From steady-state to synchronized yeast glycolytic oscillations I: Model construction

FEBS Journal

Volumn 279, Issue 16, 2012, Pages 2810-2822

  Du Preez, Franco B ^a   Van Niekerk, David D ^b   Kooi, Bob ^c   Rohwer, Johann M ^b   Snoep, Jacky L ^a,b,c  

^a UNIVERSITY OF MANCHESTER   (United Kingdom)

^b STELLENBOSCH UNIVERSITY   (South Africa)

^c VU UNIVERSITY AMSTERDAM   (Netherlands)

Author keywords

glycolysis; limit cycle oscillation; mathematical model; model construction; Saccharomyces cerevisiae

Indexed keywords

SILICON;

ARTICLE; ARTIFICIAL CELL; CELL SYNCHRONIZATION; ENZYME KINETICS; GLYCOLYSIS; MATHEMATICAL COMPUTING; MATHEMATICAL MODEL; MATHEMATICAL PARAMETERS; OSCILLATION; PRIORITY JOURNAL; SIMULATION; STEADY STATE; VALIDATION STUDY; YEAST; YEAST CELL;

ACETALDEHYDE; ADENOSINE TRIPHOSPHATASES; CELL COMMUNICATION; COMPUTER SIMULATION; DATABASES, FACTUAL; GLYCOLYSIS; KINETICS; METABOLIC NETWORKS AND PATHWAYS; MODELS, BIOLOGICAL; NAD; PHOSPHOFRUCTOKINASES; SACCHAROMYCES CEREVISIAE; SYSTEMS BIOLOGY;

SACCHAROMYCES CEREVISIAE;

EID: 84864408998     PISSN: 1742464X     EISSN: 17424658     Source Type: Journal    
DOI: 10.1111/j.1742-4658.2012.08665.x     Document Type: Article

References (44)

