Genome-guided investigation of secondary metabolites produced by a potential new strain Streptomyces BA2 isolated from an endemic plant rhizosphere in Turkey

Terrestrial actinomycetes are the important sources of secondary metabolites that serve as a major source of drugs. Recent advances in genome mining have revealed that Streptomyces genomes have a wide range of undiscovered secondary metabolite biosynthetic gene clusters. In the present study, genome mining was employed to discover biosynthetic potential of plant-associated strain Streptomyces BA2. Based on 16S rRNA gene sequencing, this strain was found to be closely related to Streptomyces durmitorensis, Streptomyces alboniger, and Streptomyces kanamyceticus with similarity of 99.71%, 99.64%, and 99.56%, respectively. The genome of BA2 contained 10.043.478 base pairs with G + C content of 69.92%. The annotation results revealed the presence of 9.056 protein coding genes, 88 tRNA and 18 rRNA genes. The dDDH and ANI values of genome sequences between strain BA2 and closely related type strains were considerably lower than the recommended threshold values. A total of 33 secondary metabolite biosynthetic gene clusters responsible for the biosynthesis of known and/or novel secondary metabolites, including non-ribosomal peptides, polyketides, terpenes, siderophores, bacteriocins, ectoines, and lassopeptides were identified. Metabolic profiling of Streptomyces sp. BA2 grown in three different culture media was determined by a non-targeted LC-MS/MS approach coupled with spectral networking. Significant bioactive natural products such as actinomycin D, desferrioxamine E, malyngamide K, and bouillonamide B were detected. Malyngamide K and bouillonamide B, known as marine cyanobacterial-derived compounds, were first reported from a Streptomyces strain in this study. Our study demonstrated the potentially novel strain Streptomyces sp. BA2 as a valuable source of new bioactive secondary metabolites.

Automated summary

Genome mining of plant-associated strain Streptomyces BA2 revealed a wide range of undiscovered secondary metabolite biosynthetic gene clusters, including novel bioactive compounds. Through analysis of genetic sequence similarity and metabolic profiling, Streptomyces sp. BA2 was identified as a potential source of new bioactive secondary metabolites.