Subtleties in control by metabolic channelling and enzyme organization

  • Boris N. Kholodenko
  • Johann M. Rohwer
  • Marta Cascante
  • Hans V. Westerhoff
Chapter
Part of the Developments in Molecular and Cellular Biochemistry book series (DMCB, volume 25)

Abstract

Because of its importance to cell function, the free-energy metabolism of the living cell is subtly and homeostatically controlled. Metabolic control analysis enables a quantitative determination of what controls the relevant fluxes. However, the original metabolic control analysis was developed for idealized metabolic systems, which were assumed to lack enzyme-enzyme association and direct metabolite transfer between enzymes (channelling). We here review the recently developed molecular control analysis, which makes it possible to study non-ideal (channelled, organized) systems quantitatively in terms of what controls the fluxes, concentrations, and transit times. We show that in real, non-ideal pathways, the central control laws, such as the summation theorem for flux control, are richer than in ideal systems: the sum of the control of the enzymes participating in a non-ideal pathway may well exceed one (the number expected in the ideal pathways), but may also drop to values below one. Precise expressions indicate how total control is determined by non-ideal phenomena such as ternary complex formation (two enzymes, one metabolite), and enzyme sequestration. The bacterial phosphotransferase system (PTS), which catalyses the uptake and concomitant phosphorylation of glucose (and also regulates catabolite repression) is analyzed as an experimental example of a non-ideal pathway. Here, the phosphoryl group is channelled between enzymes, which could increase the sum of the enzyme control coefficients to two, whereas the formation of ternary complexes could decrease the sum of the enzyme control coefficients to below one. Experimental studies have recently confirmed this identification, as well as theoretically predicted values for the total control. Macromolecular crowding was shown to be a major candidate for the factor that modulates the non-ideal behaviour of the PTS pathway and the sum of the enzyme control coefficients. (Mol Cell Biochem 184: 311–320, 1998)

Key words

metabolic channelling non-ideal metabolism control coefficient enzyme-enzyme interactions macromolecular crowding bacterial phosphotransferase system 
This is a preview of subscription content, log in to check access.

Preview

Unable to display preview. Download preview PDF.

Unable to display preview. Download preview PDF.

