Chaperone Dependency during Primary Protein Biogenesis Does Not Correlate with Chaperone Dependency during in vitro Refolding

Abstract Many proteins require molecular chaperones to fold into their functional native forms. Previously we used limited proteolysis mass-spectrometry (LiP-MS) to find that ca. 40% of the E. coli proteome do not efficiently refold spontaneously following dilution from denaturation, a frequency that drops to ca. 15% once molecular chaperones like DnaK or GroEL are provided. However, the roles of chaperones during primary biogenesis in vivo can differ from the functions they play during in vitro refolding experiments. Here, we used LiP-MS to probe structural changes incurred by the E. coli proteome when two key chaperones, trigger factor and DnaKJ, are deleted. While knocking out DnaKJ induces pervasive structural perturbations across the soluble E. coli proteome, trigger factor deletion only impacts a small number of proteins’ structures. Overall, proteins which cannot spontaneously refold (or require chaperones to refold in vitro) are not more likely to be dependent on chaperones to fold in vivo. For instance, the glycolytic enzyme, phosphoglycerate kinase (PGK), cannot refold to its native form in vitro following denaturation (even with chaperones), but by LiP-MS we find that its structure is unperturbed upon DnaKJ or Tig deletion, which is further supported with biochemical and biophysical assays. Thus, PGK folds to its native structure most efficiently during co-translational folding and does so without chaperone assistance. This behaviour is generally found among chaperone-nonrefolders (proteins that cannot refold even with chaperone assistance), strengthening the view that chaperone-nonrefolders are obligate co-translational folders. Hence, for some E. coli proteins, the vectorial nature of co-translational folding is the most important “chaperone.” Highlights - LiP-MS is used to identify which proteins in E. coli are structurally perturbed when DnaKJ or trigger factor is deleted - Very few proteins require trigger factor to assume their native structures - The proteome’s dependence on DnaKJ is increased at lower growth temperature - The enzyme PGK does not need chaperones to fold, but it cannot refold from denaturant, even with chaperone assistance - For some E. coli proteins (such as PGK) co-translational folding during primary biogenesis is the most important “chaperone” Competing Interest Statement The authors have declared no competing interest.