1887

Abstract

an ethanol-producing bacterium, possesses the Entner–Doudoroff (E-D) pathway, pyruvate decarboxylase and two alcohol dehydrogenase isoenzymes for the fermentative production of ethanol and carbon dioxide from glucose. Using available kinetic parameters, we have developed a kinetic model that incorporates the enzymic reactions of the E-D pathway, both alcohol dehydrogenases, transport reactions and reactions related to ATP metabolism. After optimizing the reaction parameters within likely physiological limits, the resulting kinetic model was capable of simulating glycolysis and in cell-free extracts with good agreement with the fluxes and steady-state intermediate concentrations reported in previous experimental studies. In addition, the model is shown to be consistent with experimental results for the coupled response of ATP concentration and glycolytic flux to ATPase inhibition. Metabolic control analysis of the model revealed that the majority of flux control resides not inside, but outside the E-D pathway itself, predominantly in ATP consumption, demonstrating why past attempts to increase the glycolytic flux through overexpression of glycolytic enzymes have been unsuccessful. Co-response analysis indicates how homeostasis of ATP concentrations starts to deteriorate markedly at the highest glycolytic rates. This kinetic model has potential for application in metabolic engineering and, since there are currently no E-D pathway models available in public databases, it can serve as a basis for the development of models for other micro-organisms possessing this type of glycolytic pathway.

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2013-12-01
2019-12-12
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References

  1. Algar E. M. , Scopes R. K. . ( 1985; ). Studies on cell-free metabolism: ethanol production by extracts of Zymomonas mobilis . . J Biotechnol 2:, 275–287. [CrossRef]
    [Google Scholar]
  2. Altintas M. M. , Eddy C. K. , Zhang M. , McMillan J. D. , Kompala D. S. . ( 2006; ). Kinetic modeling to optimize pentose fermentation in Zymomonas mobilis . . Biotechnol Bioeng 94:, 273–295. [CrossRef] [PubMed]
    [Google Scholar]
  3. Atkinson D. E. . ( 1968; ). The energy charge of the adenylate pool as a regulatory parameter. Interaction with feedback modifiers. . Biochemistry 7:, 4030–4034. [CrossRef] [PubMed]
    [Google Scholar]
  4. Arfman N. , Worrell V. , Ingram L. O. . ( 1992; ). Use of the tac promoter and lacP for the controlled expression of Zymomonas mobilis fermentative genes in Escherichia coli and Zymomonas mobilis . . J Bacteriol 174:, 7370–7378. [CrossRef]
    [Google Scholar]
  5. Barrow K. D. , Collins J. G. , Norton R. S. , Rogers P. L. , Smith G. M. . ( 1984; ). 31P nuclear magnetic resonance studies of the fermentation of glucose to ethanol by Zymomonas mobilis. . J Biol Chem 259:, 5711–5716.[PubMed]
    [Google Scholar]
  6. Bisswanger K. . ( 2002; ). Enzyme Kinetics – Principles and Methods. Weinheim:: Wiley;. [CrossRef]
    [Google Scholar]
  7. Bringer-Meyer S. , Schimz K. L. , Sahm H. . ( 1986; ). Pyruvate decarboxylase from Zymomonas mobilis: Isolation and partial characterization. . Arch Microbiol 146:, 105–110. [CrossRef]
