The whole-genome shotgun sequence of a chitinolytic actinomycete, Streptomyces californicus TBG-201, and the in-silico studies of its chitinase-19 genes

Abstract

Streptomyces species are reported to have family-19 chitinases, similar to plant chitinase-C. Streptomyces griseus HUT6037 is the first Streptomyces spp. found to produce family-19 chitinase. Chitinolytic Streptomyces have been reported to have antifungal activity against phytopathogenic fungi. Chitinase-19 (GH-19) has received much attention in recent decades because of its potential use in the biocontrol of phytopathogens like insects and fungi. According to reports, chitinase C has a significantly higher specific hydrolyzing activity than the common bacterial family-18 chitinases. This study presents the whole genome sequence of a chitinolytic isolate, S. californicus TBG-201. The genome is 7.99 Mb, with 72.60% G + C content, 6683 protein-coding genes, 31 rRNAs, 66 tRNAs, and 116 pseudogenes. Genome annotation using Glimmer, PGAP, and dbCAN provides insights into its chitinolytic activity. Multiple genes in the genome are involved in chitin degradation; based on this, a chitin degradation mechanism for S. californicus TBG-201 is presented. There are 35 biosynthetic gene clusters predicted from the whole genome sequence using the antiSMASH tool. The study further focused on the in-silico analysis of chitinase-19 genes, including phylogenetic analysis, physicochemical characterization, and functional studies. Homology modeling using the SWISS-MODEL server followed by docking studies has a better understood the enzyme structure and ligand binding features. The insights gathered from in-silico investigations would greatly assist in elucidating the in vitro characteristics of S. californicus chitinase-19.