Identifying metabolic bottlenecks for micafungin precursor production via untargeted regulatory perturbation

BACKGROUND: Micafungin, a clinically important echinocandin antifungal agent, is derived from the nonribosomal cyclic hexapeptide FR901379 produced by the filamentous fungus Coleophoma empetri. However, low fermentation efficiency remains a major constraint in its industrial production. RESULTS: In this study, we implemented an untargeted regulatory perturbation strategy to systematically identify metabolic bottlenecks affecting FR901379 biosynthesis. A mutant library was constructed by rationally engineering the key untargeted regulatory genes involved in histone modification and global regulation. The untargeted perturbation led to diverse phenotypes in both growth and secondary metabolism, ranging from enhancement (by up to 170%) to complete abolition of FR901379 production. Transcriptome profiling of high-producing strains revealed coordinated upregulation of genes in the acetyl-CoA, palmitic acid, and 3'-phosphoadenosine-5'-phosphosulfate biosynthetic pathways. Exogenous supplementation of palm oil further enhanced FR901379 titer by 87.6%, confirming the critical role of precursor supply. CONCLUSIONS: This work elucidates the metabolic network governing FR901379 biosynthesis and provides key candidates for further metabolic engineering. It also demonstrates that untargeted regulatory perturbation strategy is an effective approach for deciphering the mechanisms behind specific phenotypic traits in industrial filamentous fungi.