    [Google Scholar]
  8. Cornish-Bowden A. , Hofmeyr J.-H. S. . ( 1994; ). Determination of control coefficients in intact metabolic systems. . Biochem J 298:, 367–375.[PubMed]
    [Google Scholar]
  9. De Graaf A. A. , Striegel K. , Wittig R. M. , Laufer B. , Schmitz G. , Wiechert W. , Sprenger G. A. , Sahm H. . ( 1999; ). Metabolic state of Zymomonas mobilis in glucose-, fructose-, and xylose-fed continuous cultures as analysed by 13C- and 31P-NMR spectroscopy. . Arch Microbiol 171:, 371–385. [CrossRef] [PubMed]
    [Google Scholar]
  10. Desiniotis A. , Kouvelis V. N. , Davenport K. , Bruce D. , Detter C. , Tapia R. , Han C. , Goodwin L. A. , Woyke T. . & other authors ( 2012; ). Complete genome sequence of the ethanol-producing Zymomonas mobilis subsp. mobilis centrotype ATCC 29191. . J Bacteriol 194:, 5966–5967. [CrossRef] [PubMed]
    [Google Scholar]
  11. DiMarco A. A. , Romano A. H. . ( 1985; ). d-Glucose transport system of Zymomonas mobilis . . Appl Environ Microbiol 49:, 151–157.[PubMed]
    [Google Scholar]
  12. Doelle H. W. . ( 1982; ). Kinetic characteristics and regulatory mechanisms of glucokinase and fructokinase from Zymomonas mobilis . . European J Appl Microbiol Biotechnol 14:, 241–246. [CrossRef]
    [Google Scholar]
  13. Fell D. A. . ( 1992; ). Metabolic control analysis: a survey of its theoretical and experimental development. . Biochem J 286:, 313–330.[PubMed]
    [Google Scholar]
  14. Flamholz A. , Noor E. , Bar-Even A. , Liebermeister W. , Milo R. . ( 2013; ). Glycolytic strategy as a tradeoff between energy yield and protein cost. . Proc Natl Acad Sci U S A 110:, 10039–10044. [CrossRef] [PubMed]
    [Google Scholar]
  15. Glaser L. , Brown D. H. . ( 1955; ). Purification and properties of d-glucose-6-phosphate dehydrogenase. . J Biol Chem 216:, 67–79.[PubMed]
    [Google Scholar]
  16. Goldberg R. N. , Tewari Y. B. , Bhat T. N. . ( 2004; ). Thermodynamics of enzyme-catalyzed reactions – a database for quantitative biochemistry. . Bioinformatics 20:, 2874–2877. [CrossRef] [PubMed]
    [Google Scholar]
  17. Hofmeyr J.-H. S. , Cornish-Bowden A. , Rohwer J. M. . ( 1993; ). Taking enzyme kinetics out of control; putting control into regulation. . Eur J Biochem 212:, 833–837. [CrossRef] [PubMed]
    [Google Scholar]
  18. Hoops S. , Sahle S. , Gauges R. , Lee C. , Pahle J. , Simus N. , Singhal M. , Xu L. , Mendes P. , Kummer U. . ( 2006; ). copasi – a COmplex PAthway SImulator. . Bioinformatics 22:, 3067–3074. [CrossRef] [PubMed]
    [Google Scholar]
  19. Hoppner T. C. , Doelle H. W. . ( 1983; ). Purification and kinetic characteristics of pyruvate decarboxylase and ethanol dehydrogenase from Zymomonas mobilis in relation to ethanol production. . Eur J Appl Microbiol Biotechnol 17:, 152–157. [CrossRef]
    [Google Scholar]
  20. Jones C. W. , Doelle H. W. . ( 1991; ). Kinetic control of ethanol production by Zymomonas mobilis . . Appl Microbiol Biotechnol 35:, 4–9. [CrossRef]
    [Google Scholar]
  21. Kacser H. , Burns J. A. . ( 1979; ). Molecular democracy: who shares the controls?. Biochem Soc Trans 7:(5), 1149–1160.
