Abstract
WRKY transcription factors regulate diverse biological processes in plants, including abiotic and biotic stress responses, and constitute one of the largest transcription factor families in higher plants. Although the past decade has seen significant progress towards identifying and functionally characterizing WRKY genes in diverse species, little is known about the WRKY family in sorghum (Sorghum bicolor (L.) moench). Here we report the comprehensive identification of 94 putative WRKY transcription factors (SbWRKYs). The SbWRKYs were divided into three groups (I, II, and III), with those in group II further classified into five subgroups (IIa-IIe), based on their conserved domains and zinc finger motif types. WRKYs from the model plant Arabidopsis (Arabidopsis thaliana) were used for the phylogenetic analysis of all SbWRKY genes. Motif analysis showed that all SbWRKYs contained either one or two WRKY domains and that SbWRKYs within the same group had similar motif compositions. SbWRKY genes were located on all 10 sorghum chromosomes, and some gene clusters and two tandem duplications were detected. SbWRKY gene structure analysis showed that they contained 0-7 introns, with most SbWRKY genes consisting of two introns and three exons. Gene ontology (GO) annotation functionally categorized SbWRKYs under cellular components, molecular functions and biological processes. A cis-element analysis showed that all SbWRKYs contain at least one stress response-related cis-element. We exploited publicly available microarray datasets to analyze the expression profiles of 78 SbWRKY genes at different growth stages and in different tissues. The induction of SbWRKYs by different abiotic stresses hinted at their potential involvement in stress responses. qRT-PCR analysis revealed different expression patterns for SbWRKYs during drought stress. Functionally characterized WRKY genes in Arabidopsis and other species will provide clues for the functional characterization of putative orthologs in sorghum. Thus, the present study delivers a solid foundation for future functional studies of SbWRKY genes and their roles in the response to critical stresses such as drought.
Highlights
WRKY transcription factors (TFs), one of the largest TF families in plants, regulate various biological processes, including stress responses
The Plant Transcription Factor Database version 4 was used to download the amino acid sequences of sorghum WRKY proteins, and "WRKY" was used as a query to search against the Grassius Transcription Factor Database
Taking advantage of the availability of a complete genome assembly for sorghum, we identified SbWRKY family members using the keyword “WRKY” and the WRKY domain consensus sequence (PF03106) as queries in different databases
Summary
WRKY transcription factors (TFs), one of the largest TF families in plants, regulate various biological processes, including stress responses. WRKY proteins contain a conserved WRKYGQK motif at their N-terminus, along with a 60-amino-acid-long zinc finger motif at their C-terminus [1]. These two motifs are essential for the binding of WRKY TFs to the Wbox cis-element [(T)TGAC(C/T)] located within the promoters of their target genes. WRKY proteins can be classified into three groups (I, II, and III) according to the number of WRKY domains and the type of zinc finger motif, i.e., C2H2 or C2HC [2]. Group II members have only one WRKY domain and a C2H2 zinc finger motif and can be further classified into five subgroups (IIa, IIb, IIc, IId, and IIe) based on the sequence of the DNA-binding domain. Group III members have one WRKY domain and a C2HC-type zinc finger [3, 4]
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