Absolute metabolite concentrations and implied enzyme active site occupancy in Escherichia coli (original) (raw)

• Bajad, S.U. et al. Separation and quantitation of water soluble cellular metabolites by hydrophilic interaction chromatography-tandem mass spectrometry. J. Chromatogr. A 1125, 76–88 (2006).
  Article CAS PubMed Google Scholar
• Coulier, L. et al. Simultaneous quantitative analysis of metabolites using ion-pair liquid chromatography-electrospray ionization mass spectrometry. Anal. Chem. 78, 6573–6582 (2006).
  Article CAS PubMed Google Scholar
• Luo, B., Groenke, K., Takors, R., Wandrey, C. & Oldiges, M. Simultaneous determination of multiple intracellular metabolites in glycolysis, pentose phosphate pathway and tricarboxylic acid cycle by liquid chromatography-mass spectrometry. J. Chromatogr. A 1147, 153–164 (2007).
  Article CAS PubMed Google Scholar
• Tu, B.P. et al. Cyclic changes in metabolic state during the life of a yeast cell. Proc. Natl. Acad. Sci. USA 104, 16886–16891 (2007).
  Article CAS PubMed Google Scholar
• Brauer, M.J. et al. Conservation of the metabolomic response to starvation across two divergent microbes. Proc. Natl. Acad. Sci. USA 103, 19302–19307 (2006).
  Article CAS PubMed Google Scholar
• Oldiges, M., Kunze, M., Degenring, D., Sprenger, G.A. & Takors, R. Stimulation, monitoring, and analysis of pathway dynamics by metabolic profiling in the aromatic amino acid pathway. Biotechnol. Prog. 20, 1623–1633 (2004).
  Article CAS PubMed Google Scholar
• Villas-Bôas, S.G. & Bruheim, P. Cold glycerol-saline: the promising quenching solution for accurate intracellular metabolite analysis of microbial cells. Anal. Biochem. 370, 87–97 (2007).
  Article PubMed Google Scholar
• Mashego, M.R. et al. MIRACLE: mass isotopomer ratio analysis of U-13C-labeled extracts. A new method for accurate quantification of changes in concentrations of intracellular metabolites. Biotechnol. Bioeng. 85, 620–628 (2004).
  Article CAS PubMed Google Scholar
• Seifar, R.M. et al. Quantitative analysis of metabolites in complex biological samples using ion-pair reversed-phase liquid chromatography-isotope dilution tandem mass spectrometry. J. Chromatogr. A 1187, 103–110 (2008).
  Article CAS PubMed Google Scholar
• Wu, L. et al. Quantitative analysis of the microbial metabolome by isotope dilution mass spectrometry using uniformly 13C-labeled cell extracts as internal standards. Anal. Biochem. 336, 164–171 (2005).
  Article CAS PubMed Google Scholar
• Zamboni, N., Kummel, A. & Heinemann, M. AnNET: a tool for network-embedded thermodynamic analysis of quantitative metabolome data. BMC Bioinformatics 9, 199 (2008).
  Article PubMed PubMed Central Google Scholar
• Kümmel, A., Panke, S. & Heinemann, M. Systematic assignment of thermodynamic constraints in metabolic network models. BMC Bioinformatics 7, 512 (2006).
  Article PubMed PubMed Central Google Scholar
• Kümmel, A., Panke, S. & Heinemann, M. Putative regulatory sites unraveled by network-embedded thermodynamic analysis of metabolome data. Mol. Syst. Biol. 2, 2006.0034 (2006).
  Article PubMed PubMed Central Google Scholar
• Henry, C.S., Broadbelt, L.J. & Hatzimanikatis, V. Thermodynamics-based metabolic flux analysis. Biophys. J. 92, 1792–1805 (2007).
  Article CAS PubMed Google Scholar
• Hoppe, A., Hoffmann, S. & Holzhutter, H.G. Including metabolite concentrations into flux balance analysis: thermodynamic realizability as a constraint on flux distributions in metabolic networks. BMC Syst. Biol. 1, 23 (2007).