    [Google Scholar]
  22. Kalnenieks U. , De Graaf A. A. , Bringer-Meyer S. , Sahm H. . ( 1993; ). Oxidative phosphorylation in Zymomonas mobilis . . Arch Microbiol 160:, 74–79.[CrossRef]
    [Google Scholar]
  23. Kalnenieks U. , Galinina N. , Strazdina I. , Kravale Z. , Pickford J. L. , Rutkis R. , Poole R. K. . ( 2008; ). NADH dehydrogenase deficiency results in low respiration rate and improved aerobic growth of Zymomonas mobilis . . Microbiology 154:, 989–994. [CrossRef] [PubMed]
    [Google Scholar]
  24. Kinoshita S. , Kakizono T. , Kadota K. , Das K. , Taguchi H. . ( 1985; ). Purification of two alcohol dehydrogenases from Zymomonas mobilis and their properties. . Appl Microbiol Biotechnol 22:, 249–254. [CrossRef]
    [Google Scholar]
  25. Koebmann B. J. , Westerhoff H. V. , Snoep J. L. , Nilsson D. , Jensen P. R. . ( 2002; ). The glycolytic flux in Escherichia coli is controlled by the demand for ATP. . J Bacteriol 184:, 3909–3916. [CrossRef] [PubMed]
    [Google Scholar]
  26. Kouvelis V. N. , Davenport K. W. , Brettin T. S. , Bruce D. , Detter C. , Han C. S. , Nolan M. , Tapia R. , Damoulaki A. . & other authors ( 2011; ). Genome sequence of the ethanol-producing Zymomonas mobilis subsp. pomaceae lectotype strain ATCC 29192. . J Bacteriol 193:, 5049–5050. [CrossRef] [PubMed]
    [Google Scholar]
  27. Kouvelis V. N. , Saunders E. , Brettin T. S. , Bruce D. , Detter C. , Han C. , Typas M. A. , Pappas K. M. . ( 2009; ). Complete genome sequence of the ethanol producer Zymomonas mobilis NCIMB 11163. . J Bacteriol 191:, 7140–7141. [CrossRef] [PubMed]
    [Google Scholar]
  28. Krietsch W. K. G. , Bücher T. . ( 1970; ). 3-Phosphoglycerate kinase from rabbit skeletal muscle and yeast. . Eur J Biochem 17:, 568–580. [CrossRef] [PubMed]
    [Google Scholar]
  29. Lazdunski A. , Belaich J. P. . ( 1972; ). Uncoupling in bacterial growth: ATP pool variation in Zymomonas mobilis cells in relation to different uncoupling conditions of growth. . J Gen Microbiol 70:, 187–197. [CrossRef]
    [Google Scholar]
  30. Lee K. J. , Skotnicki M. L. , Tribe D. E. , Rogers P. L. . ( 1980; ). Kinetic studies on a highly productive strain of Zymomonas mobilis . . Biotechnol Lett 2:, 339–344. [CrossRef]
    [Google Scholar]
  31. Neale A. D. , Scopes R. K. , Kelly J. M. , Wettenhall R. E. . ( 1986; ). The two alcohol dehydrogenases of Zymomonas mobilis. Purification by differential dye ligand chromatography, molecular characterisation and physiological roles. . Eur J Biochem 154:, 119–124. [CrossRef] [PubMed]
    [Google Scholar]
  32. Osman Y. A. , Conway T. , Bonetti S. J. , Ingram L. O. . ( 1987; ). Glycolytic flux in Zymomonas mobilis: enzyme and metabolite levels during batch fermentation. . J Bacteriol 169:, 3726–3736.[PubMed]
    [Google Scholar]
  33. Pappas K. M. , Kouvelis V. N. , Saunders E. , Brettin T. S. , Bruce D. , Detter C. , Balakireva M. , Han C. S. , Savvakis G. . & other authors ( 2011; ). Genome sequence of the ethanol-producing Zymomonas mobilis subsp. mobilis lectotype strain ATCC 10988. . J Bacteriol 193:, 5051–5052. [CrossRef] [PubMed]
    [Google Scholar]
  34. Parker C. , Peekhaus N. , Zhang X. , Conway T. . ( 1997; ). Kinetics of sugar transport and phosphorylation influence glucose and fructose cometabolism by Zymomonas mobilis . . Appl Environ Microbiol 63:, 3519–3525.[PubMed]
    [Google Scholar]
  35. Pawluk A. , Scopes R. K. , Griffiths-Smith K. . ( 1986; ). Isolation and properties of the glycolytic enzymes from Zymomonas mobilis. The five enzymes from glyceraldehyde-3-phosphate dehydrogenase through to pyruvate kinase. . Biochem J 238:, 275–281.[PubMed]
    [Google Scholar]
  36. Pentjuss A. , Odzina I. , Kostromins A. , Fell D. A. , Stalidzans E. , Kalnenieks U. . ( 2013; ). Biotechnological potential of respiring Zymomonas mobilis: a stoichiometric analysis of its central metabolism. . J Biotechnol 165:, 1–10. [CrossRef] [PubMed]
    [Google Scholar]
  37. Reyes L. , Scopes R. K. . ( 1991; ). Membrane-associated ATPase from Zymomonas mobilis; purification and characterization. . Biochim Biophys Acta 1068:, 174–178. [CrossRef] [PubMed]
    [Google Scholar]
  38. Robbins E. A. , Boyer P. D. . ( 1957; ). Determination of the equilibrium of the hexokinase reaction and the free energy of hydrolysis of adenosine triphosphate. . J Biol Chem 224:, 121–135.[PubMed]
    [Google Scholar]
  39. Rogers P. L. , Lee K. J. , Tribe D. E. . ( 1979; ). Kinetics of alcohol production by Zymomonas mobilis at high sugar concentrations. . Biotechnol Lett 1:, 165–170. [CrossRef]
    [Google Scholar]
  40. Rogers P. L. , Lee K. J. , Skotnicki M. L. , Tribe D. E. . ( 1982; ). Ethanol production by Zymomonas mobilis . . Adv Biochem Eng 23:, 37–84.
