Unearthing a Cryptic Biosynthetic Gene Cluster for the Piperazic Acid-Bearing Depsipeptide Diperamycin in the Ant-Dweller Streptomyces sp. CS113

• Published in: International journal of molecular sciences 2024-02, Vol.25 (4), p.2347
• Main Authors: García-Gutiérrez, Coral, Pérez-Victoria, Ignacio, Montero, Ignacio, Fernández-De la Hoz, Jorge, Malmierca, Mónica G, Martín, Jesús, Salas, José A, Olano, Carlos, Reyes, Fernando, Méndez, Carmen
• Format: Article
• Language: English
• Subjects: Amino acids; Amino Acids - metabolism; Antibiotics; Antimicrobial Cationic Peptides - metabolism; azinothricin; Bioinformatics; Biosynthesis; depsipeptide; Depsipeptides - genetics; Depsipeptides - metabolism; diperamycin; Genes; Genomes; Metabolites; Multigene Family; N-N bond; piperazate; Polyketide Synthases - genetics; Polyketide Synthases - metabolism; Proteins; Pyridazines; Streptomyces; Streptomyces - genetics; Streptomyces - metabolism
• ISSN: 1422-0067; 1661-6596; 1422-0067
• DOI: 10.3390/ijms25042347

Piperazic acid is a cyclic nonproteinogenic amino acid that contains a hydrazine N-N bond formed by a piperazate synthase (KtzT-like). This amino acid, found in bioactive natural products synthesized by non-ribosomal peptide synthetases (NRPSs), confers conformational constraint to peptides, an important feature for their biological activities. Genome mining of strains has been revealed as a strategy to identify biosynthetic gene clusters (BGCs) for potentially active compounds. Moreover, the isolation of new strains from underexplored habitats or associated with other organisms has allowed to uncover new BGCs for unknown compounds. The in-house "Carlos Sialer (CS)" strain collection consists of seventy-one strains isolated from the cuticle of leaf-cutting ants of the tribe . Genomes from twelve of these strains have been sequenced and mined using bioinformatics tools, highlighting their potential to encode secondary metabolites. In this work, we have screened in silico those genomes, using KtzT as a hook to identify BGCs encoding piperazic acid-containing compounds. This resulted in uncovering the new BGC in sp. CS113, which encodes the biosynthesis of the hybrid polyketide-depsipeptide diperamycin. Analysis of the diperamycin polyketide synthase (PKS) and NRPS reveals their functional similarity to those from the aurantimycin A biosynthetic pathway. Experimental proof linking the BGC to its encoded compound was achieved by determining the growth conditions for the expression of the cluster and by inactivating the NRPS encoding gene and the piperazate synthase gene . The identity of diperamycin was confirmed by High-Resolution Mass Spectrometry (HRMS) and Nuclear Magnetic Resonance (NMR) and by analysis of the domain composition of modules from the DpnP PKS and DpnS NRPS. The identification of the BGC expands the number of BGCs that have been confirmed to encode the relatively scarcely represented BGCs for depsipeptides of the azinothricin family of compounds and will facilitate the generation of new-to-nature analogues by combinatorial biosynthesis.