  Article PubMed PubMed Central Google Scholar
• Yuan, J., Bennett, B.D. & Rabinowitz, J.D. Kinetic flux profiling for quantitation of cellular metabolic fluxes. Nat. Protoc. 3, 1328–1340 (2008).
  Article CAS PubMed PubMed Central Google Scholar
• Yuan, J., Fowler, W.U., Kimball, E., Lu, W. & Rabinowitz, J.D. Kinetic flux profiling of nitrogen assimilation in Escherichia coli. Nat. Chem. Biol. 2, 529–530 (2006).
  Article CAS PubMed Google Scholar
• Easterby, J.S. The effect of feedback on pathway transient response. Biochem. J. 233, 871–875 (1986).
  Article CAS PubMed PubMed Central Google Scholar
• Jamshidi, N. & Palsson, B.O. Formulating genome-scale kinetic models in the post-genome era. Mol. Syst. Biol. 4, 171 (2008).
  Article PubMed PubMed Central Google Scholar
• Gutenkunst, R.N. et al. Universally sloppy parameter sensitivities in systems biology models. PLoS Comput. Biol. 3, 1871–1878 (2007).
  Article CAS PubMed Google Scholar
• Piazza, M., Feng, X.J., Rabinowitz, J.D. & Rabitz, H. Diverse metabolic model parameters generate similar methionine cycle dynamics. J. Theor. Biol. 251, 628–639 (2008).
  Article CAS PubMed Google Scholar
• Karp, P.D. et al. Multidimensional annotation of the Escherichia coli K-12 genome. Nucleic Acids Res. 35, 7577–7590 (2007).
  Article CAS PubMed PubMed Central Google Scholar
• Ibarra, R.U., Edwards, J.S. & Palsson, B.O. Escherichia coli K-12 undergoes adaptive evolution to achieve in silico predicted optimal growth. Nature 420, 186–189 (2002).
  Article CAS PubMed Google Scholar
• Fischer, E. & Sauer, U. Metabolic flux profiling of Escherichia coli mutants in central carbon metabolism using GC-MS. Eur. J. Biochem. 270, 880–891 (2003).
  Article CAS PubMed Google Scholar
• Birkemeyer, C., Luedemann, A., Wagner, C., Erban, A. & Kopka, J. Metabolome analysis: the potential of in vivo labeling with stable isotopes for metabolite profiling. Trends Biotechnol. 23, 28–33 (2005).
  Article CAS PubMed Google Scholar
• Bennett, B.D., Yuan, J., Kimball, E.H. & Rabinowitz, J.D. Absolute quantitation of intracellular metabolite concentrations by an isotope ratio-based approach. Nat. Protoc. 3, 1299–1311 (2008).
  Article CAS PubMed PubMed Central Google Scholar
• Kimball, E. & Rabinowitz, J.D. Identifying decomposition products in extracts of cellular metabolites. Anal. Biochem. 358, 273–280 (2006).
  Article CAS PubMed PubMed Central Google Scholar
• Rabinowitz, J.D. & Kimball, E. Acidic acetonitrile for cellular metabolome extraction from Escherichia coli. Anal. Chem. 79, 6167–6173 (2007).
  Article CAS PubMed Google Scholar
• Edgar, J.R. & Bell, R.M. Biosynthesis in Escherichia coli fo sn-glycerol 3-phosphate, a precursor of phospholipid. J. Biol. Chem. 253, 6348–6353 (1978).
  CAS PubMed Google Scholar
• Lin, E.C. Glycerol dissimilation and its regulation in bacteria. Annu. Rev. Microbiol. 30, 535–578 (1976).
  Article CAS PubMed Google Scholar
• Asnis, R.E. & Brodie, A.F. A glycerol dehydrogenase from Escherichia coli. J. Biol. Chem. 203, 153–159 (1953).
