Abstract
APETALA2/ethylene-responsive element binding protein (AP2/EREBP) transcription factors constitute one of the largest and most conserved gene families in plant, and play essential roles in growth, development and stress response. Except a few members, the AP2/EREBP family has not been characterized in Brachypodium distachyon, a model plant of Poaceae. We performed a genome-wide study of this family in B. distachyon by phylogenetic analyses, transactivation assays and transcript profiling. A total of 149 AP2/EREBP genes were identified and divided into four subfamilies, i.e., ERF (ethylene responsive factor), DREB (dehydration responsive element binding gene), RAV (related to ABI3/VP) and AP2. Tandem duplication was a major force in expanding B. distachyon AP2/EREBP (BdAP2/EREBP) family. Despite a significant expansion, genomic organizations of BdAP2/EREBPs were monotonous as the majority of them, except those of AP2 subfamily, had no intron. An analysis of transcription activities of several closely related and duplicated BdDREB genes showed their functional divergence and redundancy in evolution. The expression of BdAP2/EREBPs in different tissues and the expression of DREB/ERF subfamilies in B. distachyon, wheat and rice under abiotic stresses were investigated by next-generation sequencing and microarray profiling. Our results are valuable for further function analysis of stress tolerant AP2/EREBP genes in B. distachyon.
Highlights
The APETALA2/ethylene-responsive element binding protein (AP2/EREBP) superfamily is one of the largest groups of plant specific transcription factors
Based on the amino acid sequence of the AP2 domain, the ERF family can be further divided into the dehydration-responsive element-binding protein (DREB) and ERF subfamilies, or the groups A and B, each of which consists of six groups individually
Based on a stringent Hidden Markov Model (HMM) and using restrictive BLAST searches, 189 putative AP2/EREBP proteins were identified in the B. distachyon reference genome and represent 0.44% of the annotated proteins in B. distachyon[19,44]
Summary
Identification of the AP2/EREBP superfamily in B. distachyon. Based on a stringent HMM and using restrictive BLAST searches (see Methods), 189 putative AP2/EREBP proteins were identified in the B. distachyon reference genome (version 3.0) and represent 0.44% of the annotated proteins in B. distachyon[19,44]. Together in the subgroup IIId (Figure S1) were all up-regulated significantly at least at three points after cold stress; while the expression of its paralogs in wheat were not profiled since the probe sets of these genes were not on the microarray used These results suggested functional conservation and divergence of DREBs during the Pooideae evolution. Expression analysis of the DREB/ERF subfamily genes in wheat, rice and B. distachyon under cold, high-salinity, drought or heat stresses revealed diverse differential expression of these genes and their possible roles in response to these stresses. In B. distachyon, 11 BdDREB genes that clustered together in the subgroup IIId of A1 group (Figure S1) and were all significantly induced by cold could be further studied and be exploited to enhance stress tolerance These results would help expand our knowledge of this important class of transcription factors in plant stress resistance. The functions of the superfamily genes were expanded and enhanced through gene duplication
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