    [Google Scholar]
  41. Rohwer J. M. , Hanekom A. J. , Hendrik S. , Hofmeyr J.-H. S. . ( 2007; ). A universal rate equation for systems biology. . Proceed 2nd Intern ESCEC Symp, pp. 175–187.
    [Google Scholar]
  42. Saint Girons I. , Gilles A. M. , Margarita D. , Michelson S. , Monnot M. , Fermandjian S. , Danchin A. , Bârzu O. . ( 1987; ). Structural and catalytic characteristics of Escherichia coli adenylate kinase. . J Biol Chem 262:, 622–629.[PubMed]
    [Google Scholar]
  43. Schoberth S. M. , Chapman B. E. , Kuchel P. W. , Wittig R. M. , Grotendorst J. , Jansen P. , DeGraff A. A. . ( 1996; ). Ethanol transport in Zymomonas mobilis measured by using in vivo nuclear magnetic resonance spin transfer. . J Bacteriol 178:, 1756–1761.[PubMed]
    [Google Scholar]
  44. Scopes R. K. . ( 1983; ). An iron-activated alcohol dehydrogenase. . FEBS Lett 156:, 303–306. [CrossRef] [PubMed]
    [Google Scholar]
  45. Scopes R. K. . ( 1984; ). Use of differential dye-ligand chromatography with affinity elution for enzyme purification: 2-keto-3-deoxy-6-phosphogluconate aldolase from Zymomonas mobilis . . Anal Biochem 136:, 525–529. [CrossRef] [PubMed]
    [Google Scholar]
  46. Scopes R. K. . ( 1985; ). 6-Phosphogluconolactonase from Zymomonas mobilis . . FEBS Lett 193:, 185–188. [CrossRef]
    [Google Scholar]
  47. Scopes R. K. . ( 1997; ). Allosteric control of Zymomonas mobilis glucose-6-phosphate dehydrogenase by phosphoenolpyruvate. . Biochem J 326:, 731–735.[PubMed]
    [Google Scholar]
  48. Scopes R. K. , Griffiths-Smith K. . ( 1984; ). Use of differential dye-ligand chromatography with affinity elution for enzyme purification: 6-phosphogluconate dehydratase from Zymomonas mobilis . . Anal Biochem 136:, 530–534. [CrossRef] [PubMed]
    [Google Scholar]
  49. Scopes R. K. , Griffiths-Smith K. . ( 1986; ). Fermentation capabilities of Zymomonas mobilis glycolytic enzymes. . Biotechnol Lett 8:, 653–656. [CrossRef]
    [Google Scholar]
  50. Scopes R. K. , Testolin V. , Stoter A. , Griffiths-Smith K. , Algar E. M. . ( 1985; ). Simultaneous purification and characterization of glucokinase, fructokinase and glucose-6-phosphate dehydrogenase from Zymomonas mobilis . . Biochem J 228:, 627–634.[PubMed]
    [Google Scholar]
  51. Seo J. S. , Chong H. , Park H. S. , Yoon K. O. , Jung C. , Kim J. J. , Hong J. H. , Kim H. , Kim J. H. . & other authors ( 2005; ). The genome sequence of the ethanologenic bacterium Zymomonas mobilis ZM4. . Nat Biotechnol 23:, 63–68. [CrossRef] [PubMed]
    [Google Scholar]
  52. Small J. R. , Kacser H. . ( 1993; ). Responses of metabolic systems to large changes in enzyme activities and effectors. 1. The linear treatment of unbranched chains. . Eur J Biochem 213:, 613–624. [CrossRef] [PubMed]
    [Google Scholar]
  53. Snoep J. L. , Yomano L. P. , Westerhoff H. V. , Ingram L. O. . ( 1995; ). Protein burden in Zymomonas mobilis: negative flux and growth control due to overproduction of glycolytic enzymes. . Microbiology 141:, 2329–2337. [CrossRef]
    [Google Scholar]
  54. Strazdina I. , Kravale Z. , Galinina N. , Rutkis R. , Poole R. K. , Kalnenieks U. . ( 2012; ). Electron transport and oxidative stress in Zymomonas mobilis respiratory mutants. . Arch Microbiol 194:, 461–471. [CrossRef] [PubMed]
