Organising metabolic networks: Cycles in flux distributions

Journal of Theoretical Biology

Volumn 265, Issue 3, 2010, Pages 250-260

  Kritz, Maurício Vieira ^a   Trindade dos Santos, Marcelo ^a   Urritia, Sebastián ^b   Schwartz, Jean Marc ^c  

^a LABORATÓRIO NACIONAL DE COMPUTAÇÃO CIENTÍFICA   (Brazil)

^b FEDERAL UNIVERSITY OF MINAS GERAIS   (Brazil)

^c UNIVERSITY OF MANCHESTER   (United Kingdom)

Author keywords

Cycle; Flux; Organisation; Systems biology

Indexed keywords

ALGORITHM; BIOCHEMISTRY; BIOLOGY; ENVIRONMENTAL CHANGE; HOMEOSTASIS; METABOLISM;

ALGORITHM; ARTICLE; BACTERIAL METABOLISM; DELETION MUTANT; ERYTHROCYTE METABOLISM; ESCHERICHIA COLI; METHYLOBACTERIUM EXTORQUENS; NONHUMAN; PRIORITY JOURNAL; TRANSPORT KINETICS; WILD TYPE; BIOCHEMISTRY; BIOLOGICAL MODEL; COMPUTER SIMULATION; ERYTHROCYTE; HOMEOSTASIS; HUMAN; METABOLISM; PHYSIOLOGY; SPECIES DIFFERENCE;

ALGORITHMS; BIOCHEMICAL PHENOMENA; COMPUTER SIMULATION; ERYTHROCYTES; ESCHERICHIA COLI; HOMEOSTASIS; HUMANS; METABOLIC NETWORKS AND PATHWAYS; METHYLOBACTERIUM EXTORQUENS; MODELS, BIOLOGICAL; SPECIES SPECIFICITY;

BACTERIA (MICROORGANISMS); ESCHERICHIA COLI; METHYLOBACTERIUM EXTORQUENS;

EID: 77954623243     PISSN: 00225193     EISSN: 10958541     Source Type: Journal    
DOI: 10.1016/j.jtbi.2010.04.026     Document Type: Article

References (48)

