{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"institution":[{"name":"bioRxiv"}],"indexed":{"date-parts":[[2026,7,30]],"date-time":"2026-07-30T12:13:20Z","timestamp":1785413600090,"version":"3.56.0"},"posted":{"date-parts":[[2025,6,19]]},"group-title":"Biochemistry","reference-count":109,"publisher":"openRxiv","license":[{"start":{"date-parts":[[2025,6,19]],"date-time":"2025-06-19T00:00:00Z","timestamp":1750291200000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc\/4.0\/"}],"funder":[{"DOI":"10.13039\/100000057","name":"National Institute of General Medical Sciences","doi-asserted-by":"crossref","award":["DP2-GM140926"],"award-info":[{"award-number":["DP2-GM140926"]}],"id":[{"id":"10.13039\/100000057","id-type":"DOI","asserted-by":"crossref"}]},{"name":"National Science Foundation","award":["MCB-2045844"],"award-info":[{"award-number":["MCB-2045844"]}]},{"id":[{"id":"https:\/\/ror.org\/019p8h045","id-type":"ROR","asserted-by":"publisher"}]},{"id":[{"id":"https:\/\/ror.org\/00jp8d455","id-type":"ROR","asserted-by":"publisher"}]},{"id":[{"id":"https:\/\/ror.org\/03g03ge92","id-type":"ROR","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"accepted":{"date-parts":[[2025,6,19]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                <jats:p>\n                  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\n                  <jats:italic>E. coli<\/jats:italic>\n                  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\n                  <jats:italic>in vivo<\/jats:italic>\n                  can differ from the functions they play during\n                  <jats:italic>in vitro<\/jats:italic>\n                  refolding experiments. Here, we used LiP-MS to probe structural changes incurred by the\n                  <jats:italic>E. coli<\/jats:italic>\n                  proteome when two key chaperones, trigger factor and DnaKJ, are deleted. While knocking out DnaKJ induces pervasive structural perturbations across the soluble\n                  <jats:italic>E. coli<\/jats:italic>\n                  proteome, trigger factor deletion only impacts a small number of proteins\u2019 structures. Overall, proteins which cannot spontaneously refold (or require chaperones to refold\n                  <jats:italic>in vitro<\/jats:italic>\n                  ) are\n                  <jats:italic>not<\/jats:italic>\n                  more likely to be dependent on chaperones to fold\n                  <jats:italic>in vivo<\/jats:italic>\n                  . For instance, the glycolytic enzyme, phosphoglycerate kinase (PGK), cannot refold to its native form\n                  <jats:italic>in vitro<\/jats:italic>\n                  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\n                  <jats:italic>E. coli<\/jats:italic>\n                  proteins, the vectorial nature of co-translational folding is the most important \u201cchaperone.\u201d\n                <\/jats:p>\n                <jats:sec>\n                  <jats:title>Highlights<\/jats:title>\n                  <jats:list list-type=\"simple\">\n                    <jats:list-item>\n                      <jats:label>-<\/jats:label>\n                      <jats:p>\n                        LiP-MS is used to identify which proteins in\n                        <jats:italic>E. coli<\/jats:italic>\n                        are structurally perturbed when DnaKJ or trigger factor is deleted\n                      <\/jats:p>\n                    <\/jats:list-item>\n                    <jats:list-item>\n                      <jats:label>-<\/jats:label>\n                      <jats:p>Very few proteins require trigger factor to assume their native structures<\/jats:p>\n                    <\/jats:list-item>\n                    <jats:list-item>\n                      <jats:label>-<\/jats:label>\n                      <jats:p>\n                        The proteome\u2019s dependence on DnaKJ is increased at\n                        <jats:italic>lower<\/jats:italic>\n                        growth temperature\n                      <\/jats:p>\n                    <\/jats:list-item>\n                    <jats:list-item>\n                      <jats:label>-<\/jats:label>\n                      <jats:p>The enzyme PGK does not need chaperones to fold, but it cannot refold from denaturant, even with chaperone assistance<\/jats:p>\n                    <\/jats:list-item>\n                    <jats:list-item>\n                      <jats:label>-<\/jats:label>\n                      <jats:p>\n                        For some\n                        <jats:italic>E. coli<\/jats:italic>\n                        proteins (such as PGK) co-translational folding during primary biogenesis is the most important \u201cchaperone\u201d\n                      <\/jats:p>\n                    <\/jats:list-item>\n                  <\/jats:list>\n                <\/jats:sec>","DOI":"10.1101\/2025.06.16.659923","type":"posted-content","created":{"date-parts":[[2025,6,20]],"date-time":"2025-06-20T01:15:22Z","timestamp":1750382122000},"source":"Crossref","is-referenced-by-count":1,"title":["Chaperone Dependency during Primary Protein Biogenesis Does Not Correlate with Chaperone Dependency during\n                  <i>in vitro<\/i>\n                  Refolding"],"prefix":"10.64898","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-2431-1917","authenticated-orcid":false,"given":"Divya","family":"Yadav","sequence":"first","affiliation":[{"name":"Department of Chemistry, Johns Hopkins University, Baltimore, MD 21218, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"\u0130dil I.","family":"Demiralp","sequence":"additional","affiliation":[{"name":"Department of Chemistry, Johns Hopkins University, Baltimore, MD 21218, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Mark","family":"Fakler","sequence":"additional","affiliation":[{"name":"Department of Chemistry, Johns Hopkins University, Baltimore, MD 21218, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-2494-2193","authenticated-orcid":false,"given":"Stephen D.","family":"Fried","sequence":"additional","affiliation":[{"name":"Department of Chemistry, Johns Hopkins University, Baltimore, MD 21218, USA"},{"name":"T. C. Jenkins Department of Biophysics, Johns Hopkins University, Baltimore, MD 21218, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"54368","reference":[{"key":"2026041204214305000_2025.06.16.659923v1.1","doi-asserted-by":"publisher","DOI":"10.1016\/0003-2697(90)90104-H"},{"key":"2026041204214305000_2025.06.16.659923v1.2","doi-asserted-by":"publisher","DOI":"10.1126\/science.181.4096.223"},{"key":"2026041204214305000_2025.06.16.659923v1.3","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.0809794105"},{"key":"2026041204214305000_2025.06.16.659923v1.4","doi-asserted-by":"publisher","DOI":"10.1038\/35011000"},{"key":"2026041204214305000_2025.06.16.659923v1.5","doi-asserted-by":"crossref","unstructured":"Balchin D , Hayer-Hartl M & Hartl FU (2016) In vivo aspects of protein folding and quality control. 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