Palmerolide PKS-NRPS gene clusters characterized from the microbiome of an Antarctic ascidian
Polyketides are a complex family of natural products that often serve competitive or pro-survival purposes but can also demonstrate bioactivity in human diseases as, for example cholesterol lowering agents, anti-infectives, or anti-tumor agents. Marine invertebrates and microbes are a rich source of polyketides. Palmerolide A, a polyketide isolated from the Antarctic ascidian Synoicum adareanum, is a vacuolar-ATPase inhibitor with potent bioactivity against melanoma cell lines. The biosynthetic gene clusters (BGC) responsible for production of secondary metabolites are encoded in the genomes of the producers as discrete genomic elements. A putative palmerolide BGC was identified from a S. adareanum metagenome based on a high degree of congruence with a chemical structure-based retrobiosynthetic prediction. Protein family homology analysis, conserved domain searches, and active site and motif identification were used to confirm the identity and propose the function of the 75 kb trans-acyltransferase (AT) polyketide synthase-non-ribosomal synthase (PKS-NRPS) domains responsible for the synthesis of palmerolide A. Though PKS systems often act in a predictable co-linear sequence, this BGC includes multiple trans-acting enzymatic domains, a non-canonical condensation termination domain, a bacterial luciferase-like monooxygenase (LLM), and multiple copies found within the metagenome-assembled genome (MAG) of Candidatus Synoicohabitans palmerolidicus. Detailed inspection of the five highly similar pal BGC copies suggests the potential for biosynthesis of other members of the palmerolide chemical family. This is the first delineation of a biosynthetic gene cluster from an Antarctic species. These findings have relevance for fundamental knowledge of PKS combinatorial biosynthesis and could enhance drug development efforts of palmerolide A through heterologous gene expression.