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Integration of metabolic and signaling networks

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Systems Biology

Part of the book series: Topics in Current Genetics ((TCG,volume 13))

Abstract

This contribution addresses the construction of mathematical models that provide a combined description of metabolic and regulatory processes within cells. In the first part of the article, strategies for reconstruction of metabolic and signaling networks are outlined followed by a discussion of their characteristic properties. The second part focuses on the development of integrated models of metabolism and signal transduction. The case of yeast cyclic AMP (cAMP) signaling and its interaction with energy metabolism and elements of the cell cycle machinery is used to exemplify this approach.

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References

  • 1. Aebersold R, Mann M (2003) Mass spectrometry-based proteomics. Nature 422:198-207

    Article  PubMed  Google Scholar 

  • 2. Altintas MM, Kirdar B, Onsan ZI, Ulgen KO (2001) Plasmid stability in a recombinant S. cerevisiae strain secreting a bifunctional fusion protein. J Chem Technol Biotechnol 76:612-618

    Article  Google Scholar 

  • 3. Anghileri P, Branduardi P, Sternieri F, Monti P, Visintin R, Bevilacqua A, Alberghina L, Martegani E, Baroni MD (1999) Chromosome separation and exit from mitosis in budding yeast: Dependence on growth revealed by cAMP-mediated inhibition. Exp Cell Res 250:510-523

    Article  PubMed  Google Scholar 

  • 4. Barabási A-L, Oltvai ZN (2004) Network biology: understanding the cell's functional organization. Nat Genet 5:101-113

    Article  Google Scholar 

  • 5. Baroni MD, Monti P, Alberghina L (1994) Repression of growth-regulated G1 cyclin expression by cyclic AMP in budding yeast. Nature 371:339-342

    Article  PubMed  Google Scholar 

  • 6. Bolte M, Dieckhoff P, Krause C, Braus GH, Irniger S (2003) Synergistic inhibition of APC/C by glucose and activated Ras proteins can be mediated by each of the Tpk1-3 proteins in Saccharomyces cerevisiae. Microbiology (UK) 149:1205-1216

    Google Scholar 

  • 7. Brightman FA, Fell DA (2000) Differential feedback regulation of the MAPK cascade underlies the quantitative differences in EGF and NGF signaling in PC12 cells. FEBS Lett 482:169-174

    Article  PubMed  Google Scholar 

  • 8. Buchholz A, Hurlebaus J, Wandrey C, Takors R (2002) Metabolomics: quantification of intracellular metabolite dynamics. Biomol Eng 19:5-15

    Article  PubMed  Google Scholar 

  • 9. Buziol S, Bashir I, Baumeister A, Claassen W, Noisommit-Rizzi N, Mailinger W, Reuss M (2002) New bioreactor-coupled rapid stopped-flow sampling technique for measurements of metabolite dynamics on a subsecond time scale. Biotechnol Bioeng 80:632-636

    Article  PubMed  Google Scholar 

  • 10. Chen KC, Csikasz-Nagy A, Gyorffy B, Val J, Novak B, Tyson JJ (2000) Kinetic analysis of a molecular model of the budding yeast cell cycle. Mol Biol Cell 11:369-391

    PubMed  Google Scholar 

  • 11. Cross FR (2003) Two redundant oscillatory mechanisms in the yeast cell cycle. Dev Cell 4:741-752

    Article  PubMed  Google Scholar 

  • 12. Domach MM, Shuler ML (1984) A finite representation model for an asynchronous culture of Escherichia coli. Biotechnol Bioeng 26:877-884

    Article  Google Scholar 

  • 13. Eéka A, Hawoong J, Barabási A-L (2000) Error and attack tolerance of complex networks. Nature 406:378-382

    Article  PubMed  Google Scholar 

  • 14. Engelberg D, Simchen G, Levitzki A (1990) In vitro reconstitution of Cdc25-regulated Saccharomyces cerevisiae adenylyl cyclase and its kinetic properties. EMBO J 9:641-651

    PubMed  Google Scholar 

  • 15. Francois J, Parrou JL (2001) Reserve carbohydrates metabolism in the yeast Saccharomyces cerevisiae. FEMS Microbiol Rev 25:125-145

    Article  PubMed  Google Scholar 

  • 16. Futcher B (1999) Cell cycle synchronization. Methods Cell Sci 21:79-86

    Article  PubMed  Google Scholar 

  • 17. Ghaemmaghami S, Huh W, Bower K, Howson RW, Belle A, Dephoure N, O'Shea EK, Weissman JS (2003) Global analysis of protein expression in yeast. Nature 425:737-741

