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Bacterial Hsp90 mediates the degradation of aggregation-prone Hsp70-Hsp40 substrates preferentially by HslUV proteolysis

Whereas in eukaryotic cells, the Hsp90s are profusely-studied molecular chaperones controlling protein homeostasis together with Hsp70s, in bacteria, the function of Hsp90 (HtpG) and its collaboration with Hsp70 (DnaK) remains unknown. To uncover physiological processes depending on HtpG and DnaK, we performed comparative quantitative proteomic analyses of insoluble and total protein fractions from unstressed wild type E. coli, and from knockout mutants ΔdnaKdnaJ (ΔKJ), ΔhtpG (ΔG) and ΔdnaKdnaJΔhtpG (ΔKJG) and compared their growth rates under heat-stress also with ΔdnaKdnaJΔhslV. Whereas, expectedly, mutant ΔG showed no proteomic differences with wild-type, ΔKJ expressed more chaperones, proteases and ribosomes and dramatically less metabolic and respiratory enzymes. Unexpectedly, we found that ΔKJG showed higher levels of metabolic and respiratory enzymes and both ΔKJG and ΔdnaKdnaJΔhslV grew better at 37oC than ΔKJ. The results indicate that bacterial Hsp90 mediates the degradation of aggregation-prone Hsp70-Hsp40 substrates, preferably by the HslUV protease. Significance statement: The molecular chaperones Hsp70 and Hsp90 are among the most abundant and well-conserved proteins in all realms of life, forming together the core of the cellular proteostasis network. In eukaryotes, Hsp90 functions in collaboration with Hsp70; we studied this collaboration in E. coli, combining genetic studies with label-free quantitative proteomics in which both protein abundance and protein solubility were quantified. Bacteria lacking Hsp70 (DnaK) and its co-chaperone DnaJ (ΔdnaKdnaJ) grew slower and contained significantly less key metabolic and respiratory enzymes. Unexpectedly, an additional deletion of the Hsp90 (htpG) gene partially restored the WT phenotype. Deletion of the HslV protease in the ΔdnaKdnaJ background also improved growth, suggesting that bacterial Hsp90 mediates the degradation of Hsp70 substrates, preferentially through HslV. At 37oC ΔdnaKdnaJ E. coli mutants grow slower than wild type cells. Quantitative proteomics shows that compared to wild type cells, ΔdnaKdnaJ cells grown at 30oC contain significantly less key metabolic and respiratory enzymes. Unexpectedly, deletion of the HtpG gene in the Δ dnaKdnaJ background ameliorates growth at 37oC and partially restores the cellular levels of some metabolic and respiratory enzymes.