메뉴 건너뛰기




Volumn 133, Issue 3, 2008, Pages 377-385

Modeling and stochastic simulation of the Ras/cAMP/PKA pathway in the yeast Saccharomyces cerevisiae evidences a key regulatory function for intracellular guanine nucleotides pools

Author keywords

cAMP; Phosphodiesterase; Protein kinase A; Tau leaping

Indexed keywords

ALGORITHMS; CELLS; ENZYMES; GENE EXPRESSION; NUCLEOTIDES; STOCHASTIC MODELS;

EID: 37449025422     PISSN: 01681656     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.jbiotec.2007.09.019     Document Type: Article
Times cited : (38)

References (39)
  • 1
    • 0031879114 scopus 로고    scopus 로고
    • Stochastic kinetic analysis of developmental pathway bifurcation in phage lambda-infected Escherichia coli cells
    • Arkin A., Ross J., and McAdams H.H. Stochastic kinetic analysis of developmental pathway bifurcation in phage lambda-infected Escherichia coli cells. Genetics 149 (1998) 1633-1648
    • (1998) Genetics , vol.149 , pp. 1633-1648
    • Arkin, A.1    Ross, J.2    McAdams, H.H.3
  • 2
    • 0025201012 scopus 로고    scopus 로고
    • The NF1 locus encodes a protein functionally related to mammalian GAP and yeast Ira proteins
    • Ballester R., Marchuk D., Boquski M., Letcher R., Wigler M., and Collins F. The NF1 locus encodes a protein functionally related to mammalian GAP and yeast Ira proteins. Cell 63 (1999) 851-859
    • (1999) Cell , vol.63 , pp. 851-859
    • Ballester, R.1    Marchuk, D.2    Boquski, M.3    Letcher, R.4    Wigler, M.5    Collins, F.6
  • 3
    • 0024674331 scopus 로고
    • Cell size modulation by CDC25 and RAS2 genes in Saccharomyces cerevisiae
    • Baroni M.D., Martegani E., Monti P., and Alberghina L. Cell size modulation by CDC25 and RAS2 genes in Saccharomyces cerevisiae. Mol. Cell. Biol. 9 (1989) 2715-2723
    • (1989) Mol. Cell. Biol. , vol.9 , pp. 2715-2723
    • Baroni, M.D.1    Martegani, E.2    Monti, P.3    Alberghina, L.4
  • 4
    • 31544465969 scopus 로고    scopus 로고
    • Efficient step size selection for the tau-leaping simulation method
    • Cao Y., Gillespie D.T., and Petzold L.R. Efficient step size selection for the tau-leaping simulation method. J. Chem. Phys. 124 (2006) 044109
    • (2006) J. Chem. Phys. , vol.124 , pp. 044109
    • Cao, Y.1    Gillespie, D.T.2    Petzold, L.R.3
  • 5
    • 0019256754 scopus 로고
    • Small-sized mutants of Saccharomyces cerevisiae
    • Carter B.L., and Sudbery P.E. Small-sized mutants of Saccharomyces cerevisiae. Genetics 96 (1980) 561-566
    • (1980) Genetics , vol.96 , pp. 561-566
    • Carter, B.L.1    Sudbery, P.E.2
  • 6
    • 37449007789 scopus 로고    scopus 로고
    • Cazzaniga, P., Pescini, D., Besozzi, D., Martegani, E., Colombo, S., Mauri G. 2006a. Stochastic modeling of the Ras/cAMP signal transduction pathway in yeast. Abstracts International Conference Computational Methods in Systems Biology. Trento, Italy, October 18-19.
  • 7
    • 84876559742 scopus 로고    scopus 로고
    • Tau leaping stochastic simulation method in P systems
    • Hoogeboom H.J., Pǎun G., Rozenberg G., and Salomaa A. (Eds), LNCS, 4361, 298-313
    • Cazzaniga P., Pescini D., Besozzi D., and Mauri G. Tau leaping stochastic simulation method in P systems. In: Hoogeboom H.J., Pǎun G., Rozenberg G., and Salomaa A. (Eds). Membrane Computing, 7th International Workshop, WMC 2006 (2006), LNCS, 4361, 298-313
    • (2006) Membrane Computing, 7th International Workshop, WMC 2006
