In silico identification and prediction of structural, functional, and regulatory effects of haplotypes in beta-1,3-glucanase (os09g0533200/loc_os09g36280) of rice

Abstract

The gene Os09g0533200/ LOC_Os09g36280 encoding beta-1,3-glucanase was reported to have the strongest effect against rice sheath blight (ShB). Haplotypes are sets of single nucleotide polymorphisms (SNPs) that are inherited together. The examination of haplotypes in Os09g0533200/ Loc_Os09g36280 could contribute to better understanding of the mechanisms behind sheath blight resistance. Haplotypes in Os09g0533200/ LOC_Os09g36280 have not been investigated. In this study, haplotypes were identified and their regulatory, structural, and functional effects were predicted. Transcription factor binding sites (TFBSs) were predicted to determine the effects of the haplotypes on gene regulation. Homology modeling and comparison of physicochemical properties were performed to determine if the haplotypes had any effects on the resulting protein structure. Protein networks were predicted to determine the proteins interactors of beta-1,3-glucanase. Docking of protein interactors to the wild-type and haplotype proteins was done to determine which interactions were the most stable. Twelve SNPs and three previously unreported haplotypes, designated as hap1, hap2, and hap3, were detected. hap3 was the only haplotype that resulted in an amino acid change. hap3 protein has a similar structure, folding patterns, and physicochemical properties with the wild-type protein. Seventy-five percent of protein interactors of the beta-1,3-glucanase have been found to be more spontaneous when interacted with hap3. TFBSs of the haplotype-bearing genes were not significantly changed. Hence, the identified haplotypes have minimal structural and regulatory effects but may have significant functional effects.