Toward a Protein Profile of Escherichia coli: Comparison to Its Transcription Profile

• Published in: Proceedings of the National Academy of Sciences - PNAS 2003-08, Vol.100 (16), p.9232-9237
• Main Authors: Corbin, Rebecca W., Paliy, Oleg, Yang, Feng, Shabanowitz, Jeffrey, Platt, Mark, Lyons, Charles E., Root, Karen, McAuliffe, Jon, Jordan, Michael I., Kustu, Sydney, Soupene, Eric, Hunt, Donald F.
• Format: Article
• Language: English
• Subjects: Arithmetic; Biochemistry; Biological Sciences; Cell Membrane - metabolism; Chromatography, High Pressure Liquid; Escherichia coli; Escherichia coli - metabolism; Escherichia coli - physiology; Genes; Genomes; Glycerol - chemistry; Mass Spectrometry; Membrane proteins; Membranes; Messenger RNA; Oligonucleotide Array Sequence Analysis; Open reading frames; Operons; Peptides; Proteins; Proteome; RNA, Messenger - metabolism; Signal detection; Spectrum analysis; Time Factors; Transcription, Genetic
• ISSN: 0027-8424; 1091-6490
• DOI: 10.1073/pnas.1533294100

High-pressure liquid chromatography-tandem mass spectrometry was used to obtain a protein profile of Escherichia coli strain MG1655 grown in minimal medium with glycerol as the carbon source. By using cell lysate from only 3 x 108cells, at least four different tryptic peptides were detected for each of 404 proteins in a short 4-h experiment. At least one peptide with a high reliability score was detected for 986 proteins. Because membrane proteins were under-represented, a second experiment was performed with a preparation enriched in membranes. An additional 161 proteins were detected, of which from half to two-thirds were membrane proteins. Overall, 1,147 different E. coli proteins were identified, almost 4 times as many as had been identified previously by using other tools. The protein list was compared with the transcription profile obtained on Affymetrix GeneChips. Expression of 1,113 (97%) of the genes whose protein products were found was detected at the mRNA level. The arithmetic mean mRNA signal intensity for these genes was 3-fold higher than that for all 4,300 protein-coding genes of E. coli. Thus, GeneChip data confirmed the high reliability of the protein list, which contains about one-fourth of the proteins of E. coli. Detection of even those membrane proteins and proteins of undefined function that are encoded by the same operons (transcriptional units) encoding proteins on the list remained low.