    • Cazzaniga, P.1    Pescini, D.2    Besozzi, D.3    Mauri, G.4
  • 8
    • 22944469465 scopus 로고    scopus 로고
    • Binomial distribution based tau-leap accelerated stochastic simulation
    • Chatterjee A., Vlachos D.G., and Katsoulakis M.A. Binomial distribution based tau-leap accelerated stochastic simulation. J. Chem. Phys. 122 (2005) 024112
    • (2005) J. Chem. Phys. , vol.122 , pp. 024112
    • Chatterjee, A.1    Vlachos, D.G.2    Katsoulakis, M.A.3
  • 10
    • 6344256284 scopus 로고    scopus 로고
    • Activation state of the Ras2 protein and glucose-induced signaling in Saccharomyces cerevisiae
    • Colombo S., Ronchetti D., Thevelein J.M., Winderickx J., and Martegani E. Activation state of the Ras2 protein and glucose-induced signaling in Saccharomyces cerevisiae. J. Biol. Chem. 279 (2004) 46715-46722
    • (2004) J. Biol. Chem. , vol.279 , pp. 46715-46722
    • Colombo, S.1    Ronchetti, D.2    Thevelein, J.M.3    Winderickx, J.4    Martegani, E.5
  • 11
  • 13
    • 0001144902 scopus 로고    scopus 로고
    • Efficient exact stochastic simulation of chemical systems with many species and many channels
    • Gibson M.A., and Bruck J. Efficient exact stochastic simulation of chemical systems with many species and many channels. J. Phys. Chem. A 104 (2000) 1876-1889
    • (2000) J. Phys. Chem. A , vol.104 , pp. 1876-1889
    • Gibson, M.A.1    Bruck, J.2
  • 14
    • 33645429016 scopus 로고
    • Exact stochastic simulation of coupled chemical reactions
    • Gillespie D.T. Exact stochastic simulation of coupled chemical reactions. J. Phys. Chem. 81 (1977) 2340-2361
    • (1977) J. Phys. Chem. , vol.81 , pp. 2340-2361
    • Gillespie, D.T.1
  • 15
    • 0017030517 scopus 로고
    • General method for numerically simulating stochastic time evolution of coupled chemical-reactions
    • Gillespie D.T. General method for numerically simulating stochastic time evolution of coupled chemical-reactions. J. Comput. Phys. 22 (1976) 403-434
    • (1976) J. Comput. Phys. , vol.22 , pp. 403-434
    • Gillespie, D.T.1
  • 16
    • 0035933994 scopus 로고    scopus 로고
    • Approximate accelerated stochastic simulation of chemically reacting systems
    • Gillespie D.T. Approximate accelerated stochastic simulation of chemically reacting systems. J. Chem. Phys. 115 (2001) 1716-1733
    • (2001) J. Chem. Phys. , vol.115 , pp. 1716-1733
    • Gillespie, D.T.1
  • 17
    • 0027054644 scopus 로고
    • Phosphorylation of the S. cerevisiae Cdc25 in response to glucose results in its dissociation from Ras
    • Gross E., Goldberg D., and Levitzki A. Phosphorylation of the S. cerevisiae Cdc25 in response to glucose results in its dissociation from Ras. Nature 360 (1992) 762-765
    • (1992) Nature , vol.360 , pp. 762-765
    • Gross, E.1    Goldberg, D.2    Levitzki, A.3
  • 18
    • 22144498043 scopus 로고    scopus 로고
    • Sensitivity analysis of discrete stochastic systems
    • Gunawan R., Cao Y., Petzold L., and Doyle III F.J. Sensitivity analysis of discrete stochastic systems. Biophys. J. 88 (2005) 2530-2540
    • (2005) Biophys. J. , vol.88 , pp. 2530-2540
    • Gunawan, R.1    Cao, Y.2    Petzold, L.3    Doyle III, F.J.4
  • 19
    • 0028365073 scopus 로고
    • Cdc25p, the guanine nucleotide exchange factor for the Ras proteins of Saccharomyces cerevisiae, promotes exchange by stabilizing Ras in a nucleotide-free state
