Abstract
In plants, pathogen resistance is brought about by the binding of certain transcription factor (TF) proteins to the cis-elements of certain target genes. These cis-elements are present upstream in the motif of the promoters of each gene. This ensures the binding of a specific TF 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 TF. Rice 1 kb 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. A gene with more than 4 TF bm in their promoter was selected. Ten 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 confirm the presence of the corresponding motifs in the promoter sequences of these genes. The 3D structure of WRKY13 TF and the corresponding ten 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. WRKY13 was 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 provide the mechanism of interaction. Further co-expression network helped to characterize the interaction of these selected disease resistance-related genes with the WRKY13 TF protein. This study suggests downstream target genes that are regulated by the WRKY13 TF. The molecular mechanism involving the gene network regulated by WRKY13 TF in disease resistance against rice fungal pathogens is explored.
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Data availability
All the data used in the study were retrieved from publicly available databases. Rice Genome Annotation Project (RGAP; http://rice.plantbiology.msu.edu/), Rice Annotation Project Database (RAP-DB; http://rapdb.dna.affrc.go.jp/gbl/), and Rice Oligonucleotide Array Database (ROAD; http://www.ricearray.org/) are the databases used. The commands for DNA–Protein molecular dynamic simulations can be found on the GitHub page (https://github.com/Agristars/MD-Protein-DNA).
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The authors sincerely acknowledge the support rendered by Vellore Institute of Technology, Vellore, in carrying out our research.
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JLJ—obtained the data from the databases, performed the data analysis, prepared the results, and wrote the manuscript; RK, IAE—provided the system and performed the molecular docking and simulation; SK, JLJ, SP—wrote the Perl program algorithm and sorted the genes as per the chromosomes; JLJ, CBS—contributed to identifying rice genes from the database; SB, JLJ—conceived the concept, planned the work, and contributed to result interpretation and manuscript writing. All authors read and approved the final manuscript.
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Jimmy, J.L., Karn, R., Kumari, S. et al. Rice WRKY13 TF protein binds to motifs in the promoter region to regulate downstream disease resistance-related genes. Funct Integr Genomics 23, 249 (2023). https://doi.org/10.1007/s10142-023-01167-0
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DOI: https://doi.org/10.1007/s10142-023-01167-0