Genome mining of Streptomyces bambergiensis AC-800 unravels the biosynthetic gene cluster for inhibitors of prolyl hydroxylase fibrostatins

Abstract

Abstract Streptomyces bambergiensis AC-800 is known as a producer of moenomycin family antibiotics active against gram-positive bacteria. Complete genome sequencing of S. bambergiensis revealed 3 replicons represented by the linear chromosome (7,652,101 bp) and two linear plasmids, pSB1 (418,507 bp) and pSB2 (81,486 bp). Analysis of the chromosome for the presence of secondary metabolite biosynthesis gene clusters (BGCs) revealed 25 BGCs, while other 4 were located on the linear plasmid pSB1. The bioinformatics-based analysis of the moenomycin BGC provided new insights into its biosynthesis. The largest reported polyketide synthase gene cluster spanning over 190 kb was identified on the pSB1 plasmid, with its putative product likely to be represented by a 67-membered glycosylated macrolide related to stambomycins. Co-cultivation of S. bambergiensis AC-800 with a strain of Rhodococcus isolated from a fresh-water bryozoan induced production of a red pigment tentatively identified as fibrostatin. CRISPR-BEST-assisted inactivation of the only PKSIII-encoding gene abolished the production of fibrostatin, allowing the identification of the previously unreported fibrostatin BGC. Subsequent secondary metabolomics of S. bambergiensis cultivated in different media revealed production of both known and presumably novel compounds. This study sets a stage for further investigation of this strain by means of genome mining that may result in the discovery of novel bioactive natural products.