AccR, a TetR family transcriptional repressor, coordinates short-chain acyl-CoAs homeostasis in Streptomyces avermitilis.

Malonyl- and methylmalonyl-CoA are the most common extender units for biosynthesis of fatty acids and polyketides in Streptomyces, an industrially important producer of polyketides. Carboxylation of acetyl- and propionyl-CoA is an essential source of malonyl- and methylmalonyl-CoA; therefore, acyl-CoA carboxylases (ACCases) play key roles in primary and secondary metabolism. Regulation of expression of ACCases in Streptomyces spp. has not been investigated previously. We characterized a TetR family transcriptional repressor, AccR, that mediates intracellular acetyl-, propionyl-, methylcrotonyl-, malonyl-, and methylmalonyl-CoA levels by controlling transcription of genes which encode the main ACCase and enzymes associated with branched-chain amino acid metabolism in S. avermitilis. AccR bound to a 16-nt palindromic binding motif (GTTAA-N6-TTAAC) in promoter regions and repressed transcription of accD1A1-hmgL-fadE4 operon, echA8, echA9, and fadE2, which are involved in production and assimilation of acetyl- and propionyl-CoA. Methylcrotonyl-, propionyl-, and acetyl-CoA acted as effectors to release AccR from its target DNA, resulting in enhanced transcription of target genes by derepression. The affinity of methylcrotonyl- and propionyl-CoA to AccR was stronger than that of acetyl-CoA. Deletion of accR resulted in increased concentrations of short-chain acyl-CoAs (acetyl-, propionyl-, malonyl-, and methylmalonyl-CoA), leading to enhanced avermectin production. Avermectin production was increased by 14.5% in an accR-deletion mutant of industrial high-yield strain S. avermitilis A8. Our findings clarify the regulatory mechanisms that maintain homeostasis of short-chain acyl-CoAs in Streptomyces. Importance Acyl-CoA carboxylases play key roles in primary and secondary metabolism. However, regulation of ACCase genes transcription in Streptomyces spp. remains unclear. Here, we demonstrated that AccR responded to intracellular acetyl-, propionyl-, and methylcrotonyl-CoA availability and mediated transcription of the genes related to production and assimilation of these compounds in S. avermitilis. When intracellular concentrations of these compounds are low, AccR binds to target genes and represses their transcription, resulting in low production of malonyl- and methylmalonyl-CoA. When intracellular acetyl-, propionyl-, and methylcrotonyl-CoA concentrations are high, these compounds bind to AccR to dissociate AccR from target DNA, promoting the conversion of these compounds to malonyl- and methylmalonyl-CoA. The investigation revealed how AccR coordinates short-chain acyl-CoAs homeostasis in Streptomyces.