Chaperone-Mediated Stress Sensing in Mycobacterium tuberculosis Enables Fast Activation and Sustained Response

Abstract

Dynamical properties of gene regulatory networks are tuned to ensure bacterial survival. In mycobacteria, the MprAB-σE network responds to the presence of stressors, such as surfactants that cause surface stress. Positive feedback loops in this network were previously predicted to cause hysteresis, i.e., different responses to identical stressor levels for prestressed and unstressed cells. Here, we show that hysteresis does not occur in nonpathogenic Mycobacterium smegmatis but does occur in Mycobacterium tuberculosis. However, the observed rapid temporal response in M. tuberculosis is inconsistent with the model predictions. To reconcile these observations, we implement a recently proposed mechanism for stress sensing, namely, the release of MprB from the inhibitory complex with the chaperone DnaK upon the stress exposure. Using modeling and parameter fitting, we demonstrate that this mechanism can accurately describe the experimental observations. Furthermore, we predict perturbations in DnaK expression that can strongly affect dynamical properties. Experiments with these perturbations agree with model predictions, confirming the role of DnaK in fast and sustained response. IMPORTANCE Gene regulatory networks controlling stress response in mycobacterial species have been linked to persistence switches that enable bacterial dormancy within a host. However, the mechanistic basis of switching and stress sensing is not fully understood. In this paper, combining quantitative experiments and mathematical modeling, we uncover how interactions between two master regulators of stress response—the MprAB two-component system (TCS) and the alternative sigma factor σE—shape the dynamical properties of the surface stress network. The result show hysteresis (history dependence) in the response of the pathogenic bacterium M. tuberculosis to surface stress and lack of hysteresis in nonpathogenic M. smegmatis. Furthermore, to resolve the apparent contradiction between the existence of hysteresis and fast activation of the response, we utilize a recently proposed role of chaperone DnaK in stress sensing. These result leads to a novel system-level understanding of bacterial stress response dynamics.

Mathematical modelling of SigE regulatory network reveals new insights into bistability of mycobacterial stress response

“…Indeed, taking into account RseA dynamic evolution leads the system to switch from monostability to bistability. Interestingly, our findings are in agreement with recent results [ 13 ] reporting that (modest) activation of MprA-SigE network is achieved through stress-dependent degradation of RseA. Specifically, Rao and collaborators construct a M. tuberculosis strain with suppressed MprB autokinase activity (through overexpression of the chaperone protein Dnak), and show that, following exposure to SDS, mprA gene is modestly upregulated while sigE mRNA is not significantly increased.…”

“…Our analysis confirms the importance of RseA for the emergence of bistability and, additionally, elucidates the critical role played by RseA degradation pathway. Interestingly, our findings are in agreement with recent results [ 13 ] showing that stress-dependent degradation of RseA can induce modest activation of SigE response network.

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“…Rao and colleagues hence hypothesize that degradation of RseA may be responsible, through release of SigE, for the modest activation of the MprA-SigE network. Modeling results [ 13 ] support this hypothesis and additionally show that induction of mprA is lost when stress-dependent degradation of RseA is not present in the model. The results of our analysis go in the same direction by showing that RseA degradation pathway is crucial for the activation of the stress response and hence for the emergence of bistability.…”

Two‐component sensor histidine kinases of Mycobacterium tuberculosis: Beacons for niche navigation

“…The sensory domain of the MprB SK interacts with the surface-associated chaperone DnaK involved in resolving misfolded proteins and protein aggregates (Bretl et al, 2014). MprB activation is inhibited when bound to DnaK, however, it is proposed that under conditions of cell envelope stress, dissociation of DnaK from MprB promotes SK activity (Bretl et al, 2014;Rao et al, 2021).…”

“…The sensory domain of the MprB SK interacts with the surface‐associated chaperone DnaK involved in resolving misfolded proteins and protein aggregates (Bretl et al, 2014). MprB activation is inhibited when bound to DnaK, however, it is proposed that under conditions of cell envelope stress, dissociation of DnaK from MprB promotes SK activity (Bretl et al, 2014; Rao et al, 2021). The structure of the cytoplasmically‐localized SK PdtaS has been solved (Preu et al, 2012), and two recent reports suggest cyclic diguanosine monophosphate (di‐GMP), copper, zinc, and NO may be regulatory ligands of PdtaS activity (Buglino et al, 2021; Hariharan et al, 2021).…”