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Global protein turnover quantification in Escherichia coli reveals cytoplasmic recycling under nitrogen limitation

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dc.contributor.authorGupta, Meera
dc.contributor.authorJohnson, Alex N. T.
dc.contributor.authorCruz, Edward R.
dc.contributor.authorCosta, Eli J.
dc.contributor.authorGuest, Randi L.
dc.contributor.authorLi, Sophia Hsin-Jung
dc.contributor.authorHart, Elizabeth M.
dc.contributor.authorNguyen, Thao
dc.contributor.authorStadlmeier, Michael
dc.contributor.authorBratton, Benjamin P.
dc.contributor.authorSilhavy, Thomas J.
dc.contributor.authorWingreen, Ned S.
dc.contributor.authorGitai, Zemer
dc.contributor.authorWühr, Martin
dc.date.accessioned2025-02-03T17:45:13Z
dc.date.available2025-02-03T17:45:13Z
dc.date.issued2024
dc.description.abstractProtein turnover is critical for proteostasis, but turnover quantification is challenging, and even in well-studied E. coli, proteome-wide measurements remain scarce. Here, we quantify the turnover rates of ~3200 E. coli proteins under 13 conditions by combining heavy isotope labeling with complement reporter ion quantification and find that cytoplasmic proteins are recycled when nitrogen is limited. We use knockout experiments to assign substrates to the known cytoplasmic ATP-dependent proteases. Surprisingly, none of these proteases are responsible for the observed cytoplasmic protein degradation in nitrogen limitation, suggesting that a major proteolysis pathway in E. coli remains to be discovered. Lastly, we show that protein degradation rates are generally independent of cell division rates. Thus, we present broadly applicable technology for protein turnover measurements and provide a rich resource for protein half-lives and protease substrates in E. coli, complementary to genomics data, that will allow researchers to study the control of proteostasis.
dc.identifier.citationGupta, M., Johnson, A. N. T., Cruz, E. R., Costa, E. J., Guest, R. L., Li, S. H.-J., Hart, E. M., Nguyen, T., Stadlmeier, M., Bratton, B. P., Silhavy, T. J., Wingreen, N. S., Gitai, Z., & Wuhr, M. (2024). Global protein turnover quantification in Escherichia coli reveals cytoplasmic recycling under nitrogen limitation. NATURE COMMUNICATIONS, 15(1), 5890. https://doi.org/10.1038/s41467-024-49920-8
dc.identifier.doihttps://doi.org/10.1038/s41467-024-49920-8
dc.identifier.urihttps://hdl.handle.net/20.500.14078/3783
dc.language.isoen
dc.rightsAttribution (CC BY)
dc.rights.urihttps://creativecommons.org/licenses/by/4.0/
dc.subjectprotein turnover
dc.subjectE. coli proteome
dc.subjectprotease pathways
dc.titleGlobal protein turnover quantification in Escherichia coli reveals cytoplasmic recycling under nitrogen limitationen
dc.typeArticle

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