The number of catalytic elements is crucial for the emergence of metabolic cores

PLoS ONE

Volumn 4, Issue 10, 2009, Pages

  De la Fuente, Ildefonso M ^a   Vadillo, Fernando ^a   Pérez Pinilla, Martín Blas ^a   Vera López, Antonio ^a   Veguillas, Juan ^a  

^a UNIVERSITY OF THE BASQUE COUNTRY UPV EHU   (Spain)

Author keywords

[No Author keywords available]

Indexed keywords

ALLOSTERISM; ARTICLE; CELL METABOLISM; CONTROLLED STUDY; ENZYME MECHANISM; ENZYME METABOLISM; ENZYME STRUCTURE; METABOLIC REGULATION; SIGNAL TRANSDUCTION; SIMULATION; BINDING SITE; BIOCHEMISTRY; BIOLOGICAL MODEL; BIOLOGY; CATALYSIS; CELL; COMPUTER SIMULATION; ESCHERICHIA COLI; HELICOBACTER PYLORI; KINETICS; METABOLISM; METHODOLOGY; OSCILLOMETRY; SACCHAROMYCES CEREVISIAE; STATISTICAL MODEL;

ALLOSTERIC SITE; BIOCHEMICAL PROCESSES; CATALYSIS; CELLS; COMPUTATIONAL BIOLOGY; COMPUTER SIMULATION; ESCHERICHIA COLI; HELICOBACTER PYLORI; KINETICS; METABOLIC NETWORKS AND PATHWAYS; MODELS, BIOLOGICAL; MODELS, STATISTICAL; OSCILLOMETRY; SACCHAROMYCES CEREVISIAE; SIGNAL TRANSDUCTION;

EID: 70449412122     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0007510     Document Type: Article

References (55)

