Rice WRKY13 TF protein binds to motifs in the promoter region to regulate downstream disease resistance-related genes

TLDR: In this article , the authors used the Perl program algorithm to detect WRKY13 binding motifs (bm) in the promoters of each gene and then selected nine genes reported to have a role in rice disease resistance.

Abstract: Abstract In plants, pathogen resistance is brought about due to the binding of certain transcription factors (TF) proteins to the cis-elements of certain target genes. These cis-elements are present up-stream in the motif of the promoters of each gene. This ensures the binding of a specific transcription factor to a specific promoter, therefore regulating the expression of that gene. Therefore, the study of each promoter sequence of all the rice genes would help identify the target genes of a specific transcription factor. Rice 1kb upstream promoter sequences of 55,986 annotated genes were analyzed using the Perl program algorithm to detect WRKY13 binding motifs (bm). The resulting genes were grouped using gene ontology and gene set enrichment analysis. Gene with more than 4 TFbm in their promoter was selected. Nine genes reported to have a role in rice disease resistance were selected for further analysis. Cis -acting regulatory element analysis was carried out to find the cis-elements and to confirm the presence of the corresponding motifs in the promoter sequences of these genes. The 3D structure of WRKY13 TF and the corresponding nine genes were built and the interacting residues were determined. The binding capacity of WRKY13 to the promoter of these selected genes was analyzed using docking studies. WRKY 13 was also considered for docking analysis based on the prior reports of autoregulation. Molecular dynamic simulations provided more details regarding the interactions. Expression data revealed the expression of the genes that helped to provide the mechanism of interaction. Further co-expression network helped to characterize the interaction of these selected diseases resistance-related genes with WRKY13 TF protein. This study suggests the target downstream genes that are regulated by WRKY13 TF. The molecular mechanism involving the gene network regulated by WRKY13 TF in disease resistance against rice fungal pathogens is explored.