Global mapping of MtrA-binding sites links MtrA to regulation of its targets in Mycobacterium tuberculosis

Mycobacterium tuberculosis employs two-component systems (TCSs) for survival within its host. The TCS MtrAB is conserved among mycobacteria. The response regulator MtrA is essential in M. tuberculosis. The genome-wide chromatin immunoprecipitation (ChIP) sequencing performed in this study suggested that MtrA binds upstream of at least 45 genes of M. tuberculosis, including those involved in cell wall remodelling, stress responses, persistence and regulation of transcription. It binds to the promoter regions and regulates the peptidoglycan hydrolases rpfA and rpfC, which are required for resuscitation from dormancy. It also regulates the expression of whiB4, a critical regulator of the oxidative stress response, and relF, one-half of the toxin-antitoxin locus relFG. We have identified a new consensus 9 bp loose motif for MtrA binding. Mutational changes in the consensus sequence greatly reduced the binding of MtrA to its newly identified targets. Importantly, we observed that overexpression of a gain-of-function mutant, MtrAY102C, enhanced expression of the aforesaid genes in M. tuberculosis isolated from macrophages, whereas expression of each of these targets was lower in M. tuberculosis overexpressing a phosphorylation-defective mutant, MtrAD56N. This result suggests that phosphorylated MtrA (MtrA-P) is required for the expression of its targets in macrophages. Our data have uncovered new MtrA targets that suggest that MtrA is required for a transcriptional response that likely enables M. tuberculosis to persist within its host and emerge out of dormancy when the conditions are favourable.