Quantitative analysis of the effective functional structure in yeast glycolysis

PLoS ONE

Volumn 7, Issue 2, 2012, Pages

  de la Fuente, Ildefonso M ^a,b   Cortes, Jesus M ^c  

^a INSTITUTO DE PARASITOLOGÍA Y BIOMEDICINA LÓPEZ NEYRA   (Spain)

^b BIOCRUCES BIZKAIA HEALTH RESEARCH INSTITUTE   (Spain)

^c UNIVERSITY OF GRANADA   (Spain)

Author keywords

[No Author keywords available]

Indexed keywords

6 PHOSPHOFRUCTOKINASE; ENZYME; GLUCOSE;

ARTICLE; CONTROLLED STUDY; ENTROPY; ENZYME ACTIVITY; ENZYME LOCALIZATION; ENZYME STRUCTURE; ENZYME SUBSTRATE; FEEDBACK SYSTEM; GLYCOLYSIS; MATHEMATICAL ANALYSIS; MATHEMATICAL MODEL; METABOLITE; MOLECULAR DYNAMICS; QUANTITATIVE ANALYSIS; YEAST; BINDING SITE; BIOLOGICAL MODEL; CATALYSIS; CHEMISTRY; KINETICS; METABOLISM; METHODOLOGY; NONLINEAR SYSTEM; OSCILLOMETRY; PHYSIOLOGY; PROBABILITY; STATISTICAL MODEL; TIME;

ALLOSTERIC SITE; CATALYSIS; ENTROPY; ENZYMES; GLUCOSE; GLYCOLYSIS; KINETICS; MODELS, BIOLOGICAL; MODELS, STATISTICAL; NONLINEAR DYNAMICS; OSCILLOMETRY; PROBABILITY; TIME FACTORS; YEASTS;

EID: 84857733090     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0030162     Document Type: Article

References (52)

