ArticleNature communications2024
Global protein turnover quantification in Escherichia coli reveals cytoplasmic recycling under nitrogen limitation.
Article in Nature communications, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 23 papers.
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Who cites it
23 citing papers in PubMed.
- Integrated multi-omics analysis reveals a pH-driven metabolic and translational switch inMicrobiology spectrum · 2026Article
- Enzyme kinetics shapes the growth response of metabolic networks.PLoS computational biology · 2026Article
- Advances in Decoding Bacterial N-Terminal Proteoforms: Technologies, Challenges, and Functional Insights.Microorganisms · 2026Review
- Counting to two: how phages decide between lysis and lysogeny.bioRxiv : the preprint server for biology · 2026Article
- Molecular evolution in light of regulatory-coding epistasis.EMBO reports · 2026Review
- TRAINSPOTTER: profiling nascent protein N-termini indicative of bacterial translation initiation via deformylation-assisted N-terminomics.Nucleic acids research · 2026Article
- Deep Learning-Based Protein Half-Life Prediction for Identifying Rate-Limiting Enzymes in Metabolic Pathways to Alleviate Bottleneck Reactions.Journal of microbiology and biotechnology · 2026Article
- Metabolic responses to benzoic acid stress and glutamine transport-dependent vulnerabilities in Escherichia coli revealed by NMR metabolomics.World journal of microbiology & biotechnology · 2026Article
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- Protein overabundance is driven by growth robustness.Science advances · 2026Article
- Global analysis of protein degradation reveals instability of diverse regulators inProceedings of the National Academy of Sciences of the United States of America · 2026Article
- Contrasting effects of glutamate and branched-chain amino acid metabolism on acid tolerance in aApplied and environmental microbiology · 2026Article
- Understanding the Role of pH Regulation and Neutralizing Agents in Organic Acid Production and Growth of Aspergillus oryzae.Biotechnology and bioengineering · 2026Article
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- Direct and indirect pathways linking the Lon protease to motility behaviors in the pathogen Pseudomonas aeruginosa.PLoS pathogens · 2025Article
- Design principles for engineering bacteria to maximise chemical production from batch cultures.Nature communications · 2025Article
- Evaluation of protein extraction methodologies on bacterial proteomic profiling: a comparative analysis.Frontiers in microbiology · 2025Article
- OmpA controls order in the outer membrane and shares the mechanical load.Proceedings of the National Academy of Sciences of the United States of America · 2024Article
- Divergent Molecular Responses to Heavy Water inPlants (Basel, Switzerland) · 2024Article
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Authors and funding
14 authors.
Funding
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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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the Socratic graph.