1. Arita M. The metabolic world of Escherichia coli is not small. Proc. Natl. Acad. Sci. USA 2004, 101:1543-1547.
2. Binder, B., Goede, A., Holzhütter, H.G., 2008. De novo formation of organelles in time and space. In: ECMTB 08 - European Conference on Mathematical and Theoretical Biology. 29 June-4 July 2008, Edinburgh.
3. Bluthgen, N., Platt, R., 2008. What makes a good oscillator? ECMTB 08 - European Conference on Mathematical and Theoretical Biology. 29 June-4 July 2008, Edinburgh.
4. Chenoweth M., Dunn A. Fructose-6-phosphate substrate cycling and hormonal regulation of gluconeogenesis in vivo. Am. J. Physiol. 1978, 235:E295-E303.
5. Cornish-Bowden A., Cárdenas M.L. Organizational invariance in (M,R)-systems. Chem. Biodivers. 2007, 4:2396-2406.
6. Cornish-Bowden A., Cárdenas M.L. Self-organization at the origin of life. J. Theor. Biol. 2008, 252:411-418. 10.1016/j.jtbi.2007.07.035.
7. Domijan M., Kirkilionis M. Bistability and oscillation in chemical reaction networks. J. Math. Biol. 2009, 59:467-501. 10.1007/s00285-008-0234-7.
8. Ellson J., Gansner E.R., Koutsofios E., North S.C., Woodhull G. Graphviz and Dynagraph-Static and dynamic graph drawing tools. Graph Drawing Software 2003, 127-148. Springer-Verlag. M. Junger, P. Mutzel (Eds.).
9. Famili I., Palsson B.Ø. The convex basis of the left null space of the stoichiometric matrix leads to the definition of metabolically meaningful pools. Biophys. J. 2003, 85:16-26. 10.1016/S0006-3495(03)74450-6.
10. Feist A.M., Henry C.S., Reed J.L., Krummenacker M., Joyce A.R., Karp P.D., Broadbelt L.J., Hatzimanikatis V., Palsson B.Ø. A genome-scale metabolic reconstruction for Escherichia coli K-12 MG1655 that accounts for 1260 ORFs and thermodynamic information. Mol. Syst. Biol. 2007, 3:121. 10.1038/msb4100155.
11. Fell, D.A., Poolman, M.G., 2008. Modelling the photosynthetic Calvin cycle. In: ECMTB 08 - European Conference on Mathematical and Theoretical Biology. 29 June-4 July 2008, Edinburgh.
12. Gagneur J., Klamt S. Computation of elementary modes: a unifying framework and the new binary approach. BMC Bioinformatics 2004, 5:175. 10.1186/1471-2105-5-175.
13. Handorf T., Ebenhöh O., Heinrich R. Expanding metabolic networks: scopes of compounds, robustness, and evolution. J. Mol. Evol. 2005, 61:498-512. 10.1007/s00239-005-0027-1.
14. Harold F.M. The Way of the Cell: Molecules, Organisms and the Or-der of Life 2001, Oxford University Press, Oxford.
15. Heinemann M., Kümmel A., Ruinatscha R., Panke S. In silico genome-scale reconstruction and validation of the Staphylococcus aureus metabolic network. Biotechnol. Bioeng. 2005, 92:850-864.
16. Heinrich R., Rapoport T.A. A linear steady-state treatment of enzymatic chains. General properties, control and effector strength. Eur. J. Biochem. 1974, 42:89-95.
17. Herrgård M.J., Swainston N., Dobson P., Dunn W.B., Arga K.Y., et al. A consensus yeast metabolic network reconstruction obtained from a community approach to systems biology. Nat. Biotechnol. 2008, 26:1155-1160.
18. Hervagault J.F., Canu S. Bistability and irreversible transitions in a simple substrate cycle. J. Theor. Biol. 1987, 127:439-449.
19. Holzhütter H.G. The principle of flux minimization and its application to estimate stationary fluxes in metabolic networks. Eur. J. Biochem. 2004, 271:2905-2922. 10.1111/j.1432-1033.2004.04213.x.
20. Jeong H., Tombor B., Albert R., Oltvai Z.N., Barabási A.L. The large-scale organization of metabolic networks. Nature 2000, 407:651-654.
21. Kacser H., Burns J.A. The control of flux. Biochem. Soc. Trans. 1995, 23:341-366.
22. Kanehisa M., Araki M., Goto S., Hattori M., Hirakawa M., Itoh M., Katayama T., Kawashima S., Okuda S., Tokimatsu T., Yamanishi Y. Kegg for linking genomes to life and the environment. Nucleic Acids Res. 2008, 36:D480-D484. doi.org/10.1093/nar/gkm882.
23. Kitano H. Perspectives on systems biology. New Gener. Comput. 2000, 18:199-216.
24. Klir G.J. Facets of Systems Science 2001, Plenum Press, N. York, NY. 2nd edition.
