Genome Mining of Chromobacterium Genus Reveals a Class of Nonribosomal Lipopeptides with Potent Antifungal Activity

Bacterial genomes encode numerous cryptic biosynthetic gene clusters (BGCs) that represent an untapped potential source of drugs or biopesticides. However, the limited analysis of BGCs in a specific genus has limited the discovery of their natural products through genome mining. Herein, we report the systematic analysis of the biosynthetic potential of 136 genomes of the Chromobacterium genus. A total of 1713 BGCs were identified and grouped into 190 gene cluster families (GCFs). However, only eight BGCs from seven GCFs have been functionally characterized, highlighting the vast underexplored potential of the genus for the production of novel natural products. Guided by this analysis, we investigated a cryptic BGC of GCF9 featuring a glycosyltransferase and a nonribosomal peptide synthetase (NRPS) with a starter condensation domain, leading to the identification of a class of glycolipopeptides chromorhipeptins from Chromobacterium rhizoryzae. Chromorhipeptins A and B demonstrated broad-spectrum antifungal activity against several plant pathogenic fungi, including Valsa mali, with minimum inhibitory concentrations (MICs) at 0.04 and 0.16 μM, respectively, outperforming the fungicide carbendazim (MIC = 0.78 μM). These findings revealed the biosynthetic potential of Chromobacterium and underscored the power of genome mining to unlock cryptic bacterial natural products for crop protection against plant pathogenic fungi.