Natural mutations in the sensor kinase of the PhoPR two-component regulatory system modulate virulence of ancestor-like tuberculosis bacilli

Author summaryMycobacterium tuberculosis (MTB) likely emerged from an environmental ancestor by adaptation of endogenous pathways enhancing its capacity to colonize and transmit within the human host. The closest extant relatives of the MTB ancestor are the Mycobacterium canettii strains which are opportunist pathogens responsible for rare human tuberculosis cases in East-Africa. Here we found that the sensor protein of the important two-component regulatory system PhoPR displays amino acid substitutions that modulate its activity in M. canettii in comparison to MTB. These mutations impact the production and secretion of virulence factors important for multiplication within the host and cough induction. Therefore, our findings support the hypothesis that variants of the PhoPR regulatory system were selected as key evolutionary adaptations for enhancing the epidemic capacity of the tuberculosis bacilli. The molecular factors and genetic adaptations that contributed to the emergence of Mycobacterium tuberculosis (MTB) from an environmental Mycobacterium canettii-like ancestor, remain poorly investigated. In MTB, the PhoPR two-component regulatory system controls production and secretion of proteins and lipid virulence effectors. Here, we describe that several mutations, present in phoR of M. canettii relative to MTB, impact the expression of the PhoP regulon and the pathogenicity of the strains. First, we establish a molecular model of PhoR and show that some substitutions found in PhoR of M. canettii are likely to impact the structure and activity of this protein. Second, we show that STB-K, the most attenuated available M. canettii strain, displays lower expression of PhoP-induced genes than MTB. Third, we demonstrate that genetic swapping of the phoPR allele from STB-K with the ortholog from MTB H37Rv enhances expression of PhoP-controlled functions and the capacities of the recombinant strain to colonize human macrophages, the MTB target cells, as well as to cause disease in several mouse infection models. Fourth, we extended these observations to other M. canettii strains and confirm that PhoP-controlled functions are expressed at lower levels in most M. canettii strains than in M. tuberculosis. Our findings suggest that distinct PhoR variants have been selected during the evolution of tuberculosis bacilli, contributing to higher pathogenicity and persistence of MTB in the mammalian host.

Automated summary

In this study, the authors found that the sensor protein PhoPR in Mycobacterium canettii strains has amino acid substitutions that affect its activity compared to Mycobacterium tuberculosis. These mutations impact the production and secretion of virulence factors, enhancing the capacity of the strains to colonize and transmit within the host. Therefore, these findings support the hypothesis that variants of the PhoPR regulatory system are key evolutionary adaptations for enhancing the epidemic capacity of tuberculosis.