A scalable platform to discover antimicrobials of ribosomal origin

Nat Commun. 2022 Oct 17;13(1):6135. doi: 10.1038/s41467-022-33890-w.

Abstract

Ribosomally synthesized and post-translationally modified peptides (RiPPs) are a promising source of new antimicrobials in the face of rising antibiotic resistance. Here, we report a scalable platform that combines high-throughput bioinformatics with automated biosynthetic gene cluster refactoring for rapid evaluation of uncharacterized gene clusters. As a proof of concept, 96 RiPP gene clusters that originate from diverse bacterial phyla involving 383 biosynthetic genes are refactored in a high-throughput manner using a biological foundry with a success rate of 86%. Heterologous expression of all successfully refactored gene clusters in Escherichia coli enables the discovery of 30 compounds covering six RiPP classes: lanthipeptides, lasso peptides, graspetides, glycocins, linear azol(in)e-containing peptides, and thioamitides. A subset of the discovered lanthipeptides exhibit antibiotic activity, with one class II lanthipeptide showing low µM activity against Klebsiella pneumoniae, an ESKAPE pathogen. Overall, this work provides a robust platform for rapidly discovering RiPPs.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Anti-Bacterial Agents / metabolism
  • Anti-Bacterial Agents / pharmacology
  • Danazol* / metabolism
  • Escherichia coli / genetics
  • Escherichia coli / metabolism
  • Multigene Family
  • Peptides / chemistry
  • Protein Processing, Post-Translational
  • Ribosomes* / genetics
  • Ribosomes* / metabolism

Substances

  • Anti-Bacterial Agents
  • Peptides
  • Danazol