Bioinformatic and Mechanistic Analysis of the Palmerolide PKS-NRPS Biosynthetic Pathway From the Microbiome of an Antarctic Ascidian

Abstract

Complex interactions exist between microbiomes and their hosts. Increasingly, defensive metabolites that have been attributed to host biosynthetic capability are now being recognized as products of host-associated microbes. These unique metabolites often have bioactivity targets in human disease and can be purposed as pharmaceuticals. Polyketides are a complex family of natural products that often serve as defensive metabolites for competitive or pro-survival purposes for the producing organism, while demonstrating bioactivity in human diseases as cholesterol lowering agents, anti-infectives, and 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 (BGCs) responsible for production of secondary metabolites are encoded in the genomes of the producers as discrete genomic elements. A candidate palmerolide BGC was identified from a S. adareanum microbiome-metagenome based on a high degree of congruence with a chemical structure-based retrobiosynthetic prediction. Protein family homology analysis, conserved domain searches, active site and motif identification were used to identify and propose the function of the ∼75 kbp trans-acyltransferase (AT) polyketide synthase-non-ribosomal synthase (PKS-NRPS) domains responsible for the stepwise 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 is found in multiple copies within the metagenome-assembled genome (MAG). 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 microbial species, recently proposed as Candidatus Synoicihabitans palmerolidicus. These findings have relevance for fundamental knowledge of PKS combinatorial biosynthesis and could enhance drug development efforts of palmerolide A through heterologous gene expression.

Uncovering Lasonolide A Biosynthesis Using Genome-Resolved Metagenomics

“…“ Ca. Thermopylae lasonolidus,” with multiple las BGC repeats, represents an important addition to the growing collection of symbiotic Verrucomicrobia (“ Candidatus Didemnitutus mandela” and “ Candidatus Synoicihabitans palmerolidicus”) being identified with repeated trans -AT PKS BGCs ( 62 , 69 , 70 ). Recently, two simultaneous studies have also identified a trans -AT PKS BGC for pateamine in a bacterium (“ Candidatus Patea custodiens”) belonging to phylum Kiritimatiellaeota ( 71 , 72 ), a recently proposed phylum which was previously classified within Verrucomicrobia ( 73 ).…”

Marine natural products

“…BGCs associated with the biosynthesis of palmerolides in the Antarctic ascidian Synoicum adareanum have been linked to the novel verrucomicrobium "Candidatus Synoicihabitans palmerolidicus". 691,692 This journal is © The Royal Society of Chemistry 2023…”

Integrated Metabolomic–Genomic Workflows Accelerate Microbial Natural Product Discovery

“…As demonstrated by our group with palmerolide biosynthesis, 40 a retrobiosynthetic strategy can be utilized to identify the BGC implicated in the biosynthesis of a specific secondary metabolite out of a diverse metagenome represented by many bacterial genomes. In the case of palmerolide A, key enzymatic features were used to interrogate the metagenome from environmental samples, and the modular arrangement of the biosynthetic pathway derived from the retrobiosynthetic analysis was used to identify the putative BGC.…”

“…In the case of palmerolide A, key enzymatic features were used to interrogate the metagenome from environmental samples, and the modular arrangement of the biosynthetic pathway derived from the retrobiosynthetic analysis was used to identify the putative BGC. Identification of the BGC and host-associated microbial producer now paves the way for drug development efforts through biotechnological means (i.e., through heterologous expression or targeted cultivation efforts). Other examples of BGC identification using similar strategies within genomes of previously characterized polyketide compounds with potent bioactivity include those for calyculin (cytotoxicity), , corallopyronins (broad spectrum antibiotic activity), , and bryostatins (anticancer and neuroprotective activity). − The implications for these strategies cross into the various compound classes and can help propel compounds with pharmaceutical promise through the drug discovery pipeline.…”