    Google Scholar 

  • 18. Goodacre R, Vaidyanathan S, Dunn WB, Harrigan GG, Kell DB (2004) Metabolomics by numbers: acquiring and understanding global metabolite data. Trends Biotechnol 22:245-252

    Article  PubMed  Google Scholar 

  • 19. Gross E, Goldberg D, Levitzki A (1992) Phosphorylation of the Saccharomyces cerevisiae Cdc25 in response to glucose results in its dissociation from Ras. Nature 360:762-765

    Article  PubMed  Google Scholar 

  • 20. Hall DD, Markwardt DD, Parviz F, Heideman W (1998) Regulation of the Cln3-Cdc28 kinase by cAMP in Saccharomyces cerevisiae. EMBO J 17:4370-4378

    Article  PubMed  Google Scholar 

  • 21. Hartwell LH, Hopfield JJ, Leibler S, Murray AW (1999) From molecular to modular cell biology. Nature 402:C47-C52

    Article  PubMed  Google Scholar 

  • 22. Heinrich R, Neel BG, Rapoport T (2002) Mathematical models of protein kinase signal transduction. Mol Cell 9:957-970

    Article  PubMed  Google Scholar 

  • 23. Henson MA, Müller D, Reuss M (2002) Cell population modelling of yeast glycolytic oscillations. Biochem J 368:433-446

    Article  PubMed  Google Scholar 

  • 24. Huh WK, Falvo JV, Gerke LC, Carroll AS, Howson RW, Weissman JS, O'Shea EK (2003) Global analysis of protein localization in budding yeast. Nature 425:686-691

    Article  PubMed  Google Scholar 

  • 25. Kacmar J, Zamamiri A, Carlson R, Abu-Absi NR, Srienc F (2004) Single-cell variability in growing Saccharomyces cerevisiae cell populations measured with automated flow cytometry. J Biotechnol 109:253-268

    Article  Google Scholar 

  • 26. Kholodenko BN, Demin OV, Moehren G, Hoek JB (2000) Quantification of short term signaling by the epidermal growth factor receptor. Biol Chem 274:30169-30181

    Google Scholar 

  • 27. Kitano H (2003) Cancer robustness: tumour tactics. Nature 426:125

    Article  PubMed  Google Scholar 

  • 28. Kromenaker SJ, Srienc F (1994) Cell-cycle kinetics of the accumulation of heavy and light-chain immunoglobulin proteins in a mouse hybridoma cell-line. Cytotechnology 14:205-218

    Article  PubMed  Google Scholar 

  • 29. Levsky JM, Singer RH (2003) Gene expression and the myth of the average cell. Trends Cell Biol 13:4-6

    Article  PubMed  Google Scholar 

  • 30. Ma P, Wera S, Van Dijck P, Thevelein JM (1999) The PDE1-encoded low-affinity phosphodiesterase in the yeast Saccharomyces cerevisiae has a specific function in controlling agonist-induced cAMP signaling. Mol Biol Cell 10:91-104

    PubMed  Google Scholar 

  • 31. Mann M, Jensen ON (2003) Proteomic analysis of post-translational modifications. Nat Biotechnol 21:255-261

    Article  PubMed  Google Scholar 

  • 32. Massague J (2002) How cells read TGF-beta signals. Nat Rev Mol Cell Biol 3:169-178

    Google Scholar 

  • 33. Mauch K, Buziol S, Schmid JW, Reuss M (2002) Computer aided design of metabolic networks. AIChE Symposium Series 98:82-91

    Google Scholar 

  • 34. Melton L (2004) Proteomics in multiplex. Nature 429:101-107

    Article  PubMed  Google Scholar 

  • 35. Müller D, Exler S, Aguilera-Vázquez L, Guerrero-Martín E, Reuss M (2003) Cyclic AMP mediates the cell cycle dynamics of energy metabolism in Saccharomyces cerevisiae. Yeast 20:351-367

    Article  PubMed  Google Scholar 

  • 36. Nikawa J, Cameron S, Toda T, Ferguson KM, Wigler M (1987) Rigorous feedback control of cAMP levels in Saccharomyces cerevisiae. Genes Dev 1:931-937

    PubMed  Google Scholar 

  • 37. Noble D (2002) Modeling the heart - from genes to cells to the whole organ. Science 295:1678-1682

    Article  PubMed  Google Scholar 

  • 38. Pardo LA, Lazo PS, Ramos S (1993) Activation of adenylate cyclase in Cdc25 mutants of Saccharomyces cerevisiae. FEBS Lett 319:237-243

    Article  PubMed  Google Scholar 

  • 39. Puchalka J, Kierzek AM (2004) Bridging the gap between stochastic and deterministic regimes in the kinetic simulations of the biochemical reaction networks. Biophys J 86:1357-1372