  CAS PubMed Google Scholar
• Truniger, V. & Boos, W. Mapping and cloning of gldA, the structural gene of the Escherichia coli glycerol dehydrogenase. J. Bacteriol. 176, 1796–1800 (1994).
  Article CAS PubMed PubMed Central Google Scholar
• Alberty, R.A. Standard Gibbs free energy, enthalpy, and entropy changes as a function of pH and pMg for several reactions involving adenosine phosphates. J. Biol. Chem. 244, 3290–3302 (1969).
  CAS PubMed Google Scholar
• Maskow, T. & von Stockar, U. How reliable are thermodynamic feasibility statements of biochemical pathways? Biotechnol. Bioeng. 92, 223–230 (2005).
  Article CAS PubMed Google Scholar
• Shikama, K. Standard free energy maps for the hydrolysis of ATP as a function of pH, pMg and pCa. Arch. Biochem. Biophys. 147, 311–317 (1971).
  Article CAS PubMed Google Scholar
• Shikama, K. & Nakamura, K.I. Standard free energy maps for the hydrolysis of ATP as a function of pH and metal ion concentration: comparison of metal ions. Arch. Biochem. Biophys. 157, 457–463 (1973).
  Article CAS PubMed Google Scholar
• Neidhardt, F. et al. Escherichia coli and Salmonella typhimurium, Vol. 1 (American Society for Microbiology, Washington, DC, 1987).
  Google Scholar
• Ikeda, T.P., Shauger, A.E. & Kustu, S. Salmonella typhimurium apparently perceives external nitrogen limitation as internal glutamine limitation. J. Mol. Biol. 259, 589–607 (1996).
  Article CAS PubMed Google Scholar
• McLaggan, D., Naprstek, J., Buurman, E.T. & Epstein, W. Interdependence of K+ and glutamate accumulation during osmotic adaptation of Escherichia coli. J. Biol. Chem. 269, 1911–1917 (1994).
  CAS PubMed Google Scholar
• Beg, Q.K. et al. Intracellular crowding defines the mode and sequence of substrate uptake by Escherichia coli and constrains its metabolic activity. Proc. Natl. Acad. Sci. USA 104, 12663–12668 (2007).
  Article CAS PubMed Google Scholar
• Powell, J.T. & Morrison, J.F. The purification and properties of the aspartate aminotransferase and aromatic-amino-acid aminotransferase from Escherichia coli. Eur. J. Biochem. 87, 391–400 (1978).
  Article CAS PubMed Google Scholar
• Miller, R.E. & Stadtman, E.R. Glutamate synthase from Escherichia coli. An iron-sulfide flavoprotein. J. Biol. Chem. 247, 7407–7419 (1972).
  CAS PubMed Google Scholar
• Freedberg, W.B., Kistler, W.S. & Lin, E.C. Lethal synthesis of methylglyoxal by Escherichia coli during unregulated glycerol metabolism. J. Bacteriol. 108, 137–144 (1971).
  CAS PubMed PubMed Central Google Scholar
• Benov, L., Beema, A.F. & Sequeira, F. Triosephosphates are toxic to superoxide dismutase-deficient Escherichia coli. Biochim. Biophys. Acta 1622, 128–132 (2003).
  Article CAS PubMed Google Scholar
• Soupene, E. et al. Physiological studies of Escherichia coli strain MG1655: growth defects and apparent cross-regulation of gene expression. J. Bacteriol. 185, 5611–5626 (2003).
  Article CAS PubMed PubMed Central Google Scholar
• Gutnick, D., Calvo, J.M., Klopotowski, T. & Ames, B.N. Compounds which serve as the sole source of carbon or nitrogen for Salmonella typhirium LT-2. J. Bacteriol. 100, 215–219 (1969).
  CAS PubMed PubMed Central Google Scholar
• Rosenberg, H., Russell, L.M., Jacomb, P.A. & Chegwidden, K. Phosphate exchange in the pit transport system in Escherichia coli. J. Bacteriol. 149, 123–130 (1982).
  CAS PubMed PubMed Central Google Scholar