Diverse and Abundant Secondary Metabolism Biosynthetic Gene Clusters in the Genomes of Marine Sponge Derived Streptomyces spp. Isolates

Abstract

The genus Streptomyces produces secondary metabolic compounds that are rich in biological activity. Many of these compounds are genetically encoded by large secondary metabolism biosynthetic gene clusters (smBGCs) such as polyketide synthases (PKS) and non-ribosomal peptide synthetases (NRPS) which are modular and can be highly repetitive. Due to the repeats, these gene clusters can be difficult to resolve using short read next generation datasets and are often quite poorly predicted using standard approaches. We have sequenced the genomes of 13 Streptomyces spp. strains isolated from shallow water and deep-sea sponges that display antimicrobial activities against a number of clinically relevant bacterial and yeast species. Draft genomes have been assembled and smBGCs have been identified using the antiSMASH (antibiotics and Secondary Metabolite Analysis Shell) web platform. We have compared the smBGCs amongst strains in the search for novel sequences conferring the potential to produce novel bioactive secondary metabolites. The strains in this study recruit to four distinct clades within the genus Streptomyces. The marine strains host abundant smBGCs which encode polyketides, NRPS, siderophores, bacteriocins and lantipeptides. The deep-sea strains appear to be enriched with gene clusters encoding NRPS. Marine adaptations are evident in the sponge-derived strains which are enriched for genes involved in the biosynthesis and transport of compatible solutes and for heat-shock proteins. Streptomyces spp. from marine environments are a promising source of novel bioactive secondary metabolites as the abundance and diversity of smBGCs show high degrees of novelty. Sponge derived Streptomyces spp. isolates appear to display genomic adaptations to marine living when compared to terrestrial strains.

Comparative Genomics of Microbacterium Species to Reveal Diversity, Potential for Secondary Metabolites and Heavy Metal Resistance

“…Compared to well-known Actinobacteria like Streptomyces , Microbacterium have smaller genomes (10 Mb vs. 3.5 Mb). Consequently, they host a lower number of secondary metabolite gene clusters ( Jackson et al, 2019 ). Nonetheless, several secondary metabolite gene clusters were predicted by antiSMASH.…”

Diversity and Applications of Endophytic Actinobacteria of Plants in Special and Other Ecological Niches

“…Genome mining tools have made it more convenient to look for innovations in natural product discovery (Corre and Challis, 2007 ). Majority of the bioactive compounds are encoded by large gene clusters such as polyketide synthases (PKS) and non-ribosomal peptide synthetases (NRPS) with highly repetitive modules (Jackson et al, 2018 ).…”

Streptomyces spp. From the Marine Sponge Antho dichotoma: Analyses of Secondary Metabolite Biosynthesis Gene Clusters and Some of Their Products

“…Such elements may be represented by transposons, often also hosted by GLPs, and many BGCs contain transposon-like elements, or even look like composite transposons themselves, as in the case of the enterocin biosynthetic gene cluster in marine sponge-derived Streptomyces albus (Ian et al, 2014). Recently, Jackson et al reported the analyses of 13 genomes of streptomycetes isolated from various marine sponges (Jackson et al, 2018). Many unique BGCs were identified, suggesting potential of these bacteria in terms of production of novel bioactive secondary metabolites.…”