Whole-genome Sequencing and Mining of Protease Coding Genes in Bacillus paralicheniformis MKU3, and its Degradomics in Feather Meal Medium

Abstract

Bacillus paralicheniformis MKU3 produces commercially important keratinolytic proteases by utilizing chicken feather. To unravel the genetics of these degrading keratinolytic proteases in B. paralicheniformis MKU3, we sequenced the genome of this bacterium and studied the protease distribution and their characteristics using bioinformatics tools. Also, a proteomic analysis was performed to identify the consortium of proteases involved in feather hydrolysis. A total of 2,531,755 quality reads were obtained in whole genome sequencing with an approximate coverage fold of 105. The draft genome consists of 4,370,039 bp with 45 contigs. The draft genome codes for 4874 protein-coding genes. Furthermore, 109 genes coding for RNA, including 26 rRNA and 83 tRNA, were identified. Phylogenetic analysis of B. paralicheniformis MKU3 showed closest homolog to B. paralicheniformis F47. Genes coding for proteases belonging to five families were identified with the following proportions 37%, 36%, 9%, 14%, 2%, and 2% of serine-, metallo-, cysteine-, mixed-, and uncharacterized proteases, respectively. Metallo- and serine-protease represented more than 70% of the total proteases. Major protease families distributed in the genome were S8, S9, S33, M20, M50, C26, and C40. Most of the proteases showed significant similarity with the conserved domain database and also identified conserved catalytic sites and domains. SDS-PAGE and zymogram analysis of concentrated feather hydrolysis revealed the active proteases ranging from 10 to 250 kD in size. Proteomic analysis on the feather hydrolysis of B. paralicheniformis MKU3 identified two proteases belonging to serine proteases (S8) and other two as metalloproteases.