References

  1. 1.
    Ovadi J, Srere PA: Channel your energies. Trends Biochem Sci 17: 445–447, 1992PubMedCrossRefGoogle Scholar
  2. 2.
    Welch GR, Easterby JS: Metabolic channelling versus free diffusion: Transition time analysis. Trends Biochem Sci 19:193–197, 1994PubMedCrossRefGoogle Scholar
  3. 3.
    Ovadi J: Physiological significance of metabolite channelling. J Theor Biol 152:1–22, 1991PubMedCrossRefGoogle Scholar
  4. 4.
    Keizer J, Smolen P: Mechanisms of metabolite transfer between enzymes: diffusional versus direct transfer. Curr Top Cell Regul 33:391–405, 1992PubMedGoogle Scholar
  5. 5.
    Westerhoff HV, Welch GR: Enzyme organization and the direction of metabolic flow: Physicochemical considerations. Curr Top Cell Regul 33:361–390, 1992PubMedGoogle Scholar
  6. 6.
    Kell DB, Westerhoff HV: Catalytic facilitation and membrane bioenergetics. In: GR Welch (ed). Organized Multienzyme Systems. Academic Press, New York, 1985, pp 63–138CrossRefGoogle Scholar
  7. 7.
    Minton AP: A molecular model for the dependence of the osmotic pressure of bovine serum albumin upon concentration and pH. Biophys Chem 57:65–70, 1995PubMedCrossRefGoogle Scholar
  8. 8.
    Garner M: The consequences of macromolecular crowding for metabolic channelling. In: L Agius, HSA Sherratt (eds). Channelling in Intermediary Metabolism. Portland Press, London, 1997, pp 41–52Google Scholar
  9. 9.
    Kholodenko BN, Westerhoff HV: The macroworld versus the microworld of biochemical regulation and control. Trends Biochem Sci 20:52–54, 1995PubMedCrossRefGoogle Scholar
  10. 10.
    Easterby JS: Pathway dynamics and the analysis of metabolite channelling. In: L Agius, HSA Sherratt (eds). Channelling in Intermediary Metabolism. Portland Press, London, 1997, pp 71–90Google Scholar
  11. 11.
    Kacser H, Burns JA: The control of flux. In: DD Davies (ed). Rate Control of Biological Processes. Cambridge University Press, London, 1973, pp 65–104Google Scholar
  12. 12.
    Heinrich R, Rapoport TA: A linear steady-state treatment of enzymatic chains. General properties, control and effector strength. Eur J Biochem 42:89–95, 1974PubMedCrossRefGoogle Scholar
  13. 13.
    Kholodenko BN, Molenaar D, Schuster S, Heinrich R, Westerhoff HV: Defining control coefficients in non-ideal metabolic pathways. Biophys Chem 56:215–226, 1995PubMedCrossRefGoogle Scholar
  14. 14.
    Westerhoff HV, Arents JC: Two completely rate-limiting steps in one metabolic pathway? The resolution of a paradox using control theory and bacteriorhodopsin liposomes. Biosci Rep 4:23–31, 1984PubMedCrossRefGoogle Scholar
  15. 15.
    Jensen PR, Michelsen O, Westerhoff HV: Control analysis of the dependence of E. coli physiology on the H+-ATPase. Proc Natl Acad Sci USA 90:8068–8072, 1993PubMedCrossRefGoogle Scholar
  16. 16.
    Cornish-Bowden A: Fundamentals of Enzyme Kinetics. Portland Press, London, 1995Google Scholar
  17. 17.
    Fell DA, Sauro HM: Metabolic control analysis. The effects of high enzyme concentrations. Eur JBiochem 192:183–187, 1990CrossRefGoogle Scholar
  18. 18.
    Kacser H, Sauro HM, Acerenza L: Enzyme-enzyme interactions and control analysis. 1. The case of non-additivity: Monomer-oligomer associations. Eur JBiochem 187:481–491, 1990CrossRefGoogle Scholar
  19. 19.
    Sauro HM, Kacser H: Enzyme-enzyme interactions and control analysis. 2. The case of non-independence: Heterologous associations. Eur J Biochem 187:493–500, 1990PubMedCrossRefGoogle Scholar
  20. 20.
    Kholodenko BN, Lyubarev AK, Kurganov BI: Control of metabolic flux in a system with high enzyme concentrations and moiety conserved cycles. The sum of the flux control coefficients can drop significantly below unity. Eur J Biochem 210:147–153, 1992PubMedCrossRefGoogle Scholar
