PXD009736 is an
original dataset announced via ProteomeXchange.
Dataset Summary
Title | The response of the Escherichia coli proteome to deuteration and minimal media |
Description | Substitution of hydrogen for deuterium strongly affects biological systems. While higher eukaryotes, such as plants and mammals, hardly survive >30% deuterium content of water and nutrients, many microorganisms can grow on fully deuterated media albeit at reduced rates. Due to the large relative mass change, H/D replacement leads to pronounced changes in chemical reaction rates and equilibria. Very little is known how these physico-chemical effects influence cellular life at the systems level. Here we have followed the adaptation of a large part of the E. coli proteome from growth on a protonated full medium, over a protonated minimal to a completely deuterated minimal medium. More than 1800 proteins could be quantified under all conditions and several hundreds show strong regulation in both adaptation processes. As expected, the adaption to minimal medium mostly upregulates amino acid synthesis and sugar metabolism. In contrast, deuteration causes a very wide response over many cell function categories. No morphological effects are apparent under light and electron microscopy. Most of the regulated proteins have enzymatic functions involving hydrogen transfer reactions. This indicates that kinetic isotope effects and not changes in biomolecular stability are the dominant mechanisms that affect cellular function under deuteration. |
HostingRepository | PRIDE |
AnnounceDate | 2020-05-26 |
AnnouncementXML | Submission_2020-05-26_11:52:26.xml |
DigitalObjectIdentifier | https://dx.doi.org/10.6019/PXD009736 |
ReviewLevel | Peer-reviewed dataset |
DatasetOrigin | Original dataset |
RepositorySupport | Supported dataset by repository |
PrimarySubmitter | Alexander Schmidt |
SpeciesList | scientific name: Escherichia coli; NCBI TaxID: 562; |
ModificationList | Oxidation; Acetyl; Carbamidomethyl |
Instrument | LTQ Orbitrap Elite |
Dataset History
Revision | Datetime | Status | ChangeLog Entry |
0 | 2018-05-10 01:46:06 | ID requested | |
⏵ 1 | 2020-05-26 11:52:27 | announced | |
Publication List
Opitz C, Ahrn, é E, Goldie KN, Schmidt A, Grzesiek S, proteome that correlates with the reduction in growth rate. J Biol Chem, 294(7):2279-2292(2019) [pubmed] |
Keyword List
curator keyword: Technical, Biological |
submitter keyword: Ecoli, Deuteration, label-free quantification |
Contact List
Alexander Schmidt |
contact affiliation | Proteomics Core Facilty, Biozentrum, University of Basel |
contact email | alex.schmidt@unibas.ch |
lab head | |
Alexander Schmidt |
contact affiliation | Proteomics Core Facility |
contact email | alex.schmidt@unibas.ch |
dataset submitter | |
Full Dataset Link List
Dataset FTP location
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PRIDE project URI |
Repository Record List
[ + ]
[ - ]
- PRIDE
- PXD009736
- Label: PRIDE project
- Name: The response of the Escherichia coli proteome to deuteration and minimal media