25. Kun Á., Papp B., Szathmáry E. Computational identification of obligatorily autocatalytic replicators embedded in metabolic networks. Genome Biol. 2008, 9:R51. 10.1186/gb-2008-9-3-r51.
26. Kurata H., Zhao Q., Okuda R., Shimizu K. Integration of enzyme activities into metabolic flux distributions by elementary mode analysis. BMC Syst. Biol. 2007, 1:31. 10.1186/1752-0509-1-31.
27. Letelier J.C., Soto-Andrade J., Guíñez Abarzúa F., Cornish-Bowden A., Cárdenas M.L. Organizational invariance and metabolic closure: analysis in terms of (M,R)-systems. J. Theor. Biol. 2006, 238:949-961. 10.1016/j.jtbi.2005.07.007.
28. Ma H., Sorokin A., Mazein A., Selkov A., Selkov E., Demin O., Goryanin I. The Edinburgh human metabolic network reconstruction and its functional analysis. Mol. Syst. Biol. 2007, 3:135.
29. Ma'ayan A., Cecchi G.A., Wagner J., Ravi Rao A., Iyengar R., Stolovitzky G. Ordered cyclic motifs contribute to dynamic stability in biological and engineered networks. Proc. Natl. Acad. Sci. USA 2008, 105:19235-19240.
30. Morowitz H., Smith E. Energy flow and the organization of life. Complexity 2007, 13:51-59.
31. Newsholme E.A., Crabtree B. Substrate cycles in metabolic regulation and in heat generation. Biochem. Soc. Symp. 1976, 41:61-109.
32. Papin J.A., Price N.D., Wiback S.J., Fell D.A., Palsson B.Ø. Metabolic pathways in the post-genome era. Trends Biochem. Sci. 2003, 28:250-258.
33. Ravasz E., Somera A.L., Mongru D.A., Oltvai Z.N., Barabási A.L. Hierarchical organization of modularity in metabolic networks. Science 2002, 297:1551-1555.
34. Raymond J., Segrè D. The effect of oxygen on biochemical networks and the evolution of complex life. Science 2006, 311:1764-1767.
35. Rohwer J.M., Botha F.C. Analysis of sucrose accumulation in the sugar cane culm on the basis of in vitro kinetic data. Biochem. J. 2006, 358:437-445.
36. Rosen R. Anticipatory Systems 1985, Pergamon Press, N. York, NY.
37. Rosen R. Some comments on systems and system theory. Int. J. Gen. Syst. 1986, 13(1):1-3.
38. Rossell S., van der Weijden C.C., Lindenbergh A., van Tuijl A., Francke C., Bakker B.M., Westerhoff H.V. Unraveling the complexity of flux regulation: a new method demonstrated for nutrient starvation in Saccharomyces cerevisiae. Proc. Natl. Acad. Sci. USA 2006, 103:2166-2171.
39. Sales-Pardo M., Guimera R., Moreira A.A., Amaral L.A. Extracting the hierarchical organization of complex systems. Proc. Natl. Acad. Sci. USA 2007, 104:15224-15229.
40. Schilling C.H., Letscher D., Palsson B.Ø. Theory for the systemic definition of metabolic pathways and their use in interpreting metabolic function from a pathway-oriented perspective. J. Theor. Biol. 2000, 203:229-248. 10.1006/jtbi.2000.1073.
41. Schuster S., Fell D.A., Dandekar T. A general definition of metabolic pathways useful for systematic organization and analysis of complex metabolic networks. Nat. Biotechnol. 2000, 18:326-332.
42. Schwartz J.M., Kanehisa M. Quantitative elementary mode analysis of metabolic pathways: the example of yeast glycolysis. BMC Bioinformatics 2006, 7:186. 10.1186/1471-2105-7-186.
43. Tarjan R.E. Enumeration of the elementary circuits of a directed graph. SIAM J. Comput. 1973, 2:211-216.
44. Teixeira A.P., Alves C., Alves P.M., Carrondo M.J.T., Oliveira R. Hybrid elementary flux analysis/nonparametric modeling: application for bioprocess control. BMC Bioinformatics 2007, 8:30.
45. Thieffry D. Dynamical roles of biological regulatory circuits. Brief. Bioinformatics 2007, 8(4):220-225. 10.1093/bib/bbm028.
46. Ulanowicz R.E. Identifying the structure of cycling in ecosystems. Math. Biosci. 1983, 65:219-237.
47. Wolkenhauer O. Systems biology: the reincarnation of systems theory applied to biology?. Brief. Bioinformatics 2001, 2:258-270.
48. Wright J., Wagner A. Exhaustive identification of steady state cycles in large stoichiometric networks. BMC Syst. Biol. 2008, 2:61. 10.1186/1752-0509-2-61.