DegP functions as a critical protease for bacterial acid resistance

To counteract the lethal acid stress, bacteria explore such strategies as cytoplasmic decarboxylase-catalyzed proton consumption and periplasmic chaperone-assisted protein refolding. Here, we report a periplasmic protease-mediated acid resistance mechanism in Escherichia coli. Deletion of the protease gene degP dramatically decreases the viability of late log or early stationary phase cells against the extreme acid stress (pH 2.3), which can only be minimally rescued by complementary expression of the protease-deficient DegP(S210A) mutant protein. Similarly, DegQ, a homolog of DegP, also contributes to the bacterial acid resistance, but SurA as an important periplasmic chaperone hardly exhibits protection effect. In vitro studies reveal that DegP completely loses its protease activity under acidic condition but is able to partially reactivate upon neutralization. Importantly, we demonstrate the interaction of DegP with typical cellular substrate proteins in cells during acid stress and/or recovery stages by using unnatural amino acid-mediated in vivo photo-crosslinking, as well as the degradation of periplasmic proteins by DegP during recovery after acidic denaturation. These data illustrate the role of DegP in bacterial acid resistance conceivably via degrading those acid-induced misfolded proteins. Our findings, together with earlier reports, suggest a comprehensive acid resistance strategy adopted by bacteria such that in the ATP-deficient extra-cytoplasm, the inevitable misfolded proteins induced by acid stress are refolded by a chaperone (e.g., HdeA/HdeB) and/or cleaved by a protease (e.g., DegP/DegQ) while in the cytoplasm excessive protons are directly consumed or exported.