Geodesic
Mathematical Modelling Plant Signalling Networks
D. Muraro1, 2 ; H.M. Byrne1, 3, 4 ; J.R. King1, 4 ; M.J. Bennett1
1 Centre for Plant Integrative Biology, School of Biosciences, University of Nottingham Sutton Bonington Campus, Loughborough LE12 5RD, UK
2 Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, OX3 9DS, UK
3 Oxford Centre for Collaborative Applied Mathematics, Mathematical Institute, Oxford, OX1 3LB, UK
4 School of Mathematical Sciences, University of Nottingham, University Park Nottingham NG7 2RD, UK
Mathematical modelling of natural phenomena, Tome 8 (2013) no. 4, pp. 5-24

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During the last two decades, molecular genetic studies and the completion of the sequencing of the Arabidopsis thaliana genome have increased knowledge of hormonal regulation in plants. These signal transduction pathways act in concert through gene regulatory and signalling networks whose main components have begun to be elucidated. Our understanding of the resulting cellular processes is hindered by the complex, and sometimes counter-intuitive, dynamics of the networks, which may be interconnected through feedback controls and cross-regulation. Mathematical modelling provides a valuable tool to investigate such dynamics and to perform in silico experiments that may not be easily carried out in a laboratory. In this article, we firstly review general methods for modelling gene and signalling networks and their application in plants. We then describe specific models of hormonal perception and cross-talk in plants. This mathematical analysis of sub-cellular molecular mechanisms paves the way for more comprehensive modelling studies of hormonal transport and signalling in a multi-scale setting.
DOI : 10.1051/mmnp/20138402

D. Muraro 1, 2 ; H.M. Byrne 1, 3, 4 ; J.R. King 1, 4 ; M.J. Bennett 1

1 Centre for Plant Integrative Biology, School of Biosciences, University of Nottingham Sutton Bonington Campus, Loughborough LE12 5RD, UK
2 Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, OX3 9DS, UK
3 Oxford Centre for Collaborative Applied Mathematics, Mathematical Institute, Oxford, OX1 3LB, UK
4 School of Mathematical Sciences, University of Nottingham, University Park Nottingham NG7 2RD, UK 
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D. Muraro; H.M. Byrne; J.R. King; M.J. Bennett. Mathematical Modelling Plant Signalling Networks. Mathematical modelling of natural phenomena, Tome 8 (2013) no. 4, pp. 5-24. doi: 10.1051/mmnp/20138402

[1] R. Albert, A.L. Barabási Rev. Mod. Phys. 2002 47

[2] U. Alon. An introduction to systems biology: design principles of biological circuits. Boca Raton: Chapman Hall/CRC, 2007.

[3] U. Alon Nat. Rev. Genet. 2007 450 461

[4] A. Arkin, J. Ross, H.H. Mcadams Genetics 1998 1633 48

[5] L.R. Band, S. Ubeda-Tomas, R.J. Dyson, A.M. Middleton, T.C. Hodgman, M.R. Owen, O.E. Jensen, M.J. Bennett, J.R. King. Growth-induced hormone dilution can explain the dynamics of plant root cell elongation. Published online before print PNAS (2012), doi: 10.1073/pnas.1113632109.

[6] M. Bansal, D. Di Bernardo IET Syst. Biol. 2007 306 312

[7] A.L. Barabási, E. Bonabeau Scientific American 2003 60 69

[8] A.F. Bartholomay Bull. Math. Biophysics 1958 175 90

[9] A.F. Bartholomay Bull. Math. Bio. 1959 363 373

[10] G. Batt, M. Page, I. Cantone, G. Goessler, P. Monteiro, H. De Jong Bioinformatics 2010 i603 i610

[11] M.J. Beal, F. Falciani, Z. Ghahramani, C. Rangel, D.L. Wild Bioinformatics 2005 349 356

[12] K. Bleakley, G. Biau, J.P. Vert Bioinformatics 2007 23

[13] I. Blilou, J. Xu, M. Wildwater, V. Willemsen, I. Paponov, J. Friml, R. Heidstra, M. Aida, K. Palme, B. Scheres Nature 2005 39 44

[14] S. Cavalcante, D.J. Gauthier, J.E.S. Socolar, R. Zhang Phil. Trans. R. Soc. A 2010 368

[15] V. Chandrasekaran, P.A. Parrilo, A.S. Willsky. Latent Variable Graphical Model Selection via Convex Optimization. to appear in The Annals of Statistics.