    PubMed  Google Scholar 

  • 40. Ravasz E, Somera L, Mongru DA, Oltvai ZN, Barabási A-L (2002) Hierarchical organization of modularity in metabolic networks. Science 297:1551-1555

    Article  PubMed  Google Scholar 

  • 41. Rizzi M, Baltes M, Theobald U, Reuss M (1997) In vivo analysis of metabolic dynamics in Saccharomyces cerevisiae. 2. Mathematical model. Biotechnol Bioeng 55:592-608

    Article  Google Scholar 

  • 42. Schaefer U, Boos W, Takors R, Weuster-Botz D (1999) Automated sampling device for monitoring intracellular metabolite dynamics. Anal Biochem 270:88-96

    Article  PubMed  Google Scholar 

  • 43. Schubert W (2003) Topological proteomics, toponomics, MELK-technology. Adv Biochem Eng Biotechnol 83:189-209

    PubMed  Google Scholar 

  • 44. Silljé HH, ter Schure EG, Rommens AJ, Huls PG, Woldringh CL, Verkleij AJ, Boonstra J, Verrips CT (1997) Effects of different carbon fluxes on G1 phase duration, cyclin expression, and reserve carbohydrate metabolism in Saccharomyces cerevisiae. J Bacteriol 179:6560-6565

    PubMed  Google Scholar 

  • 45. Slepchenko BM, Schaff JC, Carson JH, Loew LM (2002) Computational cell biology: Spatiotemporal simulation of cellular events. Annu Rev Biophys Biomolec Struct 31:423-441

    Article  Google Scholar 

  • 46. Smith DM, Gao G, Zhang X, Wang G, Dou QP (2000) Regulation of tumor cell apoptotic sensitivity during the cell cycle. Int J Mol Med 6:503-507

    PubMed  Google Scholar 

  • 47. Smith ME, Dickinson JR, Wheals AE (1990) Intracellular and extracellular levels of cyclic AMP during the cell cycle of Saccharomyces cerevisiae. Yeast 6:53-60

    Article  PubMed  Google Scholar 

  • 48. Takahashi K, Kaizu K, Hu B, Tomita M (2004) A multi-algorithm, multi-timescale method for cell simulation. Bioinformatics 20:538-546

    Article  PubMed  Google Scholar 

  • 49. ten Dijke P, Miyazono K, Heldin CH (2000) Signaling inputs converge on nuclear effectors in TGF-beta signaling. Trends Biochem Sci 25:64-70

    Article  PubMed  Google Scholar 

  • 50. Theobald U, Mailinger W, Reuss M, Rizzi M (1993) In vivo analysis of glucose-induced fast changes in yeast adenine nucleotide pool applying a rapid sampling technique. Anal Biochem 214:31-37

    Article  PubMed  Google Scholar 

  • 51. Thevelein JM, de Winde JH (1999) Novel sensing mechanisms and targets for the cAMP-protein kinase A pathway in the yeast Saccharomyces cerevisiae. Mol Microbiol 33:904-918

    Article  PubMed  Google Scholar 

  • 52. Tokiwa G, Tyers M, Volpe T, Futcher B (1994) Inhibition of G1 cyclin activity by the Ras/cAMP pathway in yeast. Nature 371:342-345

    Article  PubMed  Google Scholar 

  • 53. Vaseghi S, Baumeister A, Rizzi M, Reuss M (1999) In vivo dynamics of the pentose phosphate pathway in Saccharomyces cerevisiae. Metab Eng 1:128-140

    Article  PubMed  Google Scholar 

  • 54. Vasudeva K, Bhalla US (2004) Adaptive stochastic-deterministic chemical kinetic simulations. Bioinformatics 20:78-84

    Article  PubMed  Google Scholar 

  • 55. Weckwerth W (2003) Metabolomics in systems biology. Annu Rev Plant Biol 54:669-689

    Article  PubMed  Google Scholar 

  • 56. You LC, Hoonlor A, Yin J (2003) Modeling biological systems using Dynetica - a simulator of dynamic networks. Bioinformatics 19:435-436

    Article  PubMed  Google Scholar 

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Correspondence to Dirk Müller .

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Lila Alberghina H.V. Westerhoff

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Müller, D., Aguilera-Vázquez, L., Reuss, M., Mauch, K. Integration of metabolic and signaling networks. In: Alberghina, L., Westerhoff, H. (eds) Systems Biology. Topics in Current Genetics, vol 13. Springer, Berlin, Heidelberg. https://doi.org/10.1007/b136529

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