Localization, Annotation, and Comparison of the Escherichia coli K-12 Proteome under Two States of Growth*S

Here we describe a proteomic analysis of Escherichia coli in which 3,199 protein forms were detected, and 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 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 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 and amino acid metabolism, transport, and chemotaxis. Detailed information related to all 2,160 protein forms (protein and gene names, accession numbers, subcellular locations, relative abundances, sequence coverage, molecular masses, and isoelectric points) can be obtained upon request in either tabular form or as interactive gel images.

[1]  P. O’Farrell High resolution two-dimensional electrophoresis of proteins. , 1975, The Journal of biological chemistry.

[2]  D. Oxender,et al.  Genetic separation of high- and low-affinity transport systems for branched-chain amino acids in Escherichia coli K-12 , 1978, Journal of bacteriology.

[3]  A. Constans Desktop drug discovery , 2004 .

[4]  E. Egelman,et al.  Image analysis reveals that Escherichia coli RecA protein consists of two domains. , 1990, Biophysical journal.

[5]  J. Celis,et al.  Reference points for comparisons of two‐dimensional maps of proteins from different human cell types defined in a pH scale where isoelectric points correlate with polypeptide compositions , 1994, Electrophoresis.

[6]  K. Shanmugam,et al.  Cloning, sequencing, and mutational analysis of the hyb operon encoding Escherichia coli hydrogenase 2 , 1994, Journal of bacteriology.

[7]  P. Andrews,et al.  Profiling the alkaline membrane proteome of Caulobacter crescentus with two‐dimensional electrophoresis and mass spectrometry , 2002, Proteomics.

[8]  G. L. Hazelbauer Maltose chemoreceptor of Escherichia coli , 1975, Journal of bacteriology.

[9]  Constance Holden Alliance Launched to Model E. coli , 2002, Science.

[10]  N. W. Davis,et al.  The complete genome sequence of Escherichia coli K-12. , 1997, Science.

[11]  Sequence of the fruB gene of Escherichia coli encoding the diphosphoryl transfer protein (DTP) of the phosphoenolpyruvate: sugar phosphotransferase system. , 1994, FEMS microbiology letters.

[12]  R. Heath,et al.  Roles of the FabA and FabZ β-Hydroxyacyl-Acyl Carrier Protein Dehydratases in Escherichia coli Fatty Acid Biosynthesis* , 1996, The Journal of Biological Chemistry.

[13]  J. Guest,et al.  Structure, Expression, and Protein Engineering of the Pyruvate Dehydrogenase Complex of Escherichia coli a , 1989, Annals of the New York Academy of Sciences.

[14]  Richard D. Smith,et al.  Integration of capillary isoelectric focusing with capillary reversed‐phase liquid chromatography for two‐dimensional proteomics separation , 2002, Electrophoresis.

[15]  C. Hoogland,et al.  New perspectives in the Escherichia coli proteome investigation , 2001, Proteomics.

[16]  J. Weiner,et al.  Chemical and functional properties of the native and reconstituted forms of the membrane-bound, aerobic glycerol-3-phosphate dehydrogenase of Escherichia coli. , 1978, The Journal of biological chemistry.

[17]  E. Newman,et al.  Sequencing and characterization of the sdaB gene from Escherichia coli K-12. , 1993, European journal of biochemistry.

[18]  R. Wait,et al.  Fluorescence two‐dimensional difference gel electrophoresis and mass spectrometry based proteomic analysis of Escherichia coli , 2002, Proteomics.

[19]  M. Quadroni,et al.  Short- and long-term changes in proteome composition and kinetic properties in a culture of Escherichia coli during transition from glucose-excess to glucose-limited growth conditions in continuous culture and vice versa. , 2001, Environmental microbiology.

[20]  R D Appel,et al.  Protein identification and analysis tools in the ExPASy server. , 1999, Methods in molecular biology.

[21]  Monica Riley,et al.  A functional update of the Escherichia coli K-12 genome , 2001, Genome Biology.

[22]  D. Hochstrasser,et al.  The focusing positions of polypeptides in immobilized pH gradients can be predicted from their amino acid sequences , 1993, Electrophoresis.

[23]  DcrA and dcrB Escherichia coli genes can control DNA injection by phages specific for BtuB and FhuA receptors. , 2002, Research in microbiology.

[24]  C. Hoogland,et al.  '98 Escherichia coli SWISS‐2DPAGE database update , 1998, Electrophoresis.

[25]  Michael I. Jordan,et al.  Toward a protein profile of Escherichia coli: Comparison to its transcription profile , 2003, Proceedings of the National Academy of Sciences of the United States of America.

[26]  T. Silhavy,et al.  Targeting and assembly of periplasmic and outer-membrane proteins in Escherichia coli. , 1998, Annual review of genetics.

[27]  George M. Church,et al.  Comparing the predicted and observed properties of proteins encoded in the genome of Escherichia coli K‐12 , 1997, Electrophoresis.