Synthase-selected sorting approach identifies a beta-lactone synthase in a nudibranch symbiotic bacterium

Abstract

Background Nudibranchs comprise a group of > 6000 marine soft-bodied mollusk species known to use secondary metabolites (natural products) for chemical defense. The full diversity of these metabolites and whether symbiotic microbes are responsible for their synthesis remains unexplored. Another issue in searching for undiscovered natural products is that computational analysis of genomes of uncultured microbes can result in detection of novel biosynthetic gene clusters; however, their in vivo functionality is not guaranteed which limits further exploration of their pharmaceutical or industrial potential. To overcome these challenges, we used a fluorescent pantetheine probe, which produces a fluorescent CoA-analog employed in biosynthesis of secondary metabolites, to label and capture bacterial symbionts actively producing these compounds in the mantle of the nudibranch Doriopsilla fulva. Results We recovered the genome of Candidatus Doriopsillibacter californiensis from the Ca. Tethybacterales order, an uncultured lineage of sponge symbionts not found in nudibranchs previously. It forms part of the core skin microbiome of D. fulva and is nearly absent in its internal organs. We showed that crude extracts of D. fulva contained secondary metabolites that were consistent with the presence of a beta-lactone encoded in Ca. D. californiensis genome. Beta-lactones represent an underexplored group of secondary metabolites with pharmaceutical potential that have not been reported in nudibranchs previously. Conclusions Altogether, this study shows how probe-based, targeted sorting approaches can capture bacterial symbionts producing secondary metabolites in vivo.

Systematic Review of Chemical and Biological Activity Studies of Extracts and Isolated Compounds From Nudibranchs

“…However, screening programs show that if secondary metabolites are explored using approaches already in use and using easily accessible samples, such as plants, compounds are often rediscovered. In recent years, therefore, research efforts have focused on little-explored sources, such as the microbiomes of marine animals [75].…”

Fluorometric Analysis of Carrier-Protein-Dependent Biosynthesis through a Conformationally Sensitive Solvatochromic Pantetheinamide Probe

“…coli fatty acid biosynthesis and identify novel CPs from a tunicate microbiome using targeted single-cell genomics . Furthermore, we and others have exploited the environmental sensitivity of fluorophores like DMN to visualize protein–protein interactions in CP-dependent fatty acid biosynthesis. − While these studies have demonstrated the efficacy of fluorescent CP-targeting probes as chemical tools, weak intensity and low signal-to-noise ratio dampened an otherwise robust ability to manifest specific bioactivity. The work described herein was designed with the goal of improving certain aspects of solvatochromic pantetheinamides by exploring dyes which change color in addition to improved fluorescence intensity to report on their local microenvironment.…”