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

التفاصيل البيبلوغرافية
العنوان: Rice WRKY13 TF protein binds to motifs in the promoter region to regulate downstream disease resistance-related genes.
المؤلفون: Jimmy JL; School of Bio Science and Technology, Vellore Institute of Technology, Vellore, 632014, India. jimmyjohn10290@gmail.com., Karn R; School of Bio Science and Technology, Vellore Institute of Technology, Vellore, 632014, India., Kumari S; School of Bio Science and Technology, Vellore Institute of Technology, Vellore, 632014, India., Sruthilaxmi CB; School of Bio Science and Technology, Vellore Institute of Technology, Vellore, 632014, India., Pooja S; School of Science, Monash University Malaysia, Bandar Sunway, Selangor, Malaysia., Emerson IA; School of Bio Science and Technology, Vellore Institute of Technology, Vellore, 632014, India., Babu S; VIT School of Agricultural Innovations and Advanced Learning, Vellore Institute of Technology, Vellore, 632014, India.
المصدر: Functional & integrative genomics [Funct Integr Genomics] 2023 Jul 20; Vol. 23 (3), pp. 249. Date of Electronic Publication: 2023 Jul 20.
نوع المنشور: Journal Article
اللغة: English
بيانات الدورية: Publisher: Springer Country of Publication: Germany NLM ID: 100939343 Publication Model: Electronic Cited Medium: Internet ISSN: 1438-7948 (Electronic) Linking ISSN: 1438793X NLM ISO Abbreviation: Funct Integr Genomics Subsets: MEDLINE
أسماء مطبوعة: Original Publication: Berlin : Springer, c2000-
مواضيع طبية MeSH: Transcription Factors*/genetics , Transcription Factors*/metabolism , Oryza*/metabolism, Disease Resistance/genetics ; Promoter Regions, Genetic ; Gene Regulatory Networks
مستخلص: 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.
(© 2023. The Author(s), under exclusive licence to Springer-Verlag GmbH Germany, part of Springer Nature.)
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فهرسة مساهمة: Keywords: Cis-acting regulatory elements; Gene Ontology; Gene set enrichment; Motif; Promoter analysis; Transcription factor; WRKY13
المشرفين على المادة: 0 (Transcription Factors)
تواريخ الأحداث: Date Created: 20230720 Date Completed: 20230920 Latest Revision: 20230922
رمز التحديث: 20230922
DOI: 10.1007/s10142-023-01167-0
PMID: 37474674
قاعدة البيانات: MEDLINE
الوصف
تدمد:1438-7948
DOI:10.1007/s10142-023-01167-0