Paenidepsins are a Family of Lipopeptides from Paenibacillus

A new 12-membered cyclic lipopeptide with antifungal activity, paenidepsin A (1), was isolated from the common-wheat-associated bacterial strain Paenibacillus apiarius MW-14. Its chemical structure was elucidated using a combination of extensive tandem mass spectrometry (MS/MS) and nuclear magnetic resonance (NMR) spectroscopy experiments. Further paenidepsin analogs B–F (2–6) produced by the same strain were detected through molecular networking and structurally characterized via MS/MS analyses. Peptidogenomic analysis revealed the corresponding nonribosomal peptide synthetase (NRPS) biosynthetic gene cluster (BGC), while through genome mining, 72 homologous BGCs were identified from publicly available bacterial genomes. Comprehensive phylogenetic and comparative analyses demonstrated that paenidepsin-like BGCs constitute a new gene cluster family from Paenibacillus. Detailed NRPS domain-level analyses provided bioinformatic evidence for recombination-driven diversification of this BGC. Our findings illustrate the utility of integrating mass spectrometric and genomic tools to discover diverse natural products, and highlight the significant biosynthetic capacity of Paenibacillus species.