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Peer-reviewedCC BYMolecular Systems Biology

E. coli prepares for starvation by dramatically remodeling its proteome in the first hours after loss of nutrients

  • Théo Gervais1,2
  • Bjoern Kscheschinski1,2
  • Michael Mell1,2
  • Nevil Goepfert1,2
  • Erik van Nimwegen3,4
  • Thomas Julou5,6
6 affiliations
  1. 1Biozentrum, University of Basel, Spitalstrasse 41, Basel, 4056, Switzerland
  2. 2Swiss Institute of Bioinformatics, Basel, Switzerland
  3. 3Biozentrum, University of Basel, Spitalstrasse 41, Basel, 4056, Switzerland. [email protected]
  4. 4Swiss Institute of Bioinformatics, Basel, Switzerland. [email protected]
  5. 5Biozentrum, University of Basel, Spitalstrasse 41, Basel, 4056, Switzerland. [email protected]
  6. 6Swiss Institute of Bioinformatics, Basel, Switzerland. [email protected]
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Abstract

Although in the wild bacteria likely spend most of their time deprived of nutrients and slowly starving to death, very little is known about how bacteria adapt their phenotype to starvation. Here we combine microfluidics with quantitative fluorescence microscopy of transcriptional reporters to comprehensively quantify growth and gene expression at the single-cell level in E. coli during carbon starvation. We find that all cells immediately stop growing upon loss of carbon source and that almost all remain alive for over 30 hours. Furthermore, entry into starvation triggers a dynamic expression program that is remarkably homogeneous across single cells, but highly variable across genes, causing dramatic remodeling of the proteome early in starvation. We further show that, as protein production and the rate of protein degradation both decay approximately exponentially, protein concentrations become essentially ‘frozen’ after the first 5 to 10 hours, setting phenotypes for several days of starvation. Finally, using experiments in which gene expression is inhibited for different periods, we show that protein production in the first 5 hours is crucial for protecting cells from stresses late in starvation.

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Cite

BibTeXRIS
BibTeX
@article{gervais2026coli,
  title = {{E. coli prepares for starvation by dramatically remodeling its proteome in the first hours after loss of nutrients}},
  author = {Théo Gervais and Bjoern Kscheschinski and Michael Mell and Nevil Goepfert and Erik van Nimwegen and Thomas Julou},
  journal = {Molecular Systems Biology},
  year = {2026},
  month = jul,
  doi = {10.1038/s44320-026-00226-5},
  url = {https://doi.org/10.1038/s44320-026-00226-5},
  note = {CC BY},
}
RIS
TY  - JOUR
TI  - E. coli prepares for starvation by dramatically remodeling its proteome in the first hours after loss of nutrients
AU  - Théo Gervais
AU  - Bjoern Kscheschinski
AU  - Michael Mell
AU  - Nevil Goepfert
AU  - Erik van Nimwegen
AU  - Thomas Julou
PY  - 2026
DA  - 2026/07/01
JO  - Molecular Systems Biology
DO  - 10.1038/s44320-026-00226-5
UR  - https://doi.org/10.1038/s44320-026-00226-5
AB  - Although in the wild bacteria likely spend most of their time deprived of nutrients and slowly starving to death, very little is known about how bacteria adapt their phenotype to starvation. Here we combine microfluidics with quantitative fluorescence microscopy of transcriptional reporters to comprehensively quantify growth and gene expression at the single-cell level in E. coli during carbon starvation. We find that all cells immediately stop growing upon loss of carbon source and that almost all remain alive for over 30 hours. Furthermore, entry into starvation triggers a dynamic expression program that is remarkably homogeneous across single cells, but highly variable across genes, causing dramatic remodeling of the proteome early in starvation. We further show that, as protein production and the rate of protein degradation both decay approximately exponentially, protein concentrations become essentially ‘frozen’ after the first 5 to 10 hours, setting phenotypes for several days of starvation. Finally, using experiments in which gene expression is inhibited for different periods, we show that protein production in the first 5 hours is crucial for protecting cells from stresses late in starvation.
SN  - 1744-4292
ER  -