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PXD035278

PXD035278 is an original dataset announced via ProteomeXchange.

Dataset Summary
TitleEnzyme expression kinetics by Escherichia coli during transition from rich to minimal media depends on proteome reserves
DescriptionBacterial 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.
HostingRepositoryPRIDE
AnnounceDate2023-11-14
AnnouncementXMLSubmission_2023-11-14_08:10:33.234.xml
DigitalObjectIdentifier
ReviewLevelPeer-reviewed dataset
DatasetOriginOriginal dataset
RepositorySupportUnsupported dataset by repository
PrimarySubmitterChristina Ludwig
SpeciesList scientific name: Escherichia coli; NCBI TaxID: 562;
ModificationListNo PTMs are included in the dataset
InstrumentOrbitrap Exploris 480; TripleTOF 5600
Dataset History
RevisionDatetimeStatusChangeLog Entry
02022-07-12 15:59:04ID requested
12023-02-06 00:57:04announced
22023-11-14 08:10:34announced2023-11-14: 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 affiliationBavarian Center for Biomolecular Mass Spectrometry (BayBioMS) Technical University Munich Gregor-Mendel-Straße 4 85354 Freising
contact emailtina.ludwig@tum.de
lab head
Christina Ludwig
contact affiliationTU Munich
contact emailtina.ludwig@tum.de
dataset submitter
Full Dataset Link List
Dataset FTP location
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PRIDE project URI
Repository Record List
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