A qualitative continuous model of cellular auxin and brassinosteroid signaling and their crosstalk

Bioinformatics

Volumn 27, Issue 10, 2011, Pages 1404-1412

  Sankar, Martial ^a   Osmont, Karen S ^a   Rolcik, Jakub ^b   Gujas, Bojan ^a   Tarkowska, Danuse ^b   Strnad, Miroslav ^b   Xenarios, Ioannis ^c   Hardtke, Christian S ^a  

^a UNIVERSITY OF LAUSANNE   (Switzerland)

^b PALACKÝ UNIVERSITY   (Czech Republic)

^c SWISS INSTITUTE OF BIOINFORMATICS   (Switzerland)

Author keywords

[No Author keywords available]

Indexed keywords

INDOLEACETIC ACID DERIVATIVE; PHYTOHORMONE;

ARABIDOPSIS; ARTICLE; BIOLOGICAL MODEL; CELL GROWTH; METABOLISM; SIGNAL TRANSDUCTION;

ARABIDOPSIS; CELL GROWTH PROCESSES; INDOLEACETIC ACIDS; MODELS, BIOLOGICAL; PLANT GROWTH REGULATORS; SIGNAL TRANSDUCTION;

EID: 79955781219     PISSN: 13674803     EISSN: 14602059     Source Type: Journal    
DOI: 10.1093/bioinformatics/btr158     Document Type: Article

References (52)

