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Global protein turnover quantification in Escherichia coli reveals cytoplasmic recycling under nitrogen limitation.
Gupta, Meera; Johnson, Alex N T; Cruz, Edward R; Costa, Eli J; Guest, Randi L; Li, Sophia Hsin-Jung; Hart, Elizabeth M; Nguyen, Thao; Stadlmeier, Michael; Bratton, Benjamin P; Silhavy, Thomas J; Wingreen, Ned S; Gitai, Zemer; Wühr, Martin.
Afiliación
  • Gupta M; Department of Chemical and Biological Engineering, Princeton University, Princeton, NJ, USA.
  • Johnson ANT; Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, USA.
  • Cruz ER; Department of Molecular Biology, Princeton University, Princeton, NJ, USA.
  • Costa EJ; Department of Chemical and Biological Engineering, Princeton University, Princeton, NJ, USA.
  • Guest RL; Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, USA.
  • Li SH; Department of Molecular Biology, Princeton University, Princeton, NJ, USA.
  • Hart EM; Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, USA.
  • Nguyen T; Department of Molecular Biology, Princeton University, Princeton, NJ, USA.
  • Stadlmeier M; Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, USA.
  • Bratton BP; Department of Molecular Biology, Princeton University, Princeton, NJ, USA.
  • Silhavy TJ; Department of Molecular Biology, Princeton University, Princeton, NJ, USA.
  • Wingreen NS; Department of Molecular Biology, Princeton University, Princeton, NJ, USA.
  • Gitai Z; Department of Microbiology, Harvard Medical School, Boston, MA, USA.
  • Wühr M; Department of Chemical and Biological Engineering, Princeton University, Princeton, NJ, USA.
Nat Commun ; 15(1): 5890, 2024 Jul 13.
Article en En | MEDLINE | ID: mdl-39003262
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.
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Texto completo: 1 Colección: 01-internacional Base de datos: MEDLINE Asunto principal: Citoplasma / Proteínas de Escherichia coli / Escherichia coli / Proteolisis / Nitrógeno Idioma: En Revista: Nat Commun Asunto de la revista: BIOLOGIA / CIENCIA Año: 2024 Tipo del documento: Article País de afiliación: Estados Unidos Pais de publicación: Reino Unido
Texto completo
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Texto completo: 1 Colección: 01-internacional Base de datos: MEDLINE Asunto principal: Citoplasma / Proteínas de Escherichia coli / Escherichia coli / Proteolisis / Nitrógeno Idioma: En Revista: Nat Commun Asunto de la revista: BIOLOGIA / CIENCIA Año: 2024 Tipo del documento: Article País de afiliación: Estados Unidos Pais de publicación: Reino Unido