Advertisement

Kinetic modelling of the E. coli metabolism

  • Oleg V. Demin
  • Tatyana Y. Plyusnina
  • Galina V. Lebedeva
  • Ekaterina A. Zobova
  • Eugeniy A. Metelkin
  • Alex G. Kolupaev
  • Igor I. Goryanin
  • Frank Tobin
Chapter
Part of the Topics in Current Genetics book series (TCG, volume 13)

Abstract

We describe a general strategy that enables us to develop kinetic models of large-scale metabolic systems by collecting and using available metabolic and gene regulation experimental data. The approach could be used to explore the local and global regulatory properties of metabolic pathways, and to predict how cell genome modifications can meet specific biotechnological and biomedical criteria. We have successfully applied the strategy for the development and applications of detailed kinetic models of catabolic and anabolic pathways of E. coli.

Keywords

Catalytic Cycle Dihydroxy Acid Threonine Dehydratase Histidinol Phosphate Acetohydroxy Acid Isomeroreductase 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.

Preview

Unable to display preview. Download preview PDF.

Unable to display preview. Download preview PDF.

References

  1. 1. Aulabaugh A, Schloss JV (1990) Oxalyl hydroxamates as reaction-intermediate analogs for ketol-acid reductoisomerase. Biochemistry 29:2824-2830CrossRefPubMedGoogle Scholar
  2. 2. Barak Z, Chipman DM, Gollop N (1987) Physiological implications of the specificity of acetohydroxy acid synthase isozymes of enteric bacteria. J Bacteriol 169:3750-3756PubMedGoogle Scholar
  3. 3. Bar-Ilan A, Balan V, Tittmann K, Golbik R, Vyazmensky M, Hubner G, Barak Z, Chipman DM (2001) Binding and activation of thiamin diphosphate in acetohydroxyacid synthase. Biochemistry 40:11946-11954CrossRefPubMedGoogle Scholar
  4. 4. Chassagnole C, Noisommit-Rizzi N, Schmid JW, Klaus Mauch K, Reuss M (2002) Dynamic modeling of the central carbon metabolism of Escherichia coli. Biotechnol Bioeng 79:53-73CrossRefGoogle Scholar
  5. 5. Chunduru SK, Mrachko GT, Calvo KC (1998) Mechanism of ketol acid reductoisomerase. Steady-state analysis and metal ion requirement. Biochemistry 28:486-493CrossRefGoogle Scholar
  6. 6. Cleland WW The kinetics of enzyme-catalysed reactions with two or more substrates or products. Biochim Biophys Acta 67:104-137Google Scholar
  7. 7. Cornish-Bouden A (2001) Fundamentals of enzyme kinetic. Portland Press, CambridgeGoogle Scholar
  8. 8. Edwards JS, Ibarra RU, Palsson BO (2001) In silico predictions of Escherichia coli metabolic capabilities are consistent with experimental data. Nat Biotechnol 19:125-130CrossRefPubMedGoogle Scholar
  9. 9. Elijah Adams (1955) I-histidinal, a biosynthetic precursor of histidine. J Biol Chem 217:325-344PubMedGoogle Scholar
  10. 10. Engel S, Vyazmensky M, Barak Z, Chipman DM, Merchuk JC (2000) Determination of the dissociation constant of valine from acetohydroxy acid synthase by equilibrium partition in an aqueous two-phase system. J Chromatogr B 743:225-229Google Scholar
  11. 11. Eoyang L, Silverman PM (1984) Purification and subunit composition of acetohydroxyacid synthase I from Escherichia coli K-12. J Bacteriol 157:184-189PubMedGoogle Scholar
  12. 12. Goryanin I, Hodgman TC, Selkov E (1999) Mathematical simulation and analysis of cellular metabolism and regulation. Bioinformatics 15:749-758CrossRefPubMedGoogle Scholar
  13. 13. Hall TR, Wallin R, Reinhart GD, Hutson SM (1993) Branched chain amino transferase isoenzymes. Purification and characterization of the rat brain isoenzyme. J Biol Chem 268:3092-3098PubMedGoogle Scholar
  14. 14. Hill CM, Duggleby RG (1998) Escherichia coli acetohydroxyacid synthase II mutants. Biochem J 335:653-661PubMedGoogle Scholar