  21. 21.
    Kholodenko BN, Westerhoff HV: Metabolic channelling and control of the flux. FEBS Lett 320:71–74, 1993PubMedCrossRefGoogle Scholar
  22. 22.
    Kholodenko BN, Cascante M, Westerhoff HV: Control and regulation of channelled versus ideal pathways. In: L Agius, HSA Sherratt (eds). Channelling in Intermediary Metabolism. Portland Press, London, 1997, pp 91–114Google Scholar
  23. 23.
    Kholodenko BN, Sauro HM, Westerhoff HV: Control by enzymes, coenzymes and conserved moieties: A generalization of the connectivity theorem ofmetabolic control analysis. EurJBiochem 225:179–186, 1994CrossRefGoogle Scholar
  24. 24.
    Sauro HM: Moiety-conserved cycles and metabolic control analysis: Problems in sequestration and metabolic channelling. BioSystems 33:55–67, 1994PubMedCrossRefGoogle Scholar
  25. 25.
    Cori CF, Velick SF, Cori GT: Combination of diphosphopyridine nucleotide with glyceraldehyde phosphate debydrogenase. Biochim Biophys Acta 4:160–169, 1950PubMedCrossRefGoogle Scholar
  26. 26.
    Friedrich P: Dynamic compartmentation in soluble enzyme systems. Acta Biochim Biophys Acad Sci Hung 9:159–173, 1974PubMedGoogle Scholar
  27. 27.
    Srivastava DK, Bernhard SA: Biophysical chemistry of metabolic reaction sequences in concentrated enzyme solution and in the cell. Annu Rev Biophys Biophys Chem 16:175–204, 1987PubMedCrossRefGoogle Scholar
  28. 28.
    Ushiroyama T, Fukushima T, Styre JD, Spivey HO: Substrate channelling of NADH in mitochondrial redox processes. Curr Top Cell Regul 33:291–307, 1992PubMedGoogle Scholar
  29. 29.
    Kholodenko BN, Demin OV, Westerhoff HV: Channelled pathways can be more sensitive to specific regulatory signals. FEBS Lett 320:75–78, 1993PubMedCrossRefGoogle Scholar
  30. 30.
    Kholodenko BN, Cascante M, Westerhoff HV: Dramatic changes in control properties that accompany channelling and metabolite sequestration. FEBS Lett 336:381–384, 1993PubMedCrossRefGoogle Scholar
  31. 31.
    Kholodenko BN, Westerhoff HV, Puigjaner J, Cascante M: Control in channelled pathways. A matrix method calculating the enzyme control coefficients. Biophys Chem 53:247–258, 1995PubMedCrossRefGoogle Scholar
  32. 32.
    Kholodenko BN, Westerhoff HV, Brown GC: Rate limitation within a single enzyme is directly related to enzyme intermediate levels. FEBS Lett 349:131–134, 1994PubMedCrossRefGoogle Scholar
  33. 33.
    Brown GC, Westerhoff HV, Kholodenko BN: Molecular control analysis. Control within proteins and molecular processes. J Theor Biol 182:389–396, 1996PubMedCrossRefGoogle Scholar
  34. 34.
    Brown GC, Cooper CE: Control analysis applied to single enzymes: Can an isolated enzyme have a unique rate-limiting step? Biochem J 294:87–94, 1993PubMedGoogle Scholar
  35. 35.
    Kholodenko BN, Westerhoff HV: Control theory of one enzyme. Biochim Biophys Acta 1208:294–305, 1994PubMedCrossRefGoogle Scholar
  36. 36.
    Van Dam K, Van der Vlag J, Kholodenko BN, Westerhoff HV: The sum of the flux control coefficients of all enzymes on the flux through a group-transfer pathway can be as high as two. Eur J Biochem 212:791–799, 1993PubMedCrossRefGoogle Scholar
  37. 37.
    Kholodenko BN, Westerhoff HV: Control theory of group-transfer pathways. Biochim Biophys Acta 1229:256–274, 1995CrossRefGoogle Scholar
  38. 38.
    Kholodenko BN, Westerhoff HV: How to reveal various aspects of regulation in group-transfer pathways. Biochim Biophys Acta 1229:275–289, 1995CrossRefGoogle Scholar
  39. 39.
    Westerhoff HV, Van Dam K: Thermodynamics and Control of Biological Free Energy Transduction. Elsevier, Amsterdam, 1987Google Scholar
  40. 40.
