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.
This is a preview of subscription content, log in via an institution to check access.
Preview
Unable to display preview. Download preview PDF.
References
1. Aulabaugh A, Schloss JV (1990) Oxalyl hydroxamates as reaction-intermediate analogs for ketol-acid reductoisomerase. Biochemistry 29:2824-2830
2. Barak Z, Chipman DM, Gollop N (1987) Physiological implications of the specificity of acetohydroxy acid synthase isozymes of enteric bacteria. J Bacteriol 169:3750-3756
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 40:11946-11954
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 79:53-73
5. Chunduru SK, Mrachko GT, Calvo KC (1998) Mechanism of ketol acid reductoisomerase. Steady-state analysis and metal ion requirement. Biochemistry 28:486-493
6. Cleland WW The kinetics of enzyme-catalysed reactions with two or more substrates or products. Biochim Biophys Acta 67:104-137
7. Cornish-Bouden A (2001) Fundamentals of enzyme kinetic. Portland Press, Cambridge
8. Edwards JS, Ibarra RU, Palsson BO (2001) In silico predictions of Escherichia coli metabolic capabilities are consistent with experimental data. Nat Biotechnol 19:125-130
9. Elijah Adams (1955) I-histidinal, a biosynthetic precursor of histidine. J Biol Chem 217:325-344
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 743:225-229
11. Eoyang L, Silverman PM (1984) Purification and subunit composition of acetohydroxyacid synthase I from Escherichia coli K-12. J Bacteriol 157:184-189
12. Goryanin I, Hodgman TC, Selkov E (1999) Mathematical simulation and analysis of cellular metabolism and regulation. Bioinformatics 15:749-758
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 268:3092-3098
14. Hill CM, Duggleby RG (1998) Escherichia coli acetohydroxyacid synthase II mutants. Biochem J 335:653-661
15. Hill CM, Pang SS, Duggleby RG (1997) Escherichia coli acetohydroxyacid synthase II. Biochem J 327:891-898
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 28:69-104
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 104:777-784
18. Ivanitzky GR, Krinsky VI, Selkov EE (1978) Mathematical biophysics of the cell. Nauka, Moscow
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):339-345
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 3:487-494
21. Loper J, Adams E (1965) Purification and properties of histidinol dehydrogenase from Salmonella typhimurium. J Biol Chem 240:788-795
22. Myers JW (1961) Dihydroxy acid dehydrase: an enzyme involved in the biosynthesis of isoleucine and valine. J Biol Chem 236:1414-1418
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 409:529-533
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 338:83-89
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 24:26-28
26. Shomburg I, Chang A, Shomburg D (2002) BRENDA, enzyme data and metabolic information. Nucleic Acids Res 30:47-49
27. Umbarger HE (1996) Escherichia coli and Salmonella: cellular and molecular biology: ASM Press, Washington DC:442-458
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 35:10339-10346
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 39:15136-151143
Author information
Authors and Affiliations
Editor information
Rights and permissions
About this chapter
Cite this chapter
Demin, O.V. et al. Kinetic modelling of the E. coli metabolism. In: Alberghina, L., Westerhoff, H. (eds) Systems Biology. Topics in Current Genetics, vol 13. Springer, Berlin, Heidelberg. https://doi.org/10.1007/4735_85
Download citation
DOI: https://doi.org/10.1007/4735_85
Published:
Publisher Name: Springer, Berlin, Heidelberg
Print ISBN: 978-3-540-22968-1
Online ISBN: 978-3-540-31453-0
eBook Packages: Biomedical and Life SciencesBiomedical and Life Sciences (R0)