Furthermore, GO annotations revealed that these target genes are likely involved in protein amino acid phosphorylation, protein binding and Endomembrane sorting system. The results suggested that the predicted target gene candidates were adequate to meet the essential biological principle of stress-resistance in plants.

The HaDREB2 transcription factor enhances basal thermotolerance and longevity of seeds through functional interaction with HaHSFA9

“…However, functional DREs are very difficult to predict based only on DNA sequence information. The nucleotide sequence near the core DRE element is important [ 31 , 32 ], but the conclusive determination of that sequence context would require functional analyses of a number of different promoters. Lacking additional examples for sHSP promoters activated by DREB factors in plant seeds, we can only speculate on the involved sequence context.…”

“…Whatever that context may be, we propose that it is different from that in other promoters induced in vegetative tissues by DREB proteins such as AtDREB2A. This could explain why no Arabidopsis CI or CII sHSP genes were predicted as target gene candidates for the former DREB2 proteins, as predictions were based on DRE sequence contexts determined for AtDREB2A and its target genes (see [ 32 ] and references therein). Thus, if DREB2 factors different from AtDREB2A are involved in the regulation of sHSP genes in Arabidopsis seeds, they could recognize a different DRE promoter context.…”

Expression Patterns of GmAP2/EREB-Like Transcription Factors Involved in Soybean Responses to Water Deficit

“…In spite of these common domains, At DREB1 has been implicated in cold stress responses [11], whereas the functions of the At DREB2 genes have been mainly described in response to water deficit and osmotic stress [12], [13]. Using an in silico analysis strategy, Wang and colleagues [14] searched for Arabidopsis thaliana genes with DRE motifs and identified 474 target genes to which the DREB transcription factors might bind. Of these genes, 160 were responsive to abiotic stresses, 27 of which were specifically regulated in response to water deficit.…”

DRE-binding Transcription factor (DREB1A) as a master regulator induced a broad range of abiotic stress tolerance in plant

“…On the other means, the DREB1A gene play a crucial role in providing tolerance to multiple stresses and display overlapping responses to different stress conditions. In addition, stress treatments analysis has revealed that negative effects induced by abiotic stresses could be overlapped altogether, and on the other hand, Wang et al (2009) identified ten genes that act as the cross-talkers in all likelihood among the drought, salinity and cold responsive pathways and have DRE motifs within the 300 bp upstream of the start codon. Most of the environmental stresses, at least in part, have similar adverse effects on plants.…”