Integrated genomic-transcriptomic analysis of clavulanic acid production in differentially productive Streptomyces clavuligerus strains

Clavulanic acid (CA) is a specific metabolite that inhibits β-lactamases, which inactivate β-lactam antibiotics, therefore reinstating the activity of β-lactams against β-lactamase-producing pathogens, and surmounting β-lactam resistance. While extensive efforts have been made to optimize CA production through random mutagenesis, these approaches often introduce deleterious mutations, limiting further yield improvements. In this study, whole-genome sequencing, time-resolved transcriptomics, and independent component analysis (ICA)-based gene co-expression network analysis were employed to elucidate the genetic and transcriptomic factors underlying enhanced CA production in mutant Streptomyces clavuligerus strains developed through ultraviolet-induced random mutagenesis. By analyzing strains with varying CA productivities and correlating genomic and transcriptomic changes, we identified multiple candidate mutations, key transcriptional regulators, and metabolic pathways influencing CA yield. Notable findings include large plasmid deletions, an enrichment of mutations in secondary metabolite biosynthesis and regulatory genes, and metabolic shifts redirecting amino acid and carbon flux toward CA biosynthetic pathways. ICA revealed gene modules directly associated with CA biosynthesis, precursor supply, and transcriptional regulation. This integrative approach generated a comprehensive paired genomic-transcriptomic dataset for CA production. The insights gained offer targeted strategies for rational strain engineering, advancing more efficient and sustainable antibiotic production.