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

Karen W Davenport,Hajnalka E Daligault,Chien-Chi Lo,Bill J Baker,Armand E K Dichosa,Patrick S G Chain,Alison E Murray,Nicole E Avalon

doi:10.3389/fchem.2021.802574

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.

Highlights

Marine invertebrates such as corals, sponges, mollusks, and ascidians are known to be a rich source of bioactive compounds (Carroll et al, 2019)
A retrobiosynthetic scheme of the pal biosynthetic gene clusters (BGCs) was developed based on the chemical structure for palmerolide A, including modules consistent with a hybrid polyketide synthase (PKS)-nonribosomal peptide synthetase (NRPS) and tailoring enzymes for key functional groups (Figure 1)
We hypothesized that the initial module would be PKS-like in nature to utilize 3methylcrotonic acid as the starter unit followed by a NRPS domain for the incorporation of glycine

Summary

Introduction

Marine invertebrates such as corals, sponges, mollusks, and ascidians are known to be a rich source of bioactive compounds (Carroll et al, 2019). Due to their sessile or sluggish nature, chemical defenses such as secondary metabolites are often key to their survival. It is estimated that over 11,000 secondary metabolites from marine and terrestrial environments understood to be products of polyketide synthase (PKS) and NRPS origin have been isolated and described (Dejong et al, 2016). The BGCs for many natural products isolated from marine invertebrates are found in the host-associated microbiota, reflecting the role of these compounds in symbiosis (Schmidt, 2015)

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