[16] J. Cheng, R. Greiner, J. Kelly, D. A. Bell, W. Liu Artif. Intell. 2002 43 90

[17] J. Chiquet, Y. Grandvalet, C. Ambroise Inferring multiple graphical structures Stat. and Comput. 2011 537 553

[18] B. Chow, P. Mccourt Genes Dev. 2006 1998 2008

[19] F. Crick Nature 1970 420 422

[20] D. Deamer EMBO Rep. 2009 S1 S4

[21] H. De Jong J. Comput. Biol. 2002 67 103

[22] R. Dello Ioio, K. Nakamura, L. Moubayidin, S. Perilli, M. Taniguchi, M.T. Morita, T. Aoyama, P. Costantino, S. Sabatini Nature 2008 1380 1384

[23] I. De Smet, T. Tetsumura, B. Derybel, N. Frei Dit Frey, L. Laplaze, I. Casimiro, R. Swarup, M. Naudts, S. Vanneste, D. Audenaert, D. Inzé, M. Bennett, T. Beeckman Development 2007 681

[24] N. Dharmasiri, S. Dharmasiri, M. Estelle Nature 2005 441 445

[25] J. Díaz, E.R. Álvarez-Buylla Chaos 2006 023112

[26] L. Dupuy, M. Vignes, B.M. Mckenzie, P.J. White Plant Cell Environ. 2010 358 69

[27] R. Edwards Physica D 2000 165 199

[28] M.B. Elowitz, S. Leibler Nature 2000 335 338

[29] C. Espinosa-Soto, P. Padilla-Longoria, E.R. Alvarez-Buylla Plant Cell. 2004 2923 39

[30] H. Ezura, N.P. Harberd Planta 1995 301 5

[31] N. Friedman, M. Linial, I. Nachman, D. Pe’Er J. Comput. Biol. 2000 601 20

[32] N. Friedman, K. Murphy, S. Russell. Learning the structure of dynamic probabilistic networks. UAI Proc. Morgan Kaufman, 1998.

[33] N. Friedman, S. Vardi, M. Ronen, U. Alon, J. Stavans PLoS Biol. 2005 e238

[34] H. Fujita, K. Toyokura, K. Okada, M. Kawaguchi PLoS ONE 2011 e18243

[35] S. Gazzarrini, P. Mccourt Ann. Bot. 2003 605 12

[36] T. Genoud, M.B. Trevino Santa Cruz, J.P. Métraux Plant Physiol. 2001 1430 1437

[37] D.T. Gillespie J. Phys. Chem. 1977 2340 2361

[38] D.T. Gillespie Annu. Rev. Phys. Chem. 2007 35 55

[39] D.T. Gillespie J. Chem. Phys. 2001 1716 1733

[40] L. Glass, S. Kauffman J. Theor. Biol. 1973 103 129

[41] B.C. Goodwin Adv. Enzyme Regul. 1965 425 428

[42] S.P. Gordon, V.S. Chickarmane, C. Ohno, E.M. Meyerowitz PNAS 2009 16529 16534

[43] V.A. Grieneisen, J. Xu, A.F. Marée, P. Hogeweg, B. Scheres Nature 2007 1008 1013

[44] J.S. Griffith J. Theor. Biol. 1968 202 208

[45] M. Grzegorczyk, D. Husmeier Bioinformatics 2011 693 699

[46] M.L. Guerriero, A. Pokhilko, A.P. Fernández, K.J. Halliday, A.J. Millar, J. Hillston J. R. Soc. Interface 2011 1 19

[47] G. Hagen, T. Guilfoyle Plant Mol. Biol. 2002 373 385

[48] A.V. Hill J. Physiol. iv vii

[49] V.A. Huynh-Thu, A. Irrthum, L. Wehenkel, P. Geurts PLoS ONE 2010 e12776

[50] A.D. Johnson, B.J. Meyer, M. Ptashne PNAS 1979 5061 5065

[51] Y.H. Kang, V. Kirik, M. Hulskamp, K.H. Nam, K. Hagely, M.M. Lee, J. Schiefelbein Plant Cell 2009 1080 1094

[52] G. Karlebach, R. Shamir Nat. Rev. Mol. Cell Biol. 2008 770 80

[53] S. Kauffman J. Theor. Biol. 1969 437 467

[54] S. Kauffman, C. Peterson, B. Samuelsson, C. Troein PNAS 2003 14796 9

[55] S. Kepinski, O. Leyser Nature 2005 436 437

[56] B.N. Kholodenko, A. Kiyatkin, F.J. Bruggeman, E. Sontag, H.V. Westerhoff, J.B. Hoek PNAS 2002 12841 12846

[57] T.R. Kiehl, R.M. Mattheyses, M.K. Simmons Bioinformatics 2004 316 322

[58] E.M. Kramer, M.J. Bennett Trends Plant Sci. 2006 382 386

[59] Yu.A. Kuznetsov Elements of Applied Bifurcation Theory. Springer, 3rd edition, 2004.

