In-silico Analysis and Functional Characterization of Rhizoctonia solani Effector Proteins
K. Prudhvi Raj Kumar *
Department of Plant Biotechnology, Tamil Nadu Agricultural University, Coimbatore, Tamil Nadu, India.
P. Vignesh
Department of Plant Pathology, Tamil Nadu Agricultural University, Coimbatore, Tamil Nadu, India.
A. Shanthinie
Department of Plant Biotechnology, Tamil Nadu Agricultural University, Coimbatore, Tamil Nadu, India.
D. Sudhakar
Department of Plant Biotechnology, Tamil Nadu Agricultural University, Coimbatore, Tamil Nadu, India.
E. Kokiladevi
Department of Plant Biotechnology, Tamil Nadu Agricultural University, Coimbatore, Tamil Nadu, India.
R. Raghu
Department of Plant Biotechnology, Tamil Nadu Agricultural University, Coimbatore, Tamil Nadu, India.
M. Jayakanthan
Department of Plant Molecular Biology and Bioinformatics, Tamil Nadu Agricultural University, Coimbatore, Tamil Nadu, India.
S. Varanavasiappan
Department of Plant Biotechnology, Tamil Nadu Agricultural University, Coimbatore, Tamil Nadu, India.
*Author to whom correspondence should be addressed.
Abstract
Sheath blight is considered the second most prevalent disease in rice with no proper resistance genes identified for its resistance. Out of the 14 anastomosis groups in R. solani (AG1 to AG13 and AGBI), the AG1 group is mostly responsible for the infection in the rice. There are many effector proteins under this group, function as transcription factors. Many bioinformatics tools are available to determine the interaction between the promoter region and effector proteins. But in an attempt to use these effector proteins for molecular docking and simulation studies, criteria like In-silico analysis and validation of the proteins are to be analyzed. The reactivity and stability of these proteins were evaluated physicochemically, domain prediction, and secondary structure prediction using bioinformatics methods such as Protparam, Pfam, and SOPMA, respectively. These bioinformatics techniques were found to be remarkably suitable for characterizing the protein's function. Robetta an abinitio approach was used to predict the 3D structure, and the models were validated using the SAVESv6.0 (PROCHECK) server. The effector protein functional analysis and 3D structure predictions made using empirical data can shed light on the interaction studies for locating effector binding elements in the promoter regions of host genes.
Keywords: Effector binding element, In-silico analysis, PROCHECK, R. solani, Robetta