1. Westerhoff HV, &, Palsson BO, (2004) The evolution of molecular biology into systems biology. Nat Biotechnol 22, 1249-1252. (Pubitemid 39336777)
2. Snoep JL, Bruggeman F, Olivier BG, &, Westerhoff HV, (2006) Towards building the silicon cell: a modular approach. Biosystems 83, 207-216. (Pubitemid 43199821)
3. Madsen M, Danø S, &, Quistorff B, (2012) A strategy for development of realistic mathematical models of whole-body metabolism. Open J Appl Sci 2, 11-27.
4. Snoep JL, (2005) The Silicon Cell initiative: working towards a detailed kinetic description at the cellular level. Curr Opin Biotechnol 16, 336-343. (Pubitemid 40806472)
5. Le Novère N, Finney A, Hucka M, Bhalla U, Campagne F, Collado-Vides J, Crampin EJ, Halstead M, Klipp E, Mendes P, et al. (2005) Minimum information requested in the annotation of biochemical models (MIRIAM). Nat Biotechnol 23, 1509-1515. (Pubitemid 41752928)
6. Hucka M, Finney A, Sauro HM, Bolouri H, Doyle JC, and the rest of the SBML Forum (2003) The systems biology markup language (SBML): a medium for representation and exchange of biochemical network models. Bioinformatics 19, 524-531. (Pubitemid 36336519)
7. Le Novère N, Hucka M, Mi H, Moodie S, Schreiber F, Sorokin A, Demir E, Wegner K, Aladjem MI, Wimalaratne SM, et al. (2009) The systems biology graphical notation. Nat Biotechnol 27, 735-741. Erratum in Nat Biotechnol 27, 864.
8. Li C, Donizelli M, Rodriguez N, Dharuri H, Endler L, Chelliah V, Li L, He E, Henry A, Stefan MI, et al. (2011) Biomodels database: an enhanced, curated and annotated resource for published quantitative kinetic models. BMC Syst Biol 4, 92.
9. Olivier B, &, Snoep J, (2004) Web-based kinetic modelling using JWS Online. Bioinformatics 20, 2143-2144. (Pubitemid 39236569)
10. Zhou M, Cheng T, &, Chan KCC, (2010) DOCQS: a prototype system for supporting data-oriented content query. In Proceedings of the 2010 International Conference on Management of data (, Elmagarmid AK, &, Agrawal D, ed.), pp. 1211-1214. ACM New York, NY, USA.
11. Miller A, Marsh J, Reeve A, Garny A, Britten R, Halstead M, Cooper J, Nickerson DP, &, Nielsen PF, (2010) An overview of the CellML API and its implementation. BMC Bioinformatics 8, 178.
12. Wolstencroft K, Owen S, du Preez F, Krebs O, Mueller W, Goble C, &, Snoep JL, (2011) The SEEK: a platform for sharing data and models in systems biology. Methods Enzymol 500, 629-655.
13. Teusink B, Passarge J, Reijenga CA, Esgalhado E, Van der Weijden CC, Schepper M, Walsh MC, Bakker BM, van Dam K, Westerhoff HV, et al. (2000) Can yeast glycolysis be understood in terms of in vitro kinetics of the constituent enzymes? Testing biochemistry. Eur J Biochem 267, 5313-5329.
14. Pritchard L, &, Kell D, (2002) Schemes of flux control in a model of Saccharomyces cerevisiae glycolysis. Eur J Biochem 269, 3894-3904. (Pubitemid 34994884)
15. Bruck J, Liebermeister W, &, Klipp E, (2008) Exploring the effect of variable enzyme concentrations in a kinetic model of yeast glycolysis. Genome Informatics 20, 1-14.
16. Albers E, Larsson C, Andlid T, Walsh MC, &, Gustafsson L, (2007) Effect of nutrient starvation on the cellular composition and metabolic capacity of Saccharomyces cerevisiae. Appl Environ Microbiol 73, 4839-4848. (Pubitemid 47241074)
17. Rizzi M, Baltes M, Theobald U, &, Reuss M, (1997) In vivo analysis of metabolic dynamics in Saccharomyces cerevisiae: II: mathematical model. Biotechnol Bioeng 55, 592-608. (Pubitemid 27318173)
18. Hynne F, Danø S, &, Sørensen P, (2001) Full-scale model of glycolysis in Saccharomyces cerevisiae. Biophys Chem 94, 121-163. (Pubitemid 34015989)
19. Bier M, Bakker BM, &, Westerhoff HV, (2000) How yeast cells synchronize their glycolytic oscillations: a perturbation analytic treatment. Biophys J 78, 1087-1093. (Pubitemid 30141538)
20. Cronwright GR, Rohwer JM, &, Prior BA, (2002) Metabolic control analysis of glycerol synthesis in Saccharomyces cerevisiae. Appl Environ Microbiol 68, 4448-4456. (Pubitemid 34993530)
21. Galazzo J, &, Bailey J, (1990) Fermentation pathway kinetics and metabolic flux control in suspended and immobilized Saccharomyces cerevisiae. Enzyme Microb Technol 12, 162-172. (Pubitemid 20116810)
