Protease-Mediated Protein Quality Control for Bacterial Acid Resistance

The periplasm of food-borne enteric pathogens is perhaps the only internal space of living species that can be severely acidified (pH 1-3), which occurs when these pathogens pass through the acidic human stomach. Whereas the periplasmic chaperoning systems are known to deal with such a harsh unfolding stress, other protein quality control mechanisms remain unexplored. Here we report a protease-mediated degradation mechanism that facilitates bacterial acid resistance. The genetic analysis revealed that mutant in degP encoding an HtrA family serine protease rendered Escherichia coli highly acid vulnerable. Combining genetically encoded trifunctional probe with 2D-based comparative proteomics, we identified its substrates. We further demonstrated that DegP directly bound to diverse aggregation-prone periplasmic proteins upon acid stress and these pre-mixed DegP-substrate co-aggregates were subsequently digested by proteolytic-rescued DegP during acid recovery. DegP represents an unprecedented "acid protease" that maintains protein homeostasis in coping with acid-induced protein unfolding stress within E. coli periplasm.