    • Haney S.A., and Broach J.R. Cdc25p, the guanine nucleotide exchange factor for the Ras proteins of Saccharomyces cerevisiae, promotes exchange by stabilizing Ras in a nucleotide-free state. J. Biol. Chem. 269 (1994) 16541-16548
    • (1994) J. Biol. Chem. , vol.269 , pp. 16541-16548
    • Haney, S.A.1    Broach, J.R.2
  • 20
    • 0037135134 scopus 로고    scopus 로고
    • Systematic identification of pathways that couple cell growth and division in yeast
    • Jorgensen P., Nishikawa J.L., Breitkreutz B.J., and Tyers M. Systematic identification of pathways that couple cell growth and division in yeast. Science 297 (2002) 395-400
    • (2002) Science , vol.297 , pp. 395-400
    • Jorgensen, P.1    Nishikawa, J.L.2    Breitkreutz, B.J.3    Tyers, M.4
  • 21
    • 0032546533 scopus 로고    scopus 로고
    • Kinetic analysis by fluorescence of the interaction between Ras and the catalytic domain of the guanine nucleotide exchange factor Cdc25Mm
    • Lenzen C., Cool R.H., Prinz H., Kuhlmann J., and Wittinghofer A. Kinetic analysis by fluorescence of the interaction between Ras and the catalytic domain of the guanine nucleotide exchange factor Cdc25Mm. Biochemistry 37 (1998) 7420-7430
    • (1998) Biochemistry , vol.37 , pp. 7420-7430
    • Lenzen, C.1    Cool, R.H.2    Prinz, H.3    Kuhlmann, J.4    Wittinghofer, A.5
  • 22
    • 33846097600 scopus 로고    scopus 로고
    • Dynamics of single-cell gene expression
    • Longo D., and Hasty J. Dynamics of single-cell gene expression. Mol. Syst. Biol. 2 64 (2006) 1-10
    • (2006) Mol. Syst. Biol. , vol.2 , Issue.64 , pp. 1-10
    • Longo, D.1    Hasty, J.2
  • 23
    • 0032896365 scopus 로고    scopus 로고
    • The PDE1-encoded low-affinity phosphodiesterase in the yeast Saccharomyces cerevisiae has a specific function in controlling agonist-induced cAMP signaling
    • Ma P., Wera S., Van Dijck P., and Thevelein J.M. 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 (1999) 91-104
    • (1999) Mol. Biol. Cell. , vol.10 , pp. 91-104
    • Ma, P.1    Wera, S.2    Van Dijck, P.3    Thevelein, J.M.4
  • 25
    • 10044260032 scopus 로고    scopus 로고
    • Modeling and simulation of biological systems with stochasticity
    • Meng T.C., Somani S., and Dhar P. Modeling and simulation of biological systems with stochasticity. In Silico Biol. 4 (2004) 0024
    • (2004) In Silico Biol. , vol.4 , pp. 0024
    • Meng, T.C.1    Somani, S.2    Dhar, P.3
  • 26
    • 0037338995 scopus 로고    scopus 로고
    • Cyclic AMP mediates the cell cycle dynamics of energy metabolism in Saccharomyces cerevisiae
    • Müller D., Exler S., Aguilera-Vázquez L., Guerrero-Martín E., and Reuss M. Cyclic AMP mediates the cell cycle dynamics of energy metabolism in Saccharomyces cerevisiae. Yeast 20 (2003) 351-367
    • (2003) Yeast , vol.20 , pp. 351-367
    • Müller, D.1    Exler, S.2    Aguilera-Vázquez, L.3    Guerrero-Martín, E.4    Reuss, M.5
  • 28
    • 0023442858 scopus 로고
    • Rigorous feedback control of cAMP levels in Saccharomyces cerevisiae
    • Nikawa J., Cameron S., Toda T., Ferguson K.M., and Wigler M. Rigorous feedback control of cAMP levels in Saccharomyces cerevisiae. Genes. Dev. 1 (1987) 931-937
    • (1987) Genes. Dev. , vol.1 , pp. 931-937
    • Nikawa, J.1    Cameron, S.2    Toda, T.3    Ferguson, K.M.4    Wigler, M.5
  • 30
    • 33846498355 scopus 로고    scopus 로고
    • Efficient stochastic sensitivity analysis of discrete event systems
    • Plyasunov S., and Arkin A.P. Efficient stochastic sensitivity analysis of discrete event systems. J. Comput. Phys. 221 (2007) 724-738
