Whole-Genome Analysis, Biosynthetic Gene Cluster Mining of Amycolatopsis sp. nov. TRM77291 and Antibacterial Activity of Siderochelin A

Abstract

The genus Amycolatopsis, belonging to the phylum Actinobacteria, is known for producing diverse bioactive secondary metabolites and plays a significant role in microbial drug discovery. This study centers on the strain TRM77291, sourced from a unique habitat, and is postulated to represent a potential new species. This hypothesis is based on 16S rRNA gene phylogenetic analysis combined with physiological, biochemical, and chemotaxonomic characterization. The strain’s genome, consisting of 8.76 Mb with a G + C content of 68.89% and encoding 8572 genes, was analyzed through whole-genome sequencing. AntiSMASH analysis identified 38 biosynthetic gene clusters related to PKS, NRPS, and RiPPs, while BIG-SCAPE analysis indicated the potential for unique compound synthesis, including Cluster 7 and Cluster 35. Screening ten fermentation media determined millet medium as the most optimal choice. Siderochelin A, a monomeric compound isolated from a fermentation product, demonstrated antibacterial efficacy against various pathogenic bacteria. This study revealed a notable activity of Siderochelin A against Escherichia coli, providing a theoretical basis for discovering novel species, exploring secondary metabolites, and developing innovative antibiotics.