The Hsp70 Chaperone System Stabilizes a Thermo-sensitive Subproteome

Stress-inducible molecular chaperones have essential roles in maintaining protein homeostasis, but the extent to which they affect global proteome stability remains unclear. Here, we analyzed the effects of the DnaK (Hsp70) system on protein stability in Escherichia coli using pulse proteolysis combined with quantitative proteomics. We quantified ~1500 soluble proteins and found ~500 of them to be protease-sensitive under normal growth conditions, indicating a high prevalence of conformationally dynamic states. Acute heat stress resulted in unfolding of an additional ~200 proteins, reflected in exposure of otherwise buried hydrophobic regions. Overexpression of the DnaK chaperone system markedly stabilized most thermo-sensitive proteins, including numerous ribosomal proteins as well as large, hetero-oligomeric proteins that frequently contain the evolutionary ancient c.37 fold (P-loop nucleoside triphosphate hydrolases).