Kinetic flux profiling for quantitation of cellular metabolic fluxes (original) (raw)

References

  1. 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 Google Scholar
  2. Yuan, J. & Rabinowitz, J.D. Differentiating metabolites formed from de novo synthesis versus macromolecule decomposition. J. Am. Chem. Soc. 129, 9294–9295 (2007).
    Article CAS Google Scholar
  3. 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 Google Scholar
  4. Kemp, G.J., Meyerspeer, M. & Moser, E. Absolute quantification of phosphorus metabolite concentrations in human muscle in vivo by 31P MRS: a quantitative review. NMR Biomed. 20, 555–565 (2007).
    Article CAS Google Scholar
  5. Cudalbu, C., Cavassila, S., Rabeson, H., van Ormondt, D. & Graveron-Demilly, D. Influence of measured and simulated basis sets on metabolite concentration estimates. NMR Biomed. 21, 627–636 (2008).
    Article CAS Google Scholar
  6. 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 Google Scholar
  7. 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 Google Scholar
  8. 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 Google Scholar
  9. Schaub, J., Schiesling, C., Reuss, M. & Dauner, M. Integrated sampling procedure for metabolome analysis. Biotechnol. Prog. 22, 1434–1442 (2006).
    Article CAS Google Scholar
  10. Villas-Boas, S.G., Hojer-Pedersen, J., Akesson, M., Smedsgaard, J. & Nielsen, J. Global metabolite analysis of yeast: evaluation of sample preparation methods. Yeast 22, 1155–1169 (2005).
    Article CAS Google Scholar
  11. Visser, D. et al. Rapid sampling for analysis of in vivo kinetics using the BioScope: a system for continuous-pulse experiments. Biotechnol. Bioeng. 79, 674–681 (2002).
    Article CAS Google Scholar
  12. Rabinowitz, J.D. Cellular metabolomics of Escherichia coli. Expert Rev. Proteomics 4, 187–198 (2007).
    Article CAS Google Scholar
  13. Rabinowitz, J.D. & Kimball, E. Acidic acetonitrile for cellular metabolome extraction from Escherichia coli. Anal. Chem. 79, 6167–6173 (2007).
    Article CAS Google Scholar
  14. Shalwitz, R.A., Beth, T.J., MacLeod, A.M., Tucker, S.J. & Rolison, G.G. Use of 2H2O to study labeling in plasma glucose and hepatic glycogen during a hyperglycemic clamp. Am. J. Physiol. 266, E433–E437 (1994).
    PubMed Google Scholar
  15. Baranyai, J.M. & Blum, J.J. Quantitative-analysis of intermediary metabolism in rat hepatocytes incubated in the presence and absence of ethanol with a substrate mixture including ketoleucine. Biochem. J. 258, 121–140 (1989).
    Article CAS Google Scholar
  16. Wright, B.E. & Reimers, J.M. Steady-state models of glucose-perturbed Dictyostelium discoideum. J. Biol. Chem. 263, 14906–14912 (1988).
    CAS PubMed Google Scholar
  17. Rabkin, M. & Blum, J.J. Quantitative analysis of intermediary metabolism in hepatocytes incubated in the presence and absence of glucagon with a substrate mixture containing glucose, ribose, fructose, alanine and acetate. Biochem. J. 225, 761–786 (1985).
    Article CAS Google Scholar
  18. Crawford, J.M. & Blum, J.J. Quantitative-analysis of flux along the gluconeogenic, glycolytic and pentose-phosphate pathways under reducing conditions in hepatocytes isolated from fed rats. Biochem. J. 212, 595–598 (1983).
    Article Google Scholar
  19. Kelly, P.J., Kelleher, J.K. & Wright, B.E. Tricarboxylic-acid cycle in dictyostelium-discoideum—metabolite concentrations, oxygen-uptake and C-14-labeled amino-acid labeling patterns. Biochem. J. 184, 581–588 (1979).
    Article CAS Google Scholar
  20. Katz, J., Wals, P.A. & Rognstad, R. Glucose phosphorylation, glucose-6-phosphatase, and recycling in rat hepatocytes. J. Biol. Chem. 253, 4530–4536 (1978).