    [Google Scholar]
  55. Strohhäcker J. , De Graaf A. A. , Schoberth S. M. , Wittig R. M. , Sahm H. . ( 1993; ). 31P Nuclear magnetic resonance studies of ethanol inhibition in Zymomonas mobilis . . Arch Microbiol 159:, 484–490. [CrossRef]
    [Google Scholar]
  56. Swings J. , De Ley J. . ( 1977; ). The biology of Zymomonas . . Bacteriol Rev 41:, 1–46.[PubMed]
    [Google Scholar]
  57. Teusink B. , Passarge J. , Reijenga C. A. , Esgalhado E. , van der Weijden C. C. , Schepper M. , Walsh M. C. , Bakker B. M. , van Dam K. . & other authors ( 2000; ). Can yeast glycolysis be understood in terms of in vitro kinetics of the constituent enzymes? Testing biochemistry. . Eur J Biochem 267:, 5313–5329. [CrossRef] [PubMed]
    [Google Scholar]
  58. Thomas S. , Fell D. A. . ( 1996; ). Design of metabolic control for large flux changes. . J Theor Biol 182:, 285–298. [CrossRef] [PubMed]
    [Google Scholar]
  59. Thomas S. , Fell D. A. . ( 1998; ). A control analysis exploration of the role of ATP utilisation in glycolytic-flux control and glycolytic-metabolite-concentration regulation. . Eur J Biochem 258:, 956–967. [CrossRef] [PubMed]
    [Google Scholar]
  60. Thomas T. M. , Scopes R. K. . ( 1998; ). The effects of temperature on the kinetics and stability of mesophilic and thermophilic 3-phosphoglycerate kinases. . Biochem J 330:, 1087–1095.[PubMed]
    [Google Scholar]
  61. Vinogradov A. D. . ( 2000; ). Steady-state and pre-steady-state kinetics of the mitochondrial F(1)F(0) ATPase: is ATP synthase a reversible molecular machine?. J Exp Biol 203:, 41–49.[PubMed]
    [Google Scholar]
  62. Vogel G. , Steinhart R. . ( 1976; ). ATPase of Escherichia coli: purification, dissociation, and reconstitution of the active complex from the isolated subunits. . Biochemistry 15:, 208–216. [CrossRef] [PubMed]
    [Google Scholar]
  63. Weisser P. , Krämer R. , Sahm H. , Sprenger G. A. . ( 1995; ). Functional expression of the glucose transporter of Zymomonas mobilis leads to restoration of glucose and fructose uptake in Escherichia coli mutants and provides evidence for its facilitator action. . J Bacteriol 177:, 3351–3354.[PubMed]
    [Google Scholar]
  64. Wills C. , Kratofil P. , Londo D. , Martin T. . ( 1981; ). Characterization of the two alcohol dehydrogenases of Zymomonas mobilis . . Arch Biochem Biophys 210:, 775–785. [CrossRef] [PubMed]
    [Google Scholar]
  65. Wold F. , Ballou C. E. . ( 1957; ). Studies on the enzyme enolase. I. Equilibrium studies. . J Biol Chem 227:, 301–312.[PubMed]
    [Google Scholar]
  66. Wurster B. , Hess B. . ( 1970; ). Kinetic analysis of the glucosephosphate isomerase-glucose-6-phosphate dehydrogenase system from yeast in vitro . . Hoppe Seylers Z Physiol Chem 351:, 1537–1544. [CrossRef] [PubMed]
    [Google Scholar]
  67. Zikmanis P. , Kruce R. , Auzina L. . ( 2001; ). Interrelationships between growth yield, ATPase and adenylate kinase activities in Zymomonas mobilis . . Acta Biotechnol 21:, 171–178. [CrossRef]
    [Google Scholar]
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