Genome Mining of a Tribrid Biosynthetic Gene Cluster Family in Bacteria

Bacterial hybrid secondary metabolites (SMs) biosynthesized by two kinds of biosynthetic enzymes are celebrated for their intricate structures and potent bioactivities. Tribrid SMs from the biosynthetic pathways including polyunsaturated fatty acid synthases (PUFASs), non-ribosomal peptide synthetases (NRPSs) and polyketide synthases (PKSs), are exceedingly rare, as only zeamines and fabclavines, both endowed with broad-spectrum antibiotic properties, have been identified thus far. In this study, we expanded the knowledge of tribrid PUFAS-NRPS-PKS gene clusters by a bioinformatics-assisted phylogenetic analysis, and discovered a previously unknown tribrid gene cluster family in β-proteobacteria. Following complementary genome mining strategies, targeted isolation and structure elucidation, three classes of tribrid PUFA-NRP-PK metabolites: megapolipeptins, chromopeptins, and chitinimopeptins, were identified from various proteobacteria, and their biosynthetic pathways were proposed on the basis of the gene organization of corresponding gene clusters. Notably, chromopeptins are cytotoxic, chitinimopeptins exhibit antifungal bioactivity, and both of them facilitate bacterial swarming motility. The genome mining and identification of tribrid gene clusters expand the structural and bioactive diversity of bacterial SMs, highlighting the potential of applying genomics-directed approaches for the discovery of novel natural products.