Regulation of multidrug efflux pumps by TetR family transcriptional repressor negatively affects secondary metabolism in Streptomyces coelicolor A3(2)

Streptomyces spp. are well-known producers of bioactive secondary metabolites (SMs) that serve as pharmaceutical agents. In addition to their ability to produce SMs, Streptomyces spp. have evolved diverse membrane transport systems to protect cells against antibiotics produced by itself or other microorganisms. We previously screened mutants of Streptomyces coelicolor that show a phenotype of reduced undecylprodigiosin (RED) production in a combined-culture with Tsukamurella pulmonis. Here, we identified a point mutation, which reduced RED production, by performing genome resequencing and genetic complementation. We found that inactivation of the sco1718 gene encoding the TetR family transcriptional regulator (TFR) produced a deficient phenotype for several SMs in Streptomyces coelicolor A3(2). Electrophoretic mobility shift assay and quantitative reverse transcription-PCR experiments demonstrated that SCO1718 repressed the expression of adjacent two-component ATP-binding cassette (ABC) transporter genes (sco1719-20) by binding to the operator sequence in the 5'-UTR. Notably, the {Delta}sco1718 mutant showed increased resistance to several antibiotics of other actinomycete origin. In the genome of S. coelicolor A3(2), two other sets of TFR and two-component ABC transporter genes (sco4358-4360 and sco5384-5382) were found, which had similar effects on the phenotype for both secondary metabolism and antibiotic resistance. Our results imply the switching of cell metabolism to direct offence (antibiotic production) or defense (efflux pump activation) using costly and limited quantities of cell energy sources (e.g., ATP) in the soil ecosystem. IMPORTANCEThe bacterial metabolic potential to synthesize diverse secondary metabolites (SMs) in the environment has been revealed by recent (meta-)genomics of both unculturable and culturable bacteria. These studies imply that bacteria are continuously exposed to harmful chemical compounds in the environment. Streptomyces spp. contain antibiotic efflux pumps and SM biosynthetic gene clusters. However, the mechanism by which soil bacteria, including Streptomyces, survive against toxic compounds in the environment remains unclear. Here, we identified three sets of TFR-ABC transporter genes in Streptomyces coelicolor A3(2). We found that each TFR controlled the expression of a respective ABC transporter, and the expression of all ABC transporters negatively impacted SM production and increased antibiotic resistance. Notably, bioinformatic analysis indicated that these TFR-ABC transporter gene sets are highly conserved and widely distributed in the genome of Streptomyces species, indicating the importance of systematic regulation that directs antibiotic production and xenobiotic excretion.