[60] G. Lahav, N. Rosenfeld, A. Sigal, N. Geva-Zatorsky, A.J. Levine, M.B. Elowitz, U. Alon Nature Genet. 2004 147 150

[61] L. Laplaze, E. Benkova, I. Casimiro, L. Maes, S. Vanneste, R. Swarup, D. Weijers, V. Calvo, B. Parizot, M. Begoña Herrera-Rodriguez, R. Offringa, N. Graham, P. Doumas, J. Friml, D. Bogusz, T. Beeckman, M. Bennett Plant Cell 2007 3889 3900

[62] S. Lèbre, J. Becq, F. Devaux, M.P.H. Stumpf, G. Lelandais BMC Syst. Biol. 2010 130

[63] S.H. Lee, D.M. Reid Can. J. Bot. 1997 501 8

[64] P. Li, C. Zhang, E.J. Perkins, P. Gong, Y. Deng BMC Bioinformatics 2007 S13

[65] S. Liang, S. Fuhrman, R. Somogyi PSB 1998 18 29

[66] J. Liu, S. Mehdi, J. Topping, P. Tarkowski, K. Lindsey Mol. Syst. Biol. 2010

[67] J.C.W. Locke, L. Kozma-Bognár, P.D. Gould, B. Feheŕ, E. Kevei, F. Nagy, M.S. Turner, A. Hall, A.J. Millar Mol. Syst. Biol. 2006 59

[68] A. Madar, A. Greenfield, E. Vanden-Eijnden, R. Bonneau PLoS ONE 2010 3

[69] D. Marbach, R.J. Prill, T. Schaffter, C. Mattiussi, D. Floreano, G. Stolovitzky PNAS 2010 6286 6291

[70] D. Marbach, J. Costello, R. K"Uffner, N. Vega, R. Prill, D. Camacho, K. Allison, M. Kellis, J. Collins, G. Stolovitzky Nature Methods 2012 796 804

[71] A.A. Margolin, I. Nemenman, K. Basso, C. Wiggins, G. Stolovitzky, R. Dalla Favera, A. Califano BMC Bioinformatics 2006 S7

[72] H. Meinhardt J. Cell Sci. 1977 117 139

[73] A.M. Middleton, J.R. King, M.J. Bennett, M.R. Owen B. Math. Biol. 2010 1383 1407

[74] A.M. Middleton, S. Úbeda-Tomás, J. Griffiths, T. Holman, P. Hedden, S.G. Thomas, A.L. Phillips, M.J. Holdsworth, M.J. Bennett, J.R. King, M.R. Owen. Mathematical modeling elucidates the role of transcriptional feedback in gibberellin signaling. Published online before print PNAS, April 20, 2012, doi: 10.1073/pnas.1113666109.

[75] M.A. Moreno-Risueno, J.M. Van Norman, A. Moreno, J. Zhang, S.E. Ahnert, P.N. Benfey Science 2010 1306

[76] L. Moubayidin, R. Di Mambro, S. Sabatini Trends Plant Sci. 2009 557 562

[77] L. Moubayidin, S. Perilli, R. Dello Ioio, R. Di Mambro, P. Costantino, S. Sabatini Curr. Biol. 2010 1138 1143

[78] D. Muraro, H. Byrne, J. King, U. Voß, J. Kieber, M. Bennett J. Theor. Biol. 2011 152 167

[79] K. Murphy, S. Mian. Modelling gene expression data using dynamic Bayesian networks. Technical Report, University of California, Berkeley, 1999.

[80] C.J. Needham, I.W. Manfield, A.J. Bulpitt, P.M. Gilmartin, D.R. Westhead BMC Syst. Biol. 2009 85

[81] J.B. Passioura, S.C. Fry Aust. J. Plant Physiol. 1992 565 576

[82] J. Paulsson Phys. Life Rev. 2005 157 175

[83] C.A. Penfold, D.L. Wild Interface Focus 2011 857 870

[84] H. Rabitz, M. Kramer, D. Dacol Annu. Rev. Phys. Chem. 1983 419 461

[85] A. Rau, F. Jaffrézic, J.L. Foulley, R.W. Doerge Stat. Appl. Genet. Mol. Biol. 2010 1

[86] J. Rice, Y. Tu, G. Stolovitzky Bioinformatics 2005 765 773

[87] N. Rosenfeld, M.B. Elowitz, U. Alon J. Mol. Biol. 2002 785 93

[88] K. Ruzicka, M. Simaskova, J. Duclercq, J. Petrasek, E. Zazimalova, S. Simon, J. Friml, M.C.E. Van Montagu, E. Benkova PNAS 2009 4284 4289

[89] L.A. Saddic, B. Huvermann, S. Bezhani, Y. Su, C.M. Winter, C.S. Kwon, R.P. Collum, D. Wagner Development 2006 1673 1682

[90] I. Shmulevich, E. R. Dougherty. Probabilistic Boolean Networks: The Modeling and Control of Gene Regulatory Networks. SIAM Press, 2009.