    CAS PubMed Google Scholar
  21. Edwards, J.S., Covert, M. & Palsson, B. Metabolic modelling of microbes: the flux-balance approach. Environ. Microbiol. 4, 133–140 (2002).
    Article Google Scholar
  22. Sauer, U. Metabolic networks in motion: 13C-based flux analysis. Mol. Syst. Biol. 2, 62 (2006).
    Article Google Scholar
  23. Edwards, J.S., Ibarra, R.U. & Palsson, B.O. In silico predictions of Escherichia coli metabolic capabilities are consistent with experimental data. Nat. Biotechnol. 19, 125–130 (2001).
    Article CAS Google Scholar
  24. 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 Google Scholar
  25. Fong, S.S., Marciniak, J.Y. & Palsson, B.O. Description and interpretation of adaptive evolution of Escherichia coli K-12 MG1655 by using a genome-scale in silico metabolic model. J. Bacteriol. 185, 6400–6408 (2003).
    Article CAS Google Scholar
  26. Segre, D., Vitkup, D. & Church, G.M. Analysis of optimality in natural and perturbed metabolic networks. Proc. Natl. Acad. Sci. USA 99, 15112–15117 (2002).
    Article CAS Google Scholar
  27. Duarte, N.C., Herrgard, M.J. & Palsson, B.O. Reconstruction and validation of Saccharomyces cerevisiae iND750, a fully compartmentalized genome-scale metabolic model. Genome Res. 14, 1298–1309 (2004).
    Article CAS Google Scholar
  28. Duarte, N.C. et al. Global reconstruction of the human metabolic network based on genomic and bibliomic data. Proc. Natl. Acad. Sci. USA 104, 1777–1782 (2007).
    Article CAS Google Scholar
  29. Fischer, E. & Sauer, U. Large-scale in vivo flux analysis shows rigidity and suboptimal performance of Bacillus subtilis metabolism. Nat. Genet. 37, 636–640 (2005).
    Article CAS Google Scholar
  30. 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 Google Scholar
  31. van Winden, W.A. et al. Metabolic-flux analysis of Saccharomyces cerevisiae CEN.PK113-7D based on mass isotopomer measurements of (13)C-labeled primary metabolites. FEMS Yeast Res. 5, 559–568 (2005).
    Article CAS Google Scholar
  32. Schmidt, K., Carlsen, M., Nielsen, J. & Villadsen, J. Modeling isotopomer distributions in biochemical networks using isotopomer mapping matrices. Biotechnol. Bioeng. 55, 831–840 (1997).
    Article CAS Google Scholar
  33. Schmidt, K. et al. Quantification of intracellular metabolic fluxes from fractional enrichment and 13C-13C coupling constraints on the isotopomer distribution in labeled biomass components. Metab. Eng. 1, 166–179 (1999).
    Article CAS Google Scholar
  34. Kimball, E. & Rabinowitz, J.D. Identifying decomposition products in extracts of cellular metabolites. Anal. Biochem. 358, 273–280 (2006).
    Article CAS Google Scholar
  35. 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 Google Scholar
  36. 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 Google Scholar
  37. Werf, M.J., Overkamp, K.M., Muilwijk, B., Coulier, L. & Hankemeier, T. Microbial metabolomics: toward a platform with full metabolome coverage. Anal. Biochem. 370, 17–25 (2007).
    Article Google Scholar
  38. Lu, W. & Bennett, B.D. Analytical strategies for LC-MS-based targeted metabolomics. J. Chromatogr. B doi:10.1016/j.jchromb2008.04.031.
  39. 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 Google Scholar
  40. Tempest, D.W., Meers, J.L. & Brown, C.M. Synthesis of glutamate in Aerobacter aerogenes by a hitherto unknown route. Biochem. J. 117, 405–407 (1970).
    Article CAS Google Scholar
  41. Reitzer, L. Nitrogen assimilation and global regulation in Escherichia coli. Annu. Rev. Microbiol. 57, 155–176 (2003).
    Article CAS Google Scholar

Download references