1. Goldbeter A (2002) Computational approaches to cellular rhythms. Nature 420: 238-245.
2. Ho Y, Gruhler A, Heilbut A, Bader DG, Moore L, et al. (2002) Systematic identification of protein complexes in Saccharomyces cerevisiae by mass spectrometry. Nature 415: 180-183.
3. Ovádi J, Saks V (2005) On the origin of the ideas of intracellular compartmentation and organized metabolic systems. Cell Biochem 256: 5-12.
4. Gavin AC, Bosche M, Krause R, Grandi P, Marzioch M, et al. (2002) Functional organization of the yeast proteome by systematic analysis of protein complexes. Nature 415: 141-147.
5. Gillette MU, Sejnowski TJ (2005) Biological clocks coordinately keep life on time. Science 309: 1196-1198.
6. Goldbeter A (2007) Biological rhythms as temporal dissipative structures. Advances in Chemical Physics 135: 253-295.
7. Futcher B (2006) Metabolic cycle, cell cycle, and the finishing kick to start. Genome Biology 7(4): 107.
8. Hess B (2000) Periodic patterns in biology. Naturwissenschaften 87: 199-211.
9. Marquez S, Crespo P, Carlini V, Garbarino-Pico E, Baler R, et al. (2004) The metabolism of phospholipids oscillates rhythmically in cultures of fibroblasts and is regulated by the clock protein PERIOD 1 FASEB Journal 18: 519-521.
10. Hartig K, Beck E (2005) Endogenous Cytokinin Oscillations Control Cell Cycle Progression of Tobacco BY-2 Cells. Plant Biology 7(1): 33-40.
11. Hungerbuehler AK, Philippsen P, Gladfelter AS (2007) Limited Functional Redundancy and Oscillation of Cyclins in Multinucleated Ashbya gossypii Fungal Cells. Eukaryot Cell 6(3): 473-486.
12. Shaul O, Mironov V, Burssens S, Van Montagu M, Inze D (1996) Two Arabidopsis cyclin promoters mediate distinctive transcriptional oscillation in synchronized tobacco BY-2 cells. Proc Natl Acad Sci 93(10): 4868-4872.
13. Chabot JR, Pedraza JM, Luitel P, van Oudenaarden (2007) A Stochastic gene expression out-of-steady-state in the cyanobacterial circadian clock. Nature 450: 1249-1252.
14. Tian B, Nowak DE, Brasier AR (2005) A TNF-induced gene expression program under oscillatory NF-κB control. BMC Genomics 6: 137.
15. Tonozuka H, Jinqing W, Kazuhiro M, Toshiki S, Yoshiki A, et al. (2001) Analysis of the Upstream Regulatory Region of the GTS1 Gene Required for Its Oscillatory Expression. J Biochem 130: 589-595.
16. Klevecz RR, Bolen J, Forrest G, Murray DB (2004) A genomewide oscillation in transcription gates DNA replication and cell cycle. Proc Natl Acad Sci 101(5): 1200-1205.
17. Lange G, Mandelkow EM, Jagla A, Mandelklow E (2004) Tubulin oligomers and microtubule oscillations Antagonistic role of microtubule stabilizers and destabilizers. FEBS 178: 61-69.
18. Placantonakis DG, Welsh JP (2001) Two distinct oscillatory states determined by the NMDA receptor in rat inferior olive. J Physiol 534: 123-140.
19. Hans MA, Heinzle E, Wittmann Ch (2003) Free intracellular amino acid pools during autonomous oscillations in Saccharomyces cerevisiae. Biotechnol Bioeng 82(2): 143-151.
20. DeForest M, Wheeler CJ (1999) Coherent Oscillations in Membrane Potential Synchronize Impulse Bursts in Central Olfactory Neurons of the Crayfish. J Neurophysiol 81: 1231-1241.
21. Sánchez-Armáss S, Sennoune SR, Maiti D, Ortega F, Martínez-Zaguila R (2006) Spectral imaging microscopy demonstrates cytoplasmic pH oscillations in glial cells. Am J Physiol Cell Physiol 290: C524-C538.
22. Holz GG, Emma Heart E, Leech CA (2008) Synchronizing Ca2+ and cAMP oscillations in pancreatic beta cells: a role for glucose metabolism and GLP-1 receptors? Am J Physiol Cell Physiol 294: c4-c6.
23. Lloyd D, Eshantha L, Salgado J, Turner MP, Murray DB (2002) Respiratory oscillations in yeast: clock-driven mitochondrial cycles of energization. FEBS Lett 519(1-3): 41-44.
24. Rosenspire AJ, Kindzelskii AL, Petty H (2001) Pulsed DC electric fields couple to natural NAD(P)H oscillations in HT-1080 fibrosarcoma cells. Journal of Cell Science 114: 1515-1520.
25. Danù S, Sùrensen PG, Hynne F (1999) Sustained oscillations in living cells. Nature 402: 320-322.
26. Ishii K, Hirose K, Iino M (2006) Ca2+ shuttling between endoplasmic reticulum and mitochondria underlying Ca2+ oscillations. EMBO 7: 390-396.
27. Jules M, Francois J, Parrou JL (2005) Autonomous oscillations in Saccharomyces cerevisiae during batch cultures on trehalose. FEBS Journal 272: 1490-1500.
28. Getty L, Panteleon AE, Mittelman SD, Dea MK, Bergman RN (2000) Rapid oscillations in omental lipolysis are independent of changing insulin levels in vivo. J Clin Invest 106: 421-430.
