PXD055125

PXD055125 is an original dataset announced via ProteomeXchange.

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

Revision	Datetime	Status	ChangeLog Entry
0	2024-08-23 04:21:23	ID requested
⏵ 1	2024-08-29 05:39:05	announced

no publication

submitter keyword: Growth, ECOLI, Starvation

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

MassIVE dataset URI

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