Divergent transcriptional regulation of redox-homeostasis and permeability modulate rifampicin tolerance and sensitivity in Mycobacterium tuberculosis

Drug-tolerance in Mycobacterium tuberculosis (Mtb) may delay treatment response while drug hypersusceptibility should improve treatment. We investigate the transcriptional regulation of these states in Mtb using a Transcriptional Regulator Induced Phenotype screen combined with an extended, steady-state rifampicin exposure method. We identify three transcription factors (TFs): Rv1359, Rv2887, and Rv3833, whose induction enhances rifampicin tolerance, and four TFs, Rv1189 (sigI), Rv1846c (blaI), Rv2069 (sigC), and Rv3736, whose induction elicits hypersusceptibility. Inducing the TFs blaI and Rv2887 produces opposite phenotypes due to their divergent regulation of the cydA and icl1, genes that we find to reduce redox stress when overexpressed. Thus, Rv2887 induces icl1 expression which contributes to drug tolerance whereas blaI downregulates cydA, which contributes to drug hypersusceptibility. In contrast, divergent regulation of tgs1 and Rv3083 by the TF Rv3736 results in a convergent hypersusceptible phenotype due to the opposing effects of tgs1 and Rv3083 on Mtb permeability to rifampicin. Our findings demonstrate the complex transcriptional regulation of drug tolerance and hypersusceptibility that cannot be captured by studying the activity of individual effector genes. Induction of TFs that regulate Mtb response to drug exposure may either augment or diminish treatment efficacy. These TFs are thus potential new targets for drug development.