Genome assembly, analysis, and mining of Kocuria flava NIO_001: a thiopeptide antibiotic synthesizing bacterium isolated from marine sponge.

Abstract

Genome mining has been a key strategy for finding biosynthetic gene clusters (BGCs) coding for secondary metabolites in the recent past. Actinomycetia is among the important bacterial classes found in marine habitats, renowned for producing high-value secondary metabolites. Kocuria is one such gram-positive bacteria that has been reported to produce the potent antibacterial molecule kocurin/PM181104. The objective of this study was to confirm the production of kocurin/PM181104 followed by sequencing, assembly, and mining of the genome of Kocuria flava NIO_001. AntiSMASH analysis predicted the BGCs involved in the production of kocurin along with eight promising secondary metabolite-producing BGCs including non-alpha poly-amino acids like e-polylysin (NAPAA), ribosomally synthesized and post-translationally modified peptide like (RiPP-like), non-ribosomal peptide synthetase like (NRPS-like), NRPS-independent IucA/IucC-like siderophores (NI-siderophore), type III polyketide synthase (T3PKS), ε-Poly-l-lysine (NAPAA), terpene, and betalactone. Kyoto Encyclopedia for Genes and Genomes pathway analysis showed the presence of biosynthetic pathways involved in terpenoid backbone synthesis and the presence of certain hemolysin-like proteins. The present investigation is highly valuable for designing experiments to overproduce this potent antibiotic molecule by using a reverse engineering approach.