Homotypic clustering of OsMYB4 binding site motifs in promoters of the rice genome and cellular-level implications on sheath blight disease resistance

Singh Pooja; Kumari Sweta; A Mohanapriya; C Sudandiradoss; Ramamoorthy Siva; Kodiveri M Gothandam; Subramanian Babu

doi:10.1016/j.gene.2015.02.031

Homotypic clustering of OsMYB4 binding site motifs in promoters of the rice genome and cellular-level implications on sheath blight disease resistance

Gene. 2015 May 1;561(2):209-18. doi: 10.1016/j.gene.2015.02.031. Epub 2015 Feb 14.

Authors

Singh Pooja¹, Kumari Sweta¹, A Mohanapriya¹, C Sudandiradoss¹, Ramamoorthy Siva¹, Kodiveri M Gothandam¹, Subramanian Babu²

Affiliations

¹ School of Bio Sciences and Technology, VIT University, Vellore 632014, India.
² School of Bio Sciences and Technology, VIT University, Vellore 632014, India. Electronic address: [email protected].

PMID: 25688880
DOI: 10.1016/j.gene.2015.02.031

Abstract

The promoter regions (1 kb upstream sequences) of 45,836 annotated genes of rice were analyzed for the presence of OsMYB4 binding sites using a Perl program algorithm. Based on the homotypic clustering concept, 113 promoters were found to have more than 4 binding site motifs. Among the downstream genes of these promoters, five genes which are known to have a role in disease resistance were selected and the binding capacity of OsMYB4 protein in the promoter regions was analyzed by docking studies. Expression level of these genes was analyzed by RT-PCR in Rhizoctonia solani infected rice seedlings. Upon pathogen challenge, higher expression of aminotransferase, ankyrin and WRKY 12 genes was observed corresponding to higher expression of Osmyb4. Over-expression of Osmyb4 cDNA in rice leaf tissues by agro-infection failed to result in similar over-expression of aminotransferase, ankyrin and WRKY 12 as expected. Although the role of OsMYB4 in sheath blight resistance was found to be definitive based on our initial results, artificial over-expression of this TF was observed to be insufficient in regulating the disease resistance related genes.

Keywords: Homotypic clusters; OsMYB4; Rice; Sheath blight; Transcription factor.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Algorithms
Binding Sites
Computational Biology
Disease Resistance*
Gene Expression Regulation, Plant
Molecular Docking Simulation
Oryza / genetics*
Oryza / immunology*
Plant Diseases / genetics*
Plant Diseases / immunology
Plant Diseases / microbiology
Plant Proteins / chemistry
Plant Proteins / genetics*
Plant Proteins / metabolism*
Plants, Genetically Modified
Promoter Regions, Genetic
Rhizoctonia / physiology

Substances

Plant Proteins