PXD001648

PXD001648 is an original dataset announced via ProteomeXchange.

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

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.

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]

curator keyword: Biological

submitter keyword: Super-SILAC,Quantitative Proteomics,Absolute Quantitation, Stress response, E.coli

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

Dataset FTP location NOTE: Most web browsers have now discontinued native support for FTP access within the browser window. But you can usually install another FTP app (we recommend FileZilla) and configure your browser to launch the external application when you click on this FTP link. Or otherwise, launch an app that supports FTP (like FileZilla) and use this address: ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2015/02/PXD001648

PRIDE project URI

• PRIDE
  1. PXD001648
     1. Label: PRIDE project
     2. Name: Characterization of the E.coli proteome and its modifications during growth and ethanol stress