    Kholodenko BN: Control of molecular transformations in multienzyme systems: quantitative theory of metabolic regulation. Mol Biol (USSR) 22:1238–1256, 1988. Engl transi 22:990-1005, 1989Google Scholar
  41. 41.
    Giersch C: Control analysis ofmetabolic networks. Homogeneous functions and the summation theorems for control coefficients. Eur J Biochem 174:509–513, 1988PubMedCrossRefGoogle Scholar
  42. 42.
    Kholodenko BN: Modern Theory of Metabolic Control. Viniti Press, Moscow (in Russian), 1991Google Scholar
  43. 43.
    Garner MM, Burg MB: Macromolecular crowding and confinement in cells exposed to hypertonicity. Am J Physiol 266:C877–C892, 1994PubMedGoogle Scholar
  44. 44.
    Adair G: A theory of partial osmotic pressure and membrane equilibria with special reference to application of Dalton’s Law to hemoglobine solutions in the presence of salts. Proc R Soc Lond A 120:573–603, 1928CrossRefGoogle Scholar
  45. 45.
    4. Brand MD, Vallis, BPS, Kesseler A: The sum of the flux control coefficients in the electron-transport chain of mitochondria. Eur J Biochem 226:819–829, 1994PubMedCrossRefGoogle Scholar
  46. 46.
    Kholodenko BN, Westerhoff HV, Cascante M: Channelling and the concentration of bulk phase intermediates as cytosolic proteins get more concentrated. Biochem J 313:921–926, 1996PubMedGoogle Scholar
  47. 47.
    Mendes P, Kell DB, Westerhoff HV: Channelling can decrease pool size. Eur J Biochem 204:257–266, 1992PubMedCrossRefGoogle Scholar
  48. 48.
    Mendes P, Kell DB, Westerhoff HV: Why and when channelling can decrease pool size at constant net flux in a simple dynamic channel. Biochim Biophys Acta 1289:175–186, 1996PubMedCrossRefGoogle Scholar
  49. 49.
    Easterby JS: A generalized theory of the transition time for sequential enzyme reactions. Biochem J 199:155–161, 1981PubMedGoogle Scholar
  50. 50.
    Melendez-Hevia E, Torres NV, Sicilia J, Kacser H: Control analysis of transition times in metabolic systems. Biochem J 265:195–202, 1990.PubMedGoogle Scholar
  51. 51.
    Easterby JS: Temporal analysis of the transition between steady states. In: A Cornish-Bowden and ML Cardenas (eds). Control of Metabolic Processes. Plenum Press, New York, 1990, pp 281–290Google Scholar
  52. 52.
    Cascante M, Melendez-Hevia E, Kholodenko BN, Sicilia J, Kacser H: Control analysis of transit time for free and enzyme-bound metabolites. Biochem J 308:895–899, 1995PubMedGoogle Scholar
  53. 53.
    Kholodenko BN, Cascante M, Westerhoff HV: (1995b) Control theory of metabolic channelling. Mol Cell Biochem 143:151–168, 1995PubMedCrossRefGoogle Scholar
  54. 54.
    Snoep JL, Yomana LP, Westerhoff HV, Ingram LO: Protein burden in Zymomonas mobilis: Negative flux and growth control due to overproduction of glycolytic enzymes. Microbiology 141:2329–2337, 1995CrossRefGoogle Scholar
  55. 55.
    Rohwer JM: Interaction of functional units of metabolism. Control and regulation of the bacterial phoshoenolpyruvate-dependent phos-photransferase system. Ph.D. thesis, University of Amsterdam, 1997Google Scholar

Copyright information

© Springer Science+Business Media Dordrecht 1998

Authors and Affiliations

  • Boris N. Kholodenko
    • 1
    • 2
  • Johann M. Rohwer
    • 3
  • Marta Cascante
    • 2
  • Hans V. Westerhoff
    • 3
    • 4
  1. 1.A.N. Belozersky Institute of Physico-Chemical BiologyMoscow State UniversityMoscowRussia
  2. 2.Departmento de Bioquímica i Biología MolecularUniversitat de BarcelonaBarcelonaSpain
  3. 3.E.C. Slater Institute, BioCentrumUniversity of AmsterdamAmsterdamThe Netherlands
  4. 4.Department of Microbial Physiology, BioCentrumFaculty of Biology, Free UniversityHV AmsterdamThe Netherlands

Personalised recommendations