Bile acids (BAs) are a class of endogenous metabolites
with important
functions. As amphipathic molecules, BAs have strong antibacterial
effects, preventing overgrowth of the gut microbiota and defending
the invasion of pathogens. However, some disease-causing pathogens
can survive the BA stress and knowledge is limited about how they
develop BA tolerance. In this work, we applied a quantitative chemoproteomic
strategy to profile BA-interacting proteins in bacteria, aiming to
discover the sensing pathway of BAs. Using a clickable and photo-affinity
BA probe with quantitative mass spectrometry, we identified a list
of histidine kinases (HKs) of the two-component systems (TCS) in bacteria
as the novel binding targets of BA. Genetic screening revealed that
knocking out one specific HK, EnvZ, renders bacteria with significant
sensitivity to BA. Further biochemical and genetic experiments demonstrated
that BA binds to a specific pocket in EnvZ and activates a downstream
signaling pathway to help efflux of BA from bacteria, resulting in
BA tolerance. Collectively, our data revealed that EnvZ is a novel
sensor of BA in bacteria and its associated TCS signaling pathway
plays a critical role in mediating bacterial BA tolerance, which opens
new opportunities to combat BA-tolerating pathogens.