Whole-genome sequencing of a protease-producing strain isolated from fermented golden pompano and molecular docking of the protease to fish proteins

In fermented fish products, microorganisms catalyze protein degradation by secreting proteases, thereby altering the nutritional values of foods. In this study, we isolated a high proteinase-producing strain from fermented golden pompano (Trachinotus ovatus), and from the 16S rRNA, we identified the strain as Bacillus tropicus, which we named Bacillus tropicus MX-8. This strain could form a distinct proteolytic circle around the colony when plated on agar containing 3% skimmed milk powder and could grow under 0–5% salinity. Its protease significantly degraded fish proteins. Genome sequencing analysis revealed that the genome of B. tropicus MX-8 comprised one circular chromosome and three circular plasmids. A total of 27 genes encoding proteases, including a neutral protease and three serine proteases, were identified in the non-redundant protein database. Homology modeling showed that serine protease 2 had the best model quality and the highest sequence match. Molecular docking experiments revealed the presence of several amino acid active sites on serine protease 2. These active sites mainly rely on hydrogen bonding to interact with actin heavy chains and myosin to form complexes, which can promote further protein degradation. This study demonstrated that B. tropicus MX-8 has the potential to ferment fish, providing a theoretical basis for the production of rapidly fermented fish products.