  15. 15. Hill CM, Pang SS, Duggleby RG (1997) Escherichia coli acetohydroxyacid synthase II. Biochem J 327:891-898PubMedGoogle Scholar
  16. 16. Holms WH (1986) The central metabolic pathways of Escherichia coli: relationship between flux and control at a branch point, efficiency of conversion to biomass, and excretion of acetate. Curr Top Cell Regul 28:69-104PubMedGoogle Scholar
  17. 17. Inoue K, Kuramitsu S, Aki K, Watanabe Y, Takagi T, Nishigai M, Ikai A, Kagamiyama H (1988) Branched-chain amino acid amino transferase of Escherichia coli: overproduction and properties. J Biochem 104:777-784PubMedGoogle Scholar
  18. 18. Ivanitzky GR, Krinsky VI, Selkov EE (1978) Mathematical biophysics of the cell. Nauka, MoscowGoogle Scholar
  19. 19. Lee-Peng FC, Hermodson MA, Kohlhaw GB (1979) Transaminase B from Escherichia coli: quaternary structure, amino-terminal sequence, substrate specificity, and absence of a separate valine-a-ketoglutarate activity. J Bacteriol 139(2):339-345PubMedGoogle Scholar
  20. 20. Limberg G, Klaffke W, Thiem J (1995) Conversion of aldonic acids to their corresponding 2-keto-3-deoxy-analogs by the non-carbohydrate enzyme dihydroxy acid dehydratase (DHAD). Bioorg Med Chem 3:487-494CrossRefPubMedGoogle Scholar
  21. 21. Loper J, Adams E (1965) Purification and properties of histidinol dehydrogenase from Salmonella typhimurium. J Biol Chem 240:788-795PubMedGoogle Scholar
  22. 22. Myers JW (1961) Dihydroxy acid dehydrase: an enzyme involved in the biosynthesis of isoleucine and valine. J Biol Chem 236:1414-1418PubMedGoogle Scholar
  23. 23. Perna NT, Plunkett G 3rd, Burland V, Mau B, Glasner JD, Rose DJ, Mayhew GF, Evans PS, et al. (2001) Genome sequence of enterohaemorrhagic Escherichia coli O157:H7. Nature 409:529-533CrossRefPubMedGoogle Scholar
  24. 24. Rane MJ, Calvo KC (1997) Reversal of the nucleotide specificity of ketol acid reductoisomerase by site-directed mutagenesis identifies the NADPH Binding Site1. Arch Biochem Biophys 338:83-89CrossRefPubMedGoogle Scholar
  25. 25. Selkov E, Basmanova S, Gaasterland T, Goryanin I, Gretchkin Y, Maltsev N, Nenashev V, Overbeek R, Panyushkina E, Pronevitch L, Yunis I (1996) The metabolic pathway collection from EMP: the enzymes and metabolic pathways database. Nucleic Acids Res 24:26-28CrossRefPubMedGoogle Scholar
  26. 26. Shomburg I, Chang A, Shomburg D (2002) BRENDA, enzyme data and metabolic information. Nucleic Acids Res 30:47-49CrossRefPubMedGoogle Scholar
  27. 27. Umbarger HE (1996) Escherichia coli and Salmonella: cellular and molecular biology: ASM Press, Washington DC:442-458Google Scholar
  28. 28. Vyazmensky M, Sella C, Barak Z, Chipman DM (1996) Isolation and characterization of subunits of acetohydroxy acid synthase isozyme III and reconstitution of the holoenzyme. Biochemistry 35:10339-10346CrossRefPubMedGoogle Scholar
  29. 29. Wessel PM, Graciet E, Douce R, Dumas R (2000) Evidence for two distinct effector-binding sites in threonine deaminase by site-directed mutagenesis, kinetic, and binding experiments. Biochemistry 39:15136-151143CrossRefPubMedGoogle Scholar

Authors and Affiliations

  • Oleg V. Demin
    • 1
  • Tatyana Y. Plyusnina
    • 2
  • Galina V. Lebedeva
    • 1
  • Ekaterina A. Zobova
    • 1
  • Eugeniy A. Metelkin
    • 1
  • Alex G. Kolupaev
    • 1
  • Igor I. Goryanin
    • 3
  • Frank Tobin
    • 3
  1. 1.A.N. Belozersky Institute of Physico-Chemical Biology, Moscow State University, MoscowRussia
  2. 2.Biophysics Department, Faculty of Biology, Moscow State University, MoscowRussia
  3. 3.GlaxoSmithKline, Scientific Computing & Mathematical Modeling, Stevenage, SG2 8PUUK

Personalised recommendations