Abstract
Transcription factors (TFs) are major players in stress signaling and constitute an integral part of signaling networks. Among the major TFs, WRKY proteins play pivotal roles in regulation of transcriptional reprogramming associated with stress responses. In view of this, genome- and transcriptome-wide identification of WRKY TF family was performed in the C4model plants, Setaria italica (SiWRKY) and S. viridis (SvWRKY), respectively. The study identified 105 SiWRKY and 44 SvWRKY proteins that were computationally analyzed for their physicochemical properties. Sequence alignment and phylogenetic analysis classified these proteins into three major groups, namely I, II, and III with majority of WRKY proteins belonging to group II (53 SiWRKY and 23 SvWRKY), followed by group III (39 SiWRKY and 11 SvWRKY) and group I (10 SiWRKY and 6 SvWRKY). Group II proteins were further classified into 5 subgroups (IIa to IIe) based on their phylogeny. Domain analysis showed the presence of WRKY motif and zinc finger-like structures in these proteins along with additional domains in a few proteins. All SiWRKY genes were physically mapped on the S. italica genome and their duplication analysis revealed that 10 and 8 gene pairs underwent tandem and segmental duplications, respectively. Comparative mapping of SiWRKY and SvWRKY genes in related C4 panicoid genomes demonstrated the orthologous relationships between these genomes. In silico expression analysis of SiWRKY and SvWRKY genes showed their differential expression patterns in different tissues and stress conditions. Expression profiling of candidate SiWRKY genes in response to stress (dehydration and salinity) and hormone treatments (abscisic acid, salicylic acid, and methyl jasmonate) suggested the putative involvement of SiWRKY066 and SiWRKY082 in stress and hormone signaling. These genes could be potential candidates for further characterization to delineate their functional roles in abiotic stress signaling.
Highlights
Plants are exposed to diverse environmental stresses, which significantly affect their growth and development leading to drastic decrease in productivity
Being the first comprehensive study on WRKY Transcription factors (TFs) in S. italica and S. viridis, the present study provides insights into the functional aspects of these TFs in response to abiotic stress, and highlights potential candidates for further characterization toward delineating their functional role in abiotic stress signaling
HMM search for WRKY proteins in Setaria italica showed the presence of 113 WRKY proteins (SiWRKY), which was in agreement with the numbers reported in Plant Transcription Factor Database v3.0 (Jin et al, 2014) and Foxtail millet Transcription Factor Database (Bonthala et al, 2014)
Summary
Plants are exposed to diverse environmental stresses, which significantly affect their growth and development leading to drastic decrease in productivity. Transcription factors (TFs) are a class of genes that predominate as tolerance determinants in plants (Mickelbart et al, 2015) by regulating the expression of stress-inducible genes. WRKY TFs are characterized by their unique WRKYGQK motif followed by a metal chelating zinc finger motif (CX4−5CX22−23HXH or CX5−8CX25−28HX1−2C) (Eulgem et al, 2000). These WRKY proteins bind to a specific domain called W-box in the promoter region with consensus sequence (C/T)TGAC[T/C], resulting in the expression of downstream target genes (Eulgem et al, 2000). In addition to W-box, WRKY TFs can interact with a sugar responsive cis-element called SURE and activate transcription of downstream genes (Sun et al, 2003)
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