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

Meera Gupta, Alex N.T. Johnson, Edward R. Cruz, Eli J. Costa, Randi L. Guest, Sophia Hsin Jung Li, Elizabeth M. Hart, Thao Nguyen, Michael Stadlmeier, Benjamin P. Bratton, Thomas J. Silhavy, Ned S. Wingreen, Zemer Gitai, Martin Wühr

Research output: Contribution to journalArticlepeer-review

3 Scopus citations

Abstract

Protein 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.

Original languageEnglish (US)
Article number5890
JournalNature communications
Volume15
Issue number1
DOIs
StatePublished - Dec 2024

All Science Journal Classification (ASJC) codes

  • General Chemistry
  • General Biochemistry, Genetics and Molecular Biology
  • General Physics and Astronomy

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