PXD055125-1
PXD055125 is an original dataset announced via ProteomeXchange.
Dataset Summary
Title | E. coli leverages growth arrest to remodel its proteome upon entry into starvation |
Description | It is widely believed that, owing to the limitation of nutrients in natural environments, bacteria spend most of their life in a non-growing state. However, despite its major clinical and ecological implications, very little is known about what determines the phenotype of starved bacteria, in particular what controls the concentration of different gene products inside the cells. Using microfluidics and quantitative fluorescence microscopy, we monitored growth and gene expression in many independent E. coli lineages as we switched them from exponential growth to starvation. We observed that all cells stopped growing immediately and that no cell death occurred for more than two days. At the same time, gene expression undergoes a dramatic remodeling upon entry into starvation in a promoter-dependent manner. Some promoters, including ribosomal protein promoters, arrest gene expression immediately, others show a slow exponential decay of expression on a 10 h time scale, while a third category exhibits a transient burst of activity before decaying exponentially. Remarkably, the time dynamics of these changes are highly homogeneous across single cells. In addition, we demonstrated that the gene expression response does not qualitatively depend on the dynamics of starvation entry. Combining the observed time-dependent protein production and decay rates, we showed with mathematical modeling that a delay between growth arrest and shutdown of gene expression allows a massive increase in the concentration of certain proteins without requiring an upregulation of their expression. Moreover, protein concentrations deep in starvation appeared to be mainly determined by the expression dynamics during the first 10 h of starvation. Finally, we established that this expression program at the onset of starvation is critical for cell viability. In particular, by inhibiting gene expression during different periods of starvation, we were able to show that the tolerance to stress after 2 days is determined by gene expression occurring during the first 10 h, which thus constitutes a preventive response. These results provide a starting point for quantitative studies of cell maintenance and the emergence of specific phenotypes when nutrients become scarce. |
HostingRepository | MassIVE |
AnnounceDate | 2024-08-29 |
AnnouncementXML | Submission_2024-08-29_05:39:05.495.xml |
DigitalObjectIdentifier | |
ReviewLevel | Non peer-reviewed dataset |
DatasetOrigin | Original dataset |
RepositorySupport | Unsupported dataset by repository |
PrimarySubmitter | Alex Schmidt |
SpeciesList | scientific name: Escherichia coli; common name: E. coli; NCBI TaxID: 562; |
ModificationList | No PTMs are included in the dataset |
Instrument | Orbitrap Exploris 480; Orbitrap Eclipse |
Dataset History
Revision | Datetime | Status | ChangeLog Entry |
---|---|---|---|
0 | 2024-08-23 04:21:23 | ID requested | |
⏵ 1 | 2024-08-29 05:39:05 | announced |
Publication List
no publication |
Keyword List
submitter keyword: Growth, ECOLI, Starvation |
Contact List
Alexander Schmidt | |
---|---|
contact affiliation | Biozentrum, Universtiy of Basel, 4056 Basel, Switzerland |
contact email | alex.schmidt@unibas.ch |
lab head | |
Alex Schmidt | |
contact affiliation | University of Basel |
contact email | alex.schmidt@unibas.ch |
dataset submitter |
Full Dataset Link List
MassIVE dataset URI |
Dataset FTP location NOTE: Most web browsers have now discontinued native support for FTP access within the browser window. But you can usually install another FTP app (we recommend FileZilla) and configure your browser to launch the external application when you click on this FTP link. Or otherwise, launch an app that supports FTP (like FileZilla) and use this address: ftp://massive.ucsd.edu/v08/MSV000095680/ |