A tRNA modification-based regulatory strategy for Lincomycin biosynthesis in Streptomyces lincolnensis

Lincomycin is a clinically important lincosamide antibiotic. Its biosynthetic efficiency is limited by the presence of the rare UUA codon in the key positive regulators LmbU and AdpA. In this study, we developed a universal metabolic optimization strategy based on tRNA modification engineering. Co-overexpression of the UUA-decoding tRNA gene bldA and its post-transcriptional modification enzyme gene miaA markedly increased lincomycin production. Further optimization was achieved by expressing miaA under the phase-dependent promoter PlmbU. Mechanistic analysis showed that this strategy enhances the decoding efficiency of the UUA codon, thereby improving translation of LmbU and AdpA. Because bldA and miaA are highly conserved among species of Streptomyces, this approach may be broadly applicable to other rare-codon-dependent secondary metabolites. Our work provides a new and rational strategy for microbial secondary metabolic engineering through precise control of tRNA modification.