    • (2007) J. Comput. Phys. , vol.221 , pp. 724-738
    • Plyasunov, S.1    Arkin, A.P.2
  • 31
    • 0033745888 scopus 로고    scopus 로고
    • Glucose-induced cAMP signalling in yeast requires both a G-protein coupled receptor system for extracellular glucose detection and a separable hexose kinase-dependent sensing process
    • Rolland F., de Winde J., Lemaire K., Boles E., Thevelein J.M., and Winderickx J. Glucose-induced cAMP signalling in yeast requires both a G-protein coupled receptor system for extracellular glucose detection and a separable hexose kinase-dependent sensing process. Mol. Microbiol. 38 (2000) 348-358
    • (2000) Mol. Microbiol. , vol.38 , pp. 348-358
    • Rolland, F.1    de Winde, J.2    Lemaire, K.3    Boles, E.4    Thevelein, J.M.5    Winderickx, J.6
  • 32
    • 0035938253 scopus 로고    scopus 로고
    • Role of guanine nucleotides in the regulation of the Ras/cAMP pathway in Saccharomyces cerevisiae
    • Rudoni S., Colombo S., Coccetti P., and Martegani E. Role of guanine nucleotides in the regulation of the Ras/cAMP pathway in Saccharomyces cerevisiae. Biochim. Biophys. Acta 1538 (2001) 181-189
    • (2001) Biochim. Biophys. Acta , vol.1538 , pp. 181-189
    • Rudoni, S.1    Colombo, S.2    Coccetti, P.3    Martegani, E.4
  • 33
    • 33645130011 scopus 로고    scopus 로고
    • Glucose signaling in Saccharomyces cerevisiae
    • Santangelo G.M. Glucose signaling in Saccharomyces cerevisiae. Microbiol. Mol. Bio. Rev. 70 1 (2006) 253-282
    • (2006) Microbiol. Mol. Bio. Rev. , vol.70 , Issue.1 , pp. 253-282
    • Santangelo, G.M.1
  • 34
    • 0028675642 scopus 로고
    • Signal transduction in yeast
    • Thevelein J.M. Signal transduction in yeast. Yeast 10 (1994) 1753-1790
    • (1994) Yeast , vol.10 , pp. 1753-1790
    • Thevelein, J.M.1
  • 36
    • 0032835137 scopus 로고    scopus 로고
    • Novel sensing mechanisms and targets for the cAMP-protein kinase A pathway in the yeast Saccharomyces cerevisiae
    • Thevelein J.M., and de Winde J.H. Novel sensing mechanisms and targets for the cAMP-protein kinase A pathway in the yeast Saccharomyces cerevisiae. Mol. Microbiol. 33 (1999) 904-918
    • (1999) Mol. Microbiol. , vol.33 , pp. 904-918
    • Thevelein, J.M.1    de Winde, J.H.2
  • 37
    • 3142543968 scopus 로고    scopus 로고
    • Binomial leap methods for simulating stochastic chemical kinetics
    • Tian T., and Burrage K. Binomial leap methods for simulating stochastic chemical kinetics. J. Chem. Phys. 121 (2004) 10356-10364
    • (2004) J. Chem. Phys. , vol.121 , pp. 10356-10364
    • Tian, T.1    Burrage, K.2
  • 38
    • 0023658335 scopus 로고
    • Three different genes in S. cerevisiae encode the catalytic subunits of the cAMP-dependent protein kinase
    • Toda T., Cameron S., Sass P., Zoller M., and Wigler M. Three different genes in S. cerevisiae encode the catalytic subunits of the cAMP-dependent protein kinase. Cell 50 (1987) 277-287
    • (1987) Cell , vol.50 , pp. 277-287
    • Toda, T.1    Cameron, S.2    Sass, P.3    Zoller, M.4    Wigler, M.5
  • 39
    • 3142577523 scopus 로고    scopus 로고
    • Stochastic approaches for modelling in vivo reactions
    • Turner T.E., Schnell S., and Burrage K. Stochastic approaches for modelling in vivo reactions. Comput. Biol. Chem. 28 (2004) 165-178
    • (2004) Comput. Biol. Chem. , vol.28 , pp. 165-178
    • Turner, T.E.1    Schnell, S.2    Burrage, K.3


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.