PhoPR variants from several phylogenetic lineages of tuberculosis bacilli respond differently to extracellular signals

ABSTRACT The global spread of Mycobacterium tuberculosis ( MTB ) is facilitated by airborne transmission, a low infectious dose, and the pathogen’s ability to persist in a latent state. Despite sharing over 99% genomic identity, MTB strains and lineages show significant variability in transmissibility. We hypothesized that natural polymorphisms in the two-component regulatory system (TCS) PhoP-PhoR (PhoPR), a major virulence regulator, contribute to this variability. First, we identified zinc and cadmium as new inducers of PhoPR. Second, we expressed phoPR variants from strains with varying transmissibility in the MTB HN878 strain and compared the variants’ capacity to induce the expression of PhoP-controlled genes (PhoPR activity) after being submitted to various chemical or cellular signals. In vitro , PhoPR systems from HN878 and the low-transmissibility strain M. canettii STB-D responded similarly to acidic and zinc stresses. In contrast, PhoPR variants from strains M. canettii STB-J and M. bovis AN5 showed reduced responsiveness. However, the former seems constitutively activated, whereas the latter displays low activity. Interestingly, although the variant found in M. bovis B, which was responsible for direct transmission in humans in contrast to most M. bovis strains, did not respond to acidic or zinc stress in vitro , it remained inducible in macrophages. Finally, we compared the virulence of the various recombinant strains in C3HeB/FeJ mice. We found that only the strain expressing the PhoPR variant from M. bovis AN5 is associated with reduced virulence. These findings indicate that both phoPR polymorphisms and the strain-specific genetic context modulate PhoPR activity, thereby influencing MTB virulence and potentially its transmissibility. IMPORTANCE Understanding genomic adaptations favoring persistence and transmission of tuberculosis bacilli is crucial for developing new strategies to combat tuberculosis. This study explores the impact of natural mutations on the response to environmental cues of the two-component regulatory system (TCS) PhoP-PhoR (PhoPR), which controls the expression of major virulence factors, and on the virulence of Mycobacterium tuberculosis ( MTB ). Our findings identify new signals activating PhoPR and provide new insights into the molecular mechanisms of PhoPR. In addition, this study highlights how phoPR polymorphisms may influence the epidemic capacity of tuberculosis bacilli.