In-silico diversity analysis of disease resistant NBS-LRR protein variants in Oryza sativa

Abstract

Oryza sativa (rice) being the contributor of more than 2 million tons of staple food plays assorted role in agrarian economy of Pakistan. Variety of pathogens and use of insecticides result in serious loses of its yield. To develop immunity at genetic level in O. sativa crops is the crucial need of the time. A diverse disease resistant gene restricts the polycyclic epidemics development induced by pathogens in the plants. Nucleotide binding site-leucine rich repeat proteins (NBS-LRR) being associated with regulation of plant proteins targeted by pathogens and detection of diverse pathogens are considered as adaptable guards for plants. Eight genes from O. sativa encoding eight NBS-LRR protein variants have been targeted for their diversity analysis in present study. For characterization of NBS-LRR disease resistant protein in O. sativa, eight nucleotide sequences were retrieved from Rice Genome Annotation Project (RGAP) database and translated via Expasy translation tool. The eight protein variants were then assessed for their physicochemical properties, sub-cellular localizations, 2D and 3D configurations using ProtParam, CELLO2 and SOPMA tools and SWISS MODEL server. These eight forms of disease resistant protein showed great diversity in their attributes. Highest number of amino acids and molecular weights were observed in case of NBS-LRR2 and LRR4. Isoelectric point (I), instability index, aliphatic and GRAVY showed only slight variation. Extinction coefficient showed considerable variation with highest and lowest values for LBS-LRR2 and LRR1, respectively. Diversity was also observed in sub-cellular localization of these NBS-LRR variants i. e. LRR1, 2, 4 and 6 (nuclear + cytoplasmic), LRR2, 3 and 7 (nuclear only) and LRR5, 6 and 8 (cytoplasmic only). Secondary structure was highly variable in terms of extended strand (ranging between 9.51% and 12.75%) and beta turn (ranging between 1.88% and 5.65%) while only small difference was observed in case of alpha helix and random coil. The 3D configurations of all the variants of protein documented in present study showed great variation and high level of complexity. This characterization revealed significant heterogeneity among different forms of disease resistant NBS-LRR proteins. Selective breeding of rice plants containing the diverse forms of the gene, addressed in present study will help to remove homogeneity in rice crops. This might result in reduced epidemics, yield stability and resistance durability.