Abstract
Sponge metagenomes are a useful platform to mine cryptic biosynthetic gene clusters responsible for production of natural products involved in the sponge-microbe association. Since numerous sponge-derived bioactive metabolites are biosynthesized by the symbiotic bacteria, this strategy may concurrently reveal sponge-symbiont produced compounds. Accordingly, a metagenomic analysis of the Japanese marine sponge Discodermia calyx has resulted in the identification of a hybrid type I polyketide synthase-nonribosomal peptide synthetase gene (kas). Bioinformatic analysis of the gene product suggested its involvement in the biosynthesis of kasumigamide, a tetrapeptide originally isolated from freshwater free-living cyanobacterium Microcystis aeruginosa NIES-87. Subsequent investigation of the sponge metabolic profile revealed the presence of kasumigamide in the sponge extract. The kasumigamide producing bacterium was identified as an ‘Entotheonella’ sp. Moreover, an in silico analysis of kas gene homologs uncovered the presence of kas family genes in two additional bacteria from different phyla. The production of kasumigamide by distantly related multiple bacterial strains implicates horizontal gene transfer and raises the potential for a wider distribution across other bacterial groups.
Highlights
Metagenome mining strategies [1] are applicable for the discovery of unknown compounds, polyketides and nonribosomal peptides, from uncultured bacteria
Sequencing of the fosmid clones revealed the existence of a hybrid polyketide synthase (PKS)-nonribosomal peptide synthetases (NRPS) biosynthetic gene cluster (Table 1, Fig 2), composed of 9 open reading frames (ORFs), with kasA-C forming a PKS-NRPS core
The substrates for the five A domains (KasA-A1, KasB-A1, A2, KasC-A1, and A2) were predicted from the NRPS codes [19] with the exception of KasA-A1, which was unmatched to known data, but annotated to the A domain recruiting phenyl pyruvic acid (PP) based on the close resemblance to
Summary
Metagenome mining strategies [1] are applicable for the discovery of unknown compounds, polyketides and nonribosomal peptides, from uncultured bacteria. Based on the colinearity rule of domain and module organization of modular polyketide synthase (PKS) and nonribosomal peptide synthetases (NRPS) [2,3], it is possible to predict the chemical structures of products derived from orphan gene clusters comprising PKS and/or NRPS genes. As many polyketides and nonribosomal peptides have been isolated from marine sponges, and there is strong evidence that those natural products are produced by their microbial symbionts, sponge metagenomes have become a useful source for identifying the real producers of those natural products. Technology (MEXT), Japan (JSPS KAKENHI Grant Numbers JP16H06443, JP16H06448, JP16K13084, JP15H01836, JP15H03112, JP15K12740, and JP26303005). Y.N. is a recipient of the JSPS Fellowship for Young Scientist. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript
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