Absolute metabolite concentrations and implied enzyme active site occupancy in Escherichia coli.
Absolute metabolite concentrations are critical to a quantitative understanding of cellular metabolism, as concentrations impact both the free energies and rates of metabolic reactions. Here we use LC-MS/MS to quantify more than 100 metabolite concentrations in aerobic, exponentially growing Escherichia coli with glucose, glycerol or acetate as the carbon source. The total observed intracellular metabolite pool was approximately 300 mM. A small number of metabolites dominate the metabolome on a molar basis, with glutamate being the most abundant. Metabolite concentration exceeds K(m) for most substrate-enzyme pairs. An exception is lower glycolysis, where concentrations of intermediates are near the K(m) of their consuming enzymes and all reactions are near equilibrium. This may facilitate efficient flux reversibility given thermodynamic and osmotic constraints. The data and analyses presented here highlight the ability to identify organizing metabolic principles from systems-level absolute metabolite concentration data.
Bennett
Bryson D
BD
Department of Chemistry and Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, New Jersey, USA.
Kimball
Elizabeth H
EH
Gao
Melissa
M
Osterhout
Robin
R
Van Dien
Stephen J
SJ
Rabinowitz
Joshua D
JD
D000085:Acetates / Q000494:pharmacology; D001665:Binding Sites; D002853:Chromatography, Liquid; D004926:Escherichia coli / Q000201:enzymology* / Q000254:growth & development / Q000378:metabolism*; D029968:Escherichia coli Proteins / Q000378:metabolism*; D005947:Glucose / Q000494:pharmacology; D005990:Glycerol / Q000494:pharmacology; D006019:Glycolysis; D013058:Mass Spectrometry; D055442:Metabolome; D013816:Thermodynamics
D000085:Acetates; D029968:Escherichia coli Proteins; D005947:Glucose; D005990:Glycerol