[91] I. Shmulevich, E.R. Dougherty, S. Kim, W. Zhang Bioinformatics 2002 261 274

[92] F. Skoog, C.O. Miller Syrup. Soc. Exp. Biol. 1957 118 130

[93] A.N. Stepanova, J. Yun, A.V. Likhacheva, J.M. Alonso Plant Cell. 2007 2169 85

[94] T.P. Sun, F. Gubler Annu. Rev. Plant Biol. 2004 197 223

[95] R. Swarup, P. Perry, D. Hagenbeek, D. Van Der Straeten, G.T.S. Beemster, G. Sandberg, R. Bhalerao, K. Ljung, M.J. Bennett Plant Cell 2007 2186 2196

[96] L. Taiz, E. Zeiger. Plant Physiology, Fifth Edition. Sinauer Associates Inc., Publishers, Sunderland, Massachussets U.S.A., 2010.

[97] R. Thomas J. Theor. Biol. 1973 563 585

[98] R. Thomas, R. D’Ari. Biological Feedback. CRC-Press, Boca Raton, Florida, 1990.

[99] Q. Tian, N.J. Uhlir, J.W. Reed Plant Cell 2002 301 319

[100] S.B. Tiwari, G. Hagan, T. Guilfoyle The roles of Auxin response factor domains in Auxin-responsive transcription Plant Cell 2003 533 543

[101] K. Tsuda, Y. Ito, Y. Sato, N. Kurata Plant Cell 2011 4368 4381

[102] A.M. Turing Philos. Trans. R. Soc. London B 1952 37 72

[103] J.J. Tyson J. Math. Biol. 1975 311 315

[104] S. Úbeda-Tomás, G. Beemster, M. Bennett Trends Plant Sci. 2012 326 331

[105] M. Ueguchi-Tanaka, M. Ashikari, M. Nakajima, H. Itoh, E. Katoh, M. Kobayashi, T.Y. Chow, Y.I. Hsing, H. Kitano, I. Yamaguchi, M. Matsuoka Nature 2005 693 698

[106] M. Ueguchi-Tanaka, M. Nakajima, E. Katoh, H. Ohmiya, K. Asano, S. Saji, X. Hongyu, M. Ashikari, H. Kitano, I. Yamaguchi, M. Matsuoka Plant Cell 2007 2140 2155

[107] T. Ulmasov, G. Hagen, T.J. Guilfoyle Plant J. 1999 309 319

[108] M. Vignes, J. Vandel, D. Allouche, N. Ramadan-Alban, C. Cierco-Ayrolles, T. Schiex, B. Mangin, S. De-Givry Gene Regulatory Network Reconstruction Using Bayesian Networks, the Dantzig Selector, the Lasso and Their Meta-Analysis PLoS ONE 2011

[109] J.P. Vogel, K.E. Woeste, A. Theologis, J.J. Kieber PNAS 1998 4766 71

[110] J. Watkinson, K. Liang, X. Wang, T. Zheng, D. Anastassiou Ann. N. Y. Acad. Sci. 2009 302 13

[111] D. Watts, S. Strogatz Nature 1998 440 442

[112] A.V. Werhli, M. Grzegorczyk, D. Husmeier Bioinformatics 2006 2523 2531

[113] A.V. Werhli, D. Husmeier J. Bioinform. Comput. Biol. 2008 543 72

[114] N. Wermuth, S. Lauritzen Biometrika 1983 537 552

[115] B.C. Willige, S. Ghosh, C. Nill, M. Zourelidou, E.M. Dohmann, A. Maier, C. Schwechheimer Plant Cell 2007 1209 1220

[116] L. Wolpert J. Theor. Biol. 1999 1 47

[117] K.Y. Yip, R.P. Alexander, K.K. Yan, M. Gerstein PLoS ONE 2010 1

[118] T.T. Vu, J. Vohradsky Nucleic Acids Res. 2006 279 287

[119] M. Zou, S.D. Conzen Bioinformatics 2005 1

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