Direct cloning and refactoring of a silent lipopeptide biosynthetic gene cluster yields the antibiotic taromycin A

TLDR

Microbes possess many specialized compound genes, yet only a few are produced in the laboratory. The study introduces a genetic platform that enables efficient production of natural products from uncharacterized gene collections. The platform employs yeast transformation‑associated recombination to clone and express an orphan biosynthetic cluster, creating a single capture vector from sequencing data that precisely captures loci and facilitates manipulation. This plug‑and‑play method demonstrates how cryptic biosynthetic pathways can be activated to discover and develop natural product drug candidates.

Abstract

Significance Microbes have the genetic capacity to produce large numbers of specialized compounds, yet produce only a small fraction of these in the laboratory. Here we introduce a genetic platform that allows the efficient production of natural product molecules from uncharacterized gene collections. We used transformation-associated recombination in yeast to directly clone and express an orphan biosynthetic gene cluster for the production of the lipopeptide antibiotic taromycin A. With this direct cloning approach, a single genomic capture and expression vector was designed directly from next-generation sequencing data, which precisely captures genetic loci of interest and readily facilitates genetic manipulations. This study highlights a “plug-and-play” approach to cryptic biosynthetic pathways for the discovery and development of natural product drug candidates.