Genome‐based discovery, structure prediction and functional analysis of cyclic lipopeptide antibiotics in <i>Pseudomonas</i> species

TLDR

Microbial genome analyses reveal numerous NRPS gene clusters in Pseudomonads predicted to produce cyclic lipopeptide antibiotics, yet their biological functions remain largely untested. The study aims to identify previously unknown CLP gene clusters in plant pathogenic *Pseudomonas syringae* strains B728a and DC3000 and plant beneficial *Pseudomonas fluorescens* Pf0‑1 and SBW25. Using comparative genomics, the authors identified CLP gene clusters and validated them in *P. fluorescens* SBW25 through chemical characterization and targeted mutagenesis.

Abstract

Summary Analysis of microbial genome sequences have revealed numerous genes involved in antibiotic biosynthesis. In Pseudomonads, several gene clusters encoding non‐ribosomal peptide synthetases (NRPSs) were predicted to be involved in the synthesis of cyclic lipopeptide (CLP) antibiotics. Most of these predictions, however, are untested and the association between genome sequence and biological function of the predicted metabolite is lacking. Here we report the genome‐based identification of previously unknown CLP gene clusters in plant pathogenic Pseudomonas syringae strains B728a and DC3000 and in plant beneficial Pseudomonas fluorescens Pf0‐1 and SBW25. For P. fluorescens SBW25, a model strain in studying bacterial evolution and adaptation, the structure of the CLP with a predicted 9‐amino acid peptide moiety was confirmed by chemical analyses. Mutagenesis confirmed that the three identified NRPS genes are essential for CLP synthesis in strain SBW25. CLP production was shown to play a key role in motility, biofilm formation and in activity of SBW25 against zoospores of Phytophthora infestans . This is the first time that an antimicrobial metabolite is identified from strain SBW25. The results indicate that genome mining may enable the discovery of unknown gene clusters and traits that are highly relevant in the lifestyle of plant beneficial and plant pathogenic bacteria.