A ubiquitous Streptomyces biosynthetic megacluster encodes an arsenal of synergistic biotin-targeting antibiotics

Abstract

The rise of multidrug-resistant pathogens underscores the urgent need for antibiotics that act through new targets and mechanisms. Biotin metabolism, essential in most bacteria, remains underexploited therapeutically. Here, we uncover a highly conserved, co-located biosynthetic megacluster in Streptomyces, a striking "cluster of clusters", that encodes four distinct natural product families: acidomycin, stravidins, dapamycins, and -methyl-KAPA, and is flanked by genes that encode streptavidin, a high-affinity biotin-binding protein. Remarkably, all molecules target different steps in bacterial biotin metabolism, revealing a multi-pronged natural strategy for biotin starvation. This arrangement of four functionally convergent biosynthetic gene clusters at a single genomic locus is without precedent. Even more surprisingly, we find that this anti-biotin megacluster is widespread across Streptomyces bacteria, suggesting a deeply conserved evolutionary solution to microbial competition. Mechanistically, the compounds inhibit biotin biosynthesis through enzyme blockade, prodrug activation, covalent cofactor mimicry, and biotin sequestration via co-expressed streptavidin. Stravidin S2 and -methyl-KAPA are effective in a murine model of multidrug-resistant E. coli infection. These findings expose a coordinated biosynthetic logic in microbial secondary metabolites and point to higher-order biosynthetic architectures as promising reservoirs of antibiotic innovation.