1. Badescu, G.O. and Napier, R.M. (2006) Receptors for auxin: will it all end in TIRs? Trends Plant Sci., 11, 217-223.
2. Benjamins, R. and Scheres, B. (2008) Auxin: the looping star in plant development. Annu. Rev. Plant Biol., 59, 443-465.
3. Beuchat, J. et al. (2010) BRX promotes Arabidopsis shoot growth. New Phytol., 188, 23-29.
4. Braun, N. et al. (2008) Conditional repression of AUXIN BINDING PROTEIN1 reveals that it coordinates cell division and cell expansion during postembryonic shoot development in Arabidopsis and tobacco. Plant Cell, 20, 2746-2762.
5. Dharmasiri, N. et al. (2005) The F-box protein TIR1 is an auxin receptor. Nature, 435, 441-445.
6. Diaz, J. and Alvarez-Buylla, E.R. (2009) Information flow during gene activation by signaling molecules: ethylene transduction in Arabidopsis cells as a study system. BMC Syst. Biol., 3, 48.
7. Di Cara, A. et al. (2007) Dynamic simulation of regulatory networks using SQUAD. BMC Bioinformatics, 8, 462.
8. Digiuni, S. et al. (2008)Acompetitive complex formation mechanism underlies trichome patterning on Arabidopsis leaves. Mol. Syst. Biol., 4, 217.
9. Gonzalez, A.G. et al. (2006) GINsim: a software suite for the qualitative modelling, simulation and analysis of regulatory networks. Biosystems, 84, 91-100.
10. Grieneisen, V.A. et al. (2007) Auxin transport is sufficient to generate a maximum and gradient guiding root growth. Nature, 449, 1008-1013.
11. Guilfoyle, T.J. and Hagen, G. (2007) Auxin response factors. Curr. Opin. Plant. Biol., 10, 453-460.
12. Hardtke, C.S. (2007) Transcriptional auxin-brassinosteroid crosstalk: who's talking? Bioessays, 29, 1115-1123.
13. Hyduke, D.R. and Palsson, B.O. (2010) Towards genome-scale signalling-network reconstructions. Nat. Rev. Genet., 11, 297-307.
14. Kepinski, S. and Leyser, O. (2005) The Arabidopsis F-box protein TIR1 is an auxin receptor. Nature, 435, 446-451.
15. Kieffer, M. et al. (2010) Defining auxin response contexts in plant development. Curr. Opin. Plant. Biol., 13, 12-20.
16. Kim, T.W. et al. (2009) Brassinosteroid signal transduction from cell-surface receptor kinases to nuclear transcription factors. Nat. Cell. Biol., 11, 1254-1260.
17. Kim, T.W. and Wang, Z.Y. (2010) Brassinosteroid signal transduction from receptor kinases to transcription factors. Annu. Rev. Plant Biol., 61, 23.21-23.24.
18. Klamt, S. et al. (2006) A methodology for the structural and functional analysis of signaling and regulatory networks. BMC Bioinformatics, 7, 56.
19. Kuppusamy, K.T. et al. (2008) Cross-regulatory mechanisms in hormone signaling. Plant Mol. Biol., 69, 375-381.
20. Leyser, O. (2005) Auxin distribution and plant pattern formation: how many angels can dance on the point of PIN? Cell, 121, 819-822.
21. Liu, J. et al. (2010) Modelling and experimental analysis of hormonal crosstalk in Arabidopsis. Mol. Syst. Biol., 6, 373.
22. Locke, J.C. et al. (2006) Experimental validation of a predicted feedback loop in the multi-oscillator clock of Arabidopsis thaliana. Mol. Syst. Biol., 2, 59.
23. Mendoza, L. and Pardo, F. (2010) A robust model to describe the differentiation of T-helper cells. Theory Biosci., 129, 283-293.
24. Mendoza, L. and Xenarios, I. (2006) A method for the generation of standardized qualitative dynamical systems of regulatory networks. Theor. Biol. Med. Model., 3, 13.
25. Mouchel, C.F. et al. (2004) Natural genetic variation in Arabidopsis identifies BREVIS RADIX, a novel regulator of cell proliferation and elongation in the root. Genes Dev., 18, 700-714.
26. Mouchel, C.F. et al. (2006) BRX mediates feedback between brassinosteroid levels and auxin signalling in root growth. Nature, 443, 458-461.
27. Muller, B. and Sheen, J. (2008) Cytokinin and auxin interaction in root stem-cell specification during early embryogenesis. Nature, 453, 1094-1097.
28. Naldi, A. et al. (2010) Diversity and plasticity of Th cell types predicted from regulatory network modelling. PLoS Comput. Biol., 6, e1000912.
29. Nemhauser, J.L. et al. (2006) Different plant hormones regulate similar processes through largely nonoverlapping transcriptional responses. Cell, 126, 467-475.
30. Nemhauser, J.L. et al. (2004) Interdependency of brassinosteroid and auxin signaling in Arabidopsis. PLoS Biol., 2, E258.
31. Osmont, K.S. et al. (2007) Hidden branches: developments in root system architecture. Annu. Rev. Plant Biol., 58, 93-113.
32. Pandey, S. et al. (2010) Boolean modeling of transcriptome data reveals novel modes of heterotrimeric G-protein action. Mol. Syst. Biol., 6, 372.
33. Philippi, N. et al. (2009) Modeling system states in liver cells: survival, apoptosis and their modifications in response to viral infection. BMC Syst. Biol., 3, 97.
34. Sabatini, S. et al. (1999) An auxin-dependent distal organizer of pattern and polarity in the Arabidopsis root. Cell, 99, 463-472.
35. Sanchez-Corrales, Y.E. et al. (2010) TheArabidopsis thaliana flower organ specification gene regulatory network determines a robust differentiation process. J. Theor. Biol., 264, 971-983.
36. Sauer, M. et al. (2006) Canalization of auxin flow byAux/IAA-ARF-dependent feedback regulation of PIN polarity. Genes Dev., 20, 2902-2911.
37. Savaldi-Goldstein, S. et al. (2007) The epidermis both drives and restricts plant shoot growth. Nature, 446, 199-202.
38. Scacchi, E. et al. (2009) Dynamic, auxin-responsive plasma membrane-to-nucleus movement of Arabidopsis BRX. Development, 136, 2059-2067.
39. Scacchi, E. et al. (2010) Spatio-temporal sequence of cross-regulatory events in root meristem growth. Proc. Natl Acad. Sci. USA, 107, 22734-22739.
40. Scheres, B. and Xu, J. (2006) Polar auxin transport and patterning: grow with the flow. Genes Dev., 20, 922-926.
41. Sibout, R. et al. (2006) Opposite root growth phenotypes of hy5 versus hy5 hyh mutants correlate with increased constitutive auxin signaling. PLoS Genet., 2, e202.
42. Strader, L.C. et al. (2008) The IBR5 phosphatase promotes Arabidopsis auxin responses through a novel mechanism distinct from TIR1-mediated repressor degradation. BMC Plant Biol., 8, 41.
43. Tiwari, S.B. et al. (2003) The roles of auxin response factor domains in auxin-responsive transcription. Plant Cell, 15, 533-543.
44. Trigueros, M. et al. (2009) The NGATHA genes direct style development in the Arabidopsis gynoecium. Plant Cell, 21, 1394-1409.
45. Tromas, A. et al. (2009) The AUXIN BINDING PROTEIN 1 is required for differential auxin responses mediating root growth. PLoS ONE, 4, e6648.
46. Vert, G. et al. (2005) Molecular mechanisms of steroid hormone signaling in plants. Annu. Rev. Cell. Dev. Biol., 21, 177-201.
47. Vert, G. et al. (2008) Integration of auxin and brassinosteroid pathways by Auxin Response Factor 2. Proc. Natl Acad. Sci. USA, 105, 9829-9834.
48. Vieten, A. et al. (2005) Functional redundancy of PIN proteins is accompanied by auxin-dependent cross-regulation of PIN expression. Development, 132, 4521-4531.
49. Wang, S. et al. (2005) AUXIN RESPONSE FACTOR7 restores the expression of auxin-responsive genes in mutant Arabidopsis leaf mesophyll protoplasts. Plant Cell, 17, 1979-1993.
50. Weijers, D. et al. (2005) Developmental specificity of auxin response by pairs of ARF and Aux/IAA transcriptional regulators. EMBO J., 24, 1874-1885.
51. Wisniewska, J. et al. (2006) Polar PIN localization directs auxin flow in plants. Science, 312, 883.
52. Wittmann, D.M. et al. (2009) Transforming Boolean models to continuous models: methodology and application to T-cell receptor signaling. BMC Syst. Biol., 3, 98.