29. Klevecz RR, Murray DB (2001) Genome wide oscillations in expression - Wavelet analysis of time series data from yeast expression arrays uncovers the dynamic architecture of phenotype. Molecular Biology Reports 28: 73-82.
30. Kindzelskii AL, Zhou MJ, Haugland PR, Boxer AL, Petty RH (1998) Oscillatory Pericellular Proteolysis and Oxidant Deposition During Neutrophil Locomotion. Biophysical J 74: 90-97.
31. Fuentes JM, Pascual MR, Salido G, Soler JA (1994) Madrid Oscillations in rat liver cytosolic enzyme activities of the urea cycle. Archives Of Physiology And Biochemistry 102(5): 237-241.
32. Wittmann C, Hans M, Van Winden AW, Ras C, Heijnen JJ (2005) Dynamics of intracellular metabolites of glycolysis and TCA cycle during cell-cycle-related oscillation in Saccharomyces cerevisiae. Biotechnol Bioeng 89: 839-847.
33. Chiam HK, Rajagopal G (2007) Oscillations in intracellular signaling cascades. Phys Rev E 75: 061901.
34. Heinzle E, Dunn I, Furukawa K, Tanner RD (1983) Modeling of sustained oscillations observed in continuous culture of Saccharomyces cerevisiae. Proceedings of the 1st IFAC Workshop Halme A, ed. Oxford: Pergamon Press. pp 57-65.
35. De La Fuente IM, Benítez N, Santamaría A, Veguillas J, Aguirregabiria JM (1999) Persistence in Metabolic Nets. Bulletin of Mathematical Biology 61: 573-595.
36. Almaas E, Kovacs B, Vicsek T, Oltvai ZN, Barabási AL (2004) Global organization of metabolic fluxes in the bacterium Escherichia coli. Nature 427: 839-843.
37. Almaas E, Oltvai ZN, Barabasi AL (2005) The activity reaction core and plasticity of metabolic networks. PLoS Comput Biol 1(7): e680557-563.
38. Almaas E (2007) Biological impacts and context of network theory. Journal of Experimental Biology 210: 1548-1558.
39. De La Fuente IM, Martínez L, Pérez-Samartín AL, Ormaetxea L, Amezaga C, et al. (2008) Global Self-organization of the cellular metabolic structure. Plos One 3: e31001-19.
40. Csaba P, Balázs P, Martin J, Lercher P, Csermely S, et al. (2006) Chance and necessity in the evolution of minimal metabolic networks. Nature 440: 667-670.
41. Karp PD (2001) Pathway Databases: A Case Study in Computational Symbolic Theories. Science 293: 2040-2044.
42. Cyber Cell Database Statistics. http://redpoll.pharmacy.ualberta.ca/CCDB/ cgi-bin/STAT_NEW.cgi.
43. Kitano H (2004) Biological Robustness. Nature reviews Genetics 5: 826-837.
44. Jules M, Francois J, Parrou JL (2005) Autonomous oscillations in Saccharomyces cerevisiae during batch cultures on trehalose. FEBS 272: 1490-1500.
45. Smrcinová M, Sørensen PG, Krempasky J, Ballo P (1998) Chaotic oscillations in a chloroplast system under constant illumination. International Journal of Bifurcation and Chaos 8: 2467-2470.
46. Nielsen K, Sorensen 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. Biophysical Chemistry 72: 49-62.
47. MacDonald MJ, Fahien LA, Buss JD, Hasan NM, Fallon MJ, et al. (2003) Citrate Oscillates in Liver and Pancreatic Beta Cell Mitochondria and in INS-1 Insulinoma. Cells. J Biol Chem 278: 51894-51900.
48. Møller AC, Hauser MJB, Olsen LF (1998) Oscillations in peroxidase-catalyzed reactions and their potential function in vivo. Biophysical Chemistry 72: 63-72.
49. Lebrun P, Water AT (1985) Chaotic and irregular bursting electrical activity in mouse pancreatic B-cells. Biophys J 48: 529-531.
50. Garmendia-Torres C, Goldbeter A, Jacquet M Nucleocytoplasmic (2007) Oscillations of the Yeast Transcription Factor Msn2: Evidence for Periodic PKA Activation. Current Biology 17: 1044-1049.
51. Ramanujan VK, Biener G, Herman B (2006) Scaling Behavior in Mitochondrial Redox Fluctuations. Biophys J 90: L70-L72.
52. Dyachok O, Isakov Y, Sagetorp J, Tengholm A (2006) Oscillations of cyclic AMP in hormone-stimulated insulin-secreting b-cells. Nature 439: 349-352.
53. Ainscow EK, Mirsham S, Tang T, Ashford MLJ, Rutter GA (2002) Dynamic imaging of free cytosolic ATP concentration during fuel sensing by rat hypothalamic neurones: evidence for ATPindependent control of ATP-sensitive K+ channels. Journal of Physiology 544: 429-445.
54. Dixon CJ, Cobbold PH, Green AK (1995) Oscillations in cytosolic free Ca2+ induced by ADP and ATP in single rat hepatocytes display differential sensitivity to application of phorbol ester. Biochem J 309: 145-149.
55. Goldbeter A, Lefever R (1972) Dissipative structures for an allosteric model. Application to glycolytic oscillations. Biophys J 12: 1302-1315.