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Submitted on May 18, 2005
Accepted on May 19, 2005

Localization, annotation & comparison of the Escherichia coli K-12 proteome under two states of growth

Ana Lopez-Campistrous, Paul Semchuk, Lorne Burke, Taunja Palmer-Stone, Stephen J. Brokx, Gordon Broderick, Drell Bottorff, Sandra Bolch, Joel H. Weiner, and Michael J. Ellison

Institute for Biomolecular Design, University of Alberta, Edmonton, Alberta T6G 2H7

Corresponding Author: mike.ellison{at}ualberta.ca

Here we describe a proteomic analysis of Escherichia coli in which 3,199 protein forms were detected of those 2,160 were annotated and assigned to the cytosol, periplasm, inner membrane and outer membrane by biochemical fractionation followed by two-dimensional gel electrophoresis and tandem mass spectrometry. Represented within this inventory were unique and modified forms corresponding to 575 different open reading frames (ORFs) that included 151 proteins whose existence had been predicted from hypothetical ORFs, 76 proteins of completely unknown function, and 222 proteins currently without location assignments in the Swiss-Prot Database. Of the 575 unique proteins identified, 42% were found to exist in multiple forms. Using differential in gel fluorescence (DIGE), we also examined the relative changes in protein expression when cells were grown in the presence and absence of amino acids. A total of 23 different proteins were identified whose abundance changed significantly between the two conditions. Most of these changes were found to be associated with proteins involved in carbon & amino acid metabolism, transport, and chemotaxis. Detailed information related to all 2160 protein forms (protein & gene names, accession numbers, subcellular locations, relative abundances, sequence coverage, molecular masses and isoelectric points) can be found at www.projectcybercell.ca in either tabular form or as interactive gel images.


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