Differential quantitative proteome analysis of Escherichia coli grown on acetate versus glucose.
Relative protein abundances of Escherichia coli MG1655 growing exponentially on minimal medium with acetate or glucose as the sole carbon source were investigated in a quantitative shotgun proteome analysis with TMT6-plex isobaric tags. Peptides were separated by high resolution high/low pH 2D-LC, using an optimized fraction pooling scheme followed by mass spectrometric analysis. Quantitative data were acquired for 2099 proteins covering 49% of the predicted E. coli proteins, showing system-wide effects of growth conditions. In total, 507 proteins showed a fold change of at least 1.5 and 205 proteins changed by more than twofold. Significant differences in abundance were observed for most of the proteins in the central carbon metabolism and in proteins relevant for amino acid and protein synthesis, processing of environmental information and scavenging of a variety of alternate carbon sources. Periplasmic-binding proteins were also more abundant on acetate, especially proteins involved in scavenging extracellular resources such as sugars. All MS data have been deposited to the ProteomeXchange Consortium via the PRIDE partner repository (dataset identifier PXD003863).
Systematische Proteomforschung & Bioanalytik, Institut für Experimentelle Medizin, Christian-Albrechts-Universität zu Kiel, Kiel, Germany.
Christian
C
Treitz
LISBP, Université de Toulouse, CNRS, INRA, INSA, Toulouse, France.
Brice
B
Enjalbert
LISBP, Université de Toulouse, CNRS, INRA, INSA, Toulouse, France.
Jean-Charles
JC
Portais
LISBP, Université de Toulouse, CNRS, INRA, INSA, Toulouse, France.
Fabien
F
Letisse
Systematische Proteomforschung & Bioanalytik, Institut für Experimentelle Medizin, Christian-Albrechts-Universität zu Kiel, Kiel, Germany. a.tholey@iem.uni-kiel.de.
Andreas
A
Tholey
D000085:Acetates / Q000737:chemistry; D000596:Amino Acids / Q000737:chemistry; D004926:Escherichia coli / Q000235:genetics* / Q000254:growth & development; D029968:Escherichia coli Proteins / Q000096:biosynthesis* / Q000235:genetics; D005947:Glucose / Q000737:chemistry; D013058:Mass Spectrometry; D014176:Protein Biosynthesis / Q000235:genetics*; D020543:Proteome / Q000235:genetics*; D040901:Proteomics / Q000379:methods
D000085:Acetates; D000596:Amino Acids; D029968:Escherichia coli Proteins; D020543:Proteome; D005947:Glucose
2D-LC MS; Isobaric labeling; Metabolic network; Systems biology