PXD001648 is an
original dataset announced via ProteomeXchange.
Dataset Summary
Title | Characterization of the E.coli proteome and its modifications during growth and ethanol stress |
Description | We set out to provide a resource to the microbiology community especially with respect to systems biology based endeavors. To this end, we generated a comprehensive dataset monitoring the changes in protein expression, copy number, and post translational modifications in a systematic fashion during growth and ethanol stress in E.coli. We utilized high-resolution mass spectrometry combined with the Super-SILAC approach. In a single experiment, we have identified over 2,300 proteins, which represent approximately 88% of the estimated expressed proteome of E. coli and estimated protein copy numbers using the Intensity Based Absolute Quantitation (IBAQ). The dynamic range of protein expression spanned up to six orders of magnitude, with the highest protein copy per cell estimated at approximately 300,000. We focused on the proteome dynamics involved during stationary phase growth. A global up-regulation of proteins related to stress response was detected in later stages of growth. We observed the down-regulation of the methyl directed mismatch repair system containing MutS and MutL of E. coli growing in long term growth cultures, confirming that higher incidence of mutations presents an important mechanism in the increase in genetic diversity and stationary phase survival in E.coli. During ethanol stress, known markers such as alcohol dehydrogenase and aldehyde dehydrogenase were induced, further validating the dataset. Finally, we performed unbiased protein modification detection and revealed changes of many known and unknown protein modifications in both experimental conditions. |
HostingRepository | PRIDE |
AnnounceDate | 2015-02-03 |
AnnouncementXML | Submission_2015-06-01_03:53:49.xml |
DigitalObjectIdentifier | |
ReviewLevel | Peer-reviewed dataset |
DatasetOrigin | Original dataset |
RepositorySupport | Unsupported dataset by repository |
PrimarySubmitter | Karsten Krug |
SpeciesList | scientific name: Escherichia coli; NCBI TaxID: 562; |
ModificationList | No PTMs are included in the dataset |
Instrument | LTQ Orbitrap Elite |
Dataset History
Revision | Datetime | Status | ChangeLog Entry |
0 | 2015-01-05 02:42:46 | ID requested | |
1 | 2015-02-03 06:54:48 | announced | |
⏵ 2 | 2015-06-01 03:53:51 | announced | Updated publication reference for PubMed record(s): 25741329. |
Publication List
Soufi B, Krug K, Harst A, Macek B, Characterization of the E. coli proteome and its modifications during growth and ethanol stress. Front Microbiol, 6():103(2015) [pubmed] |
Keyword List
curator keyword: Biological |
submitter keyword: Super-SILAC,Quantitative Proteomics,Absolute Quantitation, Stress response, E.coli |
Contact List
Boris Macek |
contact affiliation | Protoeme Center Tuebingen, University of Tuebingen, Germany |
contact email | boris.macek@uni-tuebingen.de |
lab head | |
Karsten Krug |
contact affiliation | Proteome Center |
contact email | karsten.krug@uni-tuebingen.de |
dataset submitter | |
Full Dataset Link List
Dataset FTP location
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PRIDE project URI |
Repository Record List
[ + ]
[ - ]
- PRIDE
- PXD001648
- Label: PRIDE project
- Name: Characterization of the E.coli proteome and its modifications during growth and ethanol stress