Genome mining of coastal cenote sediment-associated Streptomyces sp. NCA360 strain uncovers novel biosynthetic gene clusters and their regulatory architecture

Abstract

The rise of antibiotic resistance has intensified the search for novel antimicrobial compounds, and bioprospecting of natural products from underexplored environments remains an effective strategy. The genus Streptomyces is one of the most prolific sources of pharmacologically active secondary metabolites, whose biosynthetic information is encoded in biosynthetic gene clusters (BGCs). However, many BGCs remain transcriptionally silent under standard laboratory conditions, underscoring the need to characterize the regulatory mechanisms governing their activation. In this study, we sequenced and analyzed the genome of Streptomyces sp. NCA360. The strain was isolated from sediments of the coastal cenote (a natural sinkhole) in the Yucatan Peninsula and selected for its antimicrobial and enzymatic activities. The high-quality genome assembly (89.7% completeness, <1% contamination) encoded 26 BGCs, of which 11 showed low similarity to characterized clusters and were classified as putatively novel (nBGCs). Resistance-guided prioritization identified duplicated resistance determinants, including an additional glyceraldehyde-3-phosphate dehydrogenase copy within a PKS-II cluster and Biotin_lipoyl/Carboxyl_trans domains within two divergent NRPS/PKS-I clusters, that were classified as candidate chemotherapeutic gene clusters. Biosynthetic pathways associated with clinically relevant antibiotics, including monobactams, carbapenems, and cephalosporins, were also detected. The regulatory architecture of the nBGCs revealed 26 regulatory genes, 20 transcription factor binding sites, and 20 rare TTA codons, reflecting heterogeneous and often multifactorial regulatory schemes. In silico protein-protein interaction analysis further revealed a coordinated cross-cluster regulation. The analysis of the Streptomyces sp. NCA360 genome expands our understanding of the biosynthetic and regulatory diversity of Streptomyces and highlights the potential of cenotes as unique environments and reservoirs of new bioactive compounds with pharmaceutical relevance.