22. Nielsen K, Sørensen PG, Hynne F, &, Busse HG, (1998) Sustained oscillations in glycolysis: an experimental and theoretical study of chaotic and complex periodic behavior and of quenching of simple oscillations. Biophys Chem 72, 49-62. (Pubitemid 28267516)
23. Poulsen AK, Ostergaard Petersen M, &, Olsen LF, (2007) Single cell studies and simulation of cell-cell interactions using oscillating glycolysis in yeast cells. Biophys Chem 125, 275-280. (Pubitemid 46123763)
24. Wolf J, Passarge J, Somsen OJ, Snoep JL, Heinrich R, &, Westerhoff HV, (2000) Transduction of intracellular and intercellular dynamics in yeast glycolytic oscillations. Biophys J 78, 1145-1153. (Pubitemid 30141543)
25. Richard P, Teusink B, Hemker MB, Dam KV, &, Westerhoff HV, (1996) Sustained oscillations in free-energy state and hexose phosphates in yeast. Yeast 12, 731-740. (Pubitemid 26201773)
26. Das J, &, Busse H, (1991) Analysis of the dynamics of relaxation type oscillation in glycolysis of yeast extracts. Biophys J 60, 369-379.
27. Ghosh A, Chance B, &, Pye E, (1971) Metabolic coupling and synchronization of NADH oscillations in yeast cell populations. Arch Biochem Biophys 145, 319-331.
28. Richard P, Bakker BM, Teusink B, Dam KV, &, Westerhoff HV, (1996) Acetaldehyde mediates the synchronization of sustained glycolytic oscillations in populations of yeast cells. Eur J Biochem 235, 238-241. (Pubitemid 26048625)
29. Boiteux A, Goldbeter A, &, Hess B, (1975) Control of oscillating glycolysis of yeast by stochastic, periodic, and steady source of substrate: a model and experimental study. Proc Natl Acad Sci USA 72, 3829-3833.
30. Goldbeter A, &, Lefever R, (1972) Dissipative structures for an allosteric model: application to glycolytic oscillations. Biophys J 10, 1302-1315.
31. Reijenga KA, van Megen YM, Kooi BW, Bakker BM, Snoep JL, van Verseveld HW, &, Westerhoff HV, (2005) Yeast glycolytic oscillations that are not controlled by a single oscillophore: a new definition of oscillophore strength. J Theor Biol 232, 385-398. (Pubitemid 39585158)
32. du Preez FB, van Niekerk DD, &, Snoep JL, (2012) From steady-state to synchronized yeast glycolytic oscillations II: model validation. FEBS J 279, 2823-2836.
33. Kacser H, &, Burns JA, (1973) The control of flux. Symp Soc Exp Biol 27, 65-104.
34. Heinrich R, &, Rapoport TA, (1974) A linear steady-state treatment of enzymatic chains. General properties, control and effector strength. Eur J Biochem 42, 89-95.
35. Guijarro JM, &, Lagunas R, (1984) Saccharomyces cerevisiae does not accumulate ethanol against a concentration gradient. J Bacteriol 160, 874-878. (Pubitemid 15219451)
36. Tehrany E, &, Desobry S, (2005) Comparison between different calculation methods of partition coefficient of aroma compounds of different chemical classes in the octanol-water system. Sci Aliments 25, 23-36. (Pubitemid 40534417)
37. Park YSPS, (2000) Determination and prediction of octanol/water partition coefficients and air-water partition coefficients for environmental toxic chemicals. J Indust Eng Chem 11, 773-779.
38. Wolf J, &, Heinrich R, (2000) Effect of cellular interaction on glycolytic oscillations in yeast: a theoretical investigation. Biochem J 345, 321-334. (Pubitemid 30077173)
39. De Monte S, d'Ovidio F, Danø S, &, Sorensen PG, (2007) Dynamical quorum sensing: population density encoded in cellular dynamics. Proc Natl Acad Sci USA 104, 18377-18381. (Pubitemid 350210704)
40. Ashyraliyev M, Fomekong-Nanfack Y, Kaandorp JA, &, Blom JG, (2009) Systems biology: parameter estimation for biochemical models. FEBS J 276, 886-902.
41. Cedersund G, &, Roll J, (2009) Systems biology: model based evaluation and comparison of potential explanations for given biological data. FEBS J 276, 903-922.
42. Kreutz C, &, Timmer J, (2009) Systems biology: experimental design. FEBS J 276, 923-942.
43. Rossell S, van der Weijden C, Lindenbergh A, van Tuijl A, Francke C, Bakker BM, &, Westerhoff HV, (2006) Unraveling the complexity of flux regulation: a new method demonstrated for nutrient starvation in Saccharomyces cerevisiae. Proc Natl Acad Sci USA 103, 2166-2171. (Pubitemid 43271641)
44. Madsen MF, Danø S, &, Sørensen PG, (2005) On the mechanisms of glycolytic oscillations in yeast. FEBS J 272, 2648-2660. (Pubitemid 40825413)