PXD035278 is an
original dataset announced via ProteomeXchange.
Dataset Summary
Title | Enzyme expression kinetics by Escherichia coli during transition from rich to minimal media depends on proteome reserves |
Description | Bacterial fitness depends on adaptability to changing environments. In rich growth medium, which is replete with amino acids, Escherichia coli primarily expresses protein synthesis machineries, which comprise ~40% of cellular proteins and are required for rapid growth. Upon transition to minimal medium, which lacks amino acids, biosynthetic enzymes are synthesized, eventually reaching ~15% of cellular proteins when growth fully resumes. We applied quantitative proteomics to analyse the timing of enzyme expression during such transitions, and established a simple positive relation between the onset time of enzyme synthesis and the fractional enzyme ‘reserve’ maintained by E. coli while growing in rich media. We devised and validated a coarse-grained kinetic model that quantitatively captures the enzyme recovery kinetics in different pathways, solely on the basis of proteomes immediately preceding the transition and well after its completion. Our model enables us to infer regulatory strategies underlying the ‘as-needed’ gene expression programme adopted by E. coli. |
HostingRepository | PRIDE |
AnnounceDate | 2023-11-14 |
AnnouncementXML | Submission_2023-11-14_08:10:33.234.xml |
DigitalObjectIdentifier | |
ReviewLevel | Peer-reviewed dataset |
DatasetOrigin | Original dataset |
RepositorySupport | Unsupported dataset by repository |
PrimarySubmitter | Christina Ludwig |
SpeciesList | scientific name: Escherichia coli; NCBI TaxID: 562; |
ModificationList | No PTMs are included in the dataset |
Instrument | Orbitrap Exploris 480; TripleTOF 5600 |
Dataset History
Revision | Datetime | Status | ChangeLog Entry |
0 | 2022-07-12 15:59:04 | ID requested | |
1 | 2023-02-06 00:57:04 | announced | |
⏵ 2 | 2023-11-14 08:10:34 | announced | 2023-11-14: Updated project metadata. |
Publication List
Wu C, Mori M, Abele M, Banaei-Esfahani A, Zhang Z, Okano H, Aebersold R, Ludwig C, Hwa T, Enzyme expression kinetics by Escherichia coli during transition from rich to minimal media depends on proteome reserves. Nat Microbiol, 8(2):347-359(2023) [pubmed] |
Keyword List
submitter keyword: proteomics, amino acid biosynthesis,growth transition, ribosome biogenesis, coarse-grained theory |
Contact List
Christina Ludwig |
contact affiliation | Bavarian Center for Biomolecular Mass Spectrometry (BayBioMS) Technical University Munich Gregor-Mendel-Straße 4 85354 Freising |
contact email | tina.ludwig@tum.de |
lab head | |
Christina Ludwig |
contact affiliation | TU Munich |
contact email | tina.ludwig@tum.de |
dataset submitter | |
Full Dataset Link List
Dataset FTP location
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PRIDE project URI |
Repository Record List
[ + ]
[ - ]
- PRIDE
- PXD035278
- Label: PRIDE project
- Name: Enzyme expression kinetics by Escherichia coli during transition from rich to minimal media depends on proteome reserves