1. Duysens L, Amesz J, (1957) Fluorescence espectrophotometry of reduced phosphopyridine nucleotide in intact cells in the near-ultraviolet and visible region. Biochem Biophys Acta 24: 19-26.
2. Chance B, Hess B, Betz A, (1964) DPNH oscillations in a cell-free extract of S. carlsbergensis. Biochem Biophys Res Commun 16: 182-187.
3. Goldbeter A, Lefeber R, (1972) Disipative estructures for an allosteric model. Biophys J 12: 1302-1315.
4. Goldbeter A, Lefeber R, (1973) Patterns of spatiotemporal organization in an allosteric enzyme model. Proc Natl Acad Sci USA 70: 3255-3259.
5. Bagheri S, Nosrati M, Li S, Fong S, Torabian S, et al. (2006) Genes and pathways downstream of telomerase in melanoma metastasis. Proc Natl Acad Sci USA 103: 11306-11311.
6. Almeidaa A, Bolaos J, Moncada S, (2010) E3 ubiquitin ligase APC/C-Cdh1 accounts for the War-burg effect by linking glycolysis to cell proliferation. Proc Natl Acad Sci USA 107: 738741.
7. Vlassenkoa A, Vaishnavia S, Couturea L, Saccoa D, Shannona B, et al. (2010) Spatial correlation between brain aerobic glycolysis and amyloid- (a) deposition. Proc Natl Acad Sci USA:www.pnas.org/cgi/doi/10.1073/pnas.1010461107.
8. Garriga-Canut M, Schoenike B, Qazi R, Bergendah K, Daley T, et al. (2006) 2-Deoxy-D-glucose reduces epilepsy progression by NRSF-CtBPdependent metabolic regulation of chromatin structure. Nat Neurosci 9: 1382-1387.
9. Colussi C, Albertini M, Coppola S, Rovidati S, Galli F, et al. (2006) H2O2-induced block of glycolysis as an active ADP-ribosylation reaction protecting cells from apoptosis. FASEB J 14: 22662276.
10. Danial N, Gramm C, Scorrano L, Zhang C, Krauss S, et al. (2003) BAD and glucokinase reside in a mitochondrial complex that integrates glycolysis and apoptosis. Nature 424: 952-956.
11. Termonia Y, Ross J, (1981) Oscillations and control features in glycolysis: Numerical analysis of a comprehensive models. Proc Natl Acad Sci USA 78: 29522956.
12. Dano S, Sorensen P, Hynne F, (1999) Sustained oscillations in living cells. Nature 402: 320-322.
13. Wolf J, Passarge J, Somsen O, Snoep J, Heinrich R, et al. (2000) Transduction of intracellular and intercellular dynamics in yeast glycolytic oscillation. Biophys J 78: 1145-1153.
14. nad S Dano MM, Sorensen P, (2005) On the mechanisms of glycolytic oscillations in yeast. FEBS J 272: 26482660.
15. Olsen L, Andersen A, Lunding A, Brasen J, Poulsen A, (2009) Regulation of Glycolytic Oscillations by Mitochondrial and Plasma Membrane H+-ATPases. Biophys J 96: 38503861.
16. Goldbeter A, (2002) Computational approaches to cellular rhythms. Nature 420: 238-245.
17. Goldbeter A, (2007) Biological rhythms as temporal dissipative structures. Advances in Chemical Physics 135: 253-295.
18. Nicolis G, Prigogine I, (1977) Self-organization in nonequilibrium systems. From dissipative structures to order through uctuations. Wiley. New York.
19. De la Fuente ID, Vadillo F, Perez-Samartin A, Perez-Pinilla M, Bidaurrazaga J, et al. (2010) Global self-regulations of the cellular metabolic structure. Plos One 5: e9484.
20. Prigogine I, Mayne F, George C, Haan MD, (1977) Microscopic theory of irreversible processes. Proc Nat Acad Sci USA 74: 4152-4156.
21. Ebeling W, Engel-Herbert H, Herzel H, (1986) Selforganization by non-linear irreversible processes Springer-Verlag.
22. 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.
23. Gerstein G, Perkel D, (1969) Simultaneously recorded trains of action potentials: analysis and functional interpretation. Science 164: 828-830.
24. Friston K, (1994) Functional and effective connectivity in neuroimaging: A synthesis. Hum Brain Mapping 2: 56-78.
25. Fujita A, Sato J, Garay-Malpartida H, Morettin P, Sogayar M, et al. (2007) Time-varying modeling of gene expression regulatory networks using the wavelet dynamic vector autoregressive method. Bioinformatics 23: 1623-1630.
26. Mukhopadhyay N, Chatterjee S, (2007) Causality and pathway search in microarray time series experiment. Bioinformatics 23: 442-449.
27. Pahle J, Green A, Dixon C, Kummer U, (2008) Information transfer in signaling pathways: a study using coupled simulated and experimental data. BMC Bioinformatics 9: 139.
28. Viola E, Raushel M, Rendina R, Cleland W, (1982) Substrate synergism and the kinetic mechanism of yeast hexokinase. Biochem 21: 1295-1302.
29. Markus M, Plesser T, Boiteux A, Hess B, Malcovati M, (1980) Rate law of pyruvate kinase type I from Escherichia coli. Biochem J 189: 421-433.
30. De la Fuente ID, Martinez L, Veguillas J, Aguirregabiria J, (1996) Quasiperiodicity route to chaos in a biochemical system. Biophys J 71: 2375-2379.
31. Schreiber T, (2000) Measuring information transfer. Phys Rev Lett 85: 461-464.
32. Markus M, Muller S, Hess B, (1985) Observation of entrainment quasiperiodicity and chaos in glycolyzing yeast extracts under periodic glucose input. Ber Bunsen-Ges Phys Chem 89: 651-654.
33. Markus M, Kuschmitz D, Hess B, (1985) Properties of strange attractors in yeast glycolysis. Biophys Chem 22: 95-105.
34. Markus M, Kuschmitz D, Hess B, (1984) Chaotic Dynamics in Yeast Glycolisys Under Periodic Substrate Input Flux. FEBS 172: 235-238.
35. De la Fuente IM, (1999) Diversity of temporal self-organized behaviors in a biochemical system. Biosystems 50: 83-97.
36. De la Fuente IM, Benitez N, Santamaria A, Veguillas J, Aguirregabiria J, (1999) Persistence in metabolic nets. Bull Mathemat Biol 61: 573-595.
37. De la Fuente IM, Martinez L, Veguillas J, (1996) Intermittency route to chaos in a biochemical system. Biosystems 39: 87-92.
38. Ruelle D, Takens F, (1971) On the nature of turbulence. Commun Math Phys 20: 167-172.
39. Cover T, Thomas J, (1991) Elements of Information Theory John Wiley & Sons, Inc.
40. Kaufmann SS, (1991) Coevolution to the edge of chaos: Coupled fitness landscapes, poised states, and coevolutionary avalanches. J Theo Biol 149: 467-505.
41. Bertschinger N, Natschlager T, (2004) Real-Time Computation at the Edge of Chaos in Recurrent Neural Networks. Neural Comput 16: 1413-1436.
42. Serrano G, (1989) The Yeasts Academic Press.
43. JJ Heinisch EB, Timpel C, (1996) A yeast phosphofructokinase insensitive to the allosteric activator fructose-2,6-bisphosphate. J Biol Chem 271: 15928-15933.
44. Stryer L, (1995) Biochemistry W.H. Freeman.
45. De la Fuente ID, Martinez L, Perez-Samartin A, Ormaetxea L, Amezaga C, et al. (2008) Global self-organization of the cellular metabolic structure. Plos One 3: 1-19.
46. Almaas E, Kovacs B, Vicsek T, Oltvai Z, Barabasi A, (2004) Global organization of metabolic uxes in the bacterium Escherichia coli. Nature 427: 839-843.
47. Almaas E, Oltvai Z, Barabasi A, (2005) The activity reaction core and plasticity of metabolic networks. PLoS Comput Biol 1: e68.
48. De la Fuente ID, Vadillo F, Perez-Pinilla M, Lopez-Vera A, Veguillas J, (2009) The number of catalytic elements is crucial for the emergence of metabolic cores. Plos One 4: e7510.
49. De la Fuente ID, Cortes J, Perez-Pinilla M, Ruiz-Rodriguez V, Veguillas J, (2011) The metabolic core and catalytic switches are fundamental elements in the self-regulation of the Systemic Metabolic Structure of Cells. Plos One 6: e27224.
50. Peng H, Long F, Ding C, (2005) Feature Selection Based on Mutual Information: Criteria of Max-Dependency, Max-Relevance, and Min-Redundancy. IEEE Trans Pattern Anal Mach Intell 27: 1226-1238.
51. Granger C, (1969) Investigating causal relations by econometric models and cross-spectral methods. Econometrica 37: 424-438.
52. Barnett L, Barrett A, Seth A, (2009) Granger causality and transfer entropy are equivalent for gaussian variables. Phys Rev Lett 103: 238701.