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BIOMD0000000351 - Vernoux2011_AuxinSignaling_AuxinSingleStepInput

 

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Reference Publication
Publication ID: 21734647
Vernoux T, Brunoud G, Farcot E, Morin V, Van den Daele H, Legrand J, Oliva M, Das P, Larrieu A, Wells D, Guédon Y, Armitage L, Picard F, Guyomarc'h S, Cellier C, Parry G, Koumproglou R, Doonan JH, Estelle M, Godin C, Kepinski S, Bennett M, De Veylder L, Traas J.
The auxin signalling network translates dynamic input into robust patterning at the shoot apex.
Mol. Syst. Biol. 2011; 7: 508
Laboratoire de Reproduction et Développement des Plantes, CNRS, INRA, ENS Lyon, UCBL, Université de Lyon, Lyon, France. teva.vernoux@ens-lyon.fr  [more]
Model
Original Model: Vernoux2010_AuxinSignaling
Submitter: Farcot Etienne
Submission ID: MODEL1105290000
Submission Date: 29 May 2011 14:26:46 UTC
Last Modification Date: 23 Aug 2011 14:13:38 UTC
Creation Date: 01 Apr 2011 10:17:29 UTC
Encoders:  Vijayalakshmi Chelliah
   Farcot Etienne
   Teva Vernoux
set #1
bqbiol:occursIn Taxonomy Arabidopsis
bqbiol:isVersionOf Gene Ontology auxin-activated signaling pathway
Notes

This model is from the article:
The auxin signalling network translates dynamic input into robust patterning at the shoo t apex.
Vernoux T, Brunoud G, Farcot E, Morin V, Van den Daele H, Legrand J, Oliva M, Das P, Larrieu A, Wells D , Guédon Y, Armitage L, Picard F, Guyomarc'h S, Cellier C, Parry G, Koumproglou R, Doonan JH, Estelle M , Godin C, Kepinski S, Bennett M, De Veylder L, Traas J. Mol Syst Biol. 2011 Jul 5;7:508. 21734647 ,
Abstract:
The plant hormone auxin is thought to provide positional information for patterning during development. It is still unclear, however, precisely how auxin is distributed across tissues and how the hormone is sensed in space and time. The control of gene expression in response to auxin involves a complex netwo rk of over 50 potentially interacting transcriptional activators and repressors, the auxin response fac tors (ARFs) and Aux/IAAs. Here, we perform a large-scale analysis of the Aux/IAA-ARF pathway in the sho ot apex of Arabidopsis, where dynamic auxin-based patterning controls organogenesis. A comprehensive ex pression map and full interactome uncovered an unexpectedly simple distribution and structure of this p athway in the shoot apex. A mathematical model of the Aux/IAA-ARF network predicted a strong buffering capacity along with spatial differences in auxin sensitivity. We then tested and confirmed these predic tions using a novel auxin signalling sensor that reports input into the signalling pathway, in conjunct ion with the published DR5 transcriptional output reporter. Our results provide evidence that the auxin signalling network is essential to create robust patterns at the shoot apex.

Note:

Figure 3 of the supplementary material of the reference article has been reproduced here. Time evolution of all the variables in the model are plotted, under the influence of a step input of auxin level (auxin=5, when time>1000; 0.11, otherwise). pi_A is varied between 0 and 2 by steps of 0.1.

This model originates from BioModels Database: A Database of Annotated Published Models (http://www.ebi.ac.uk/biomodels/). It is copyright (c) 2005-2011 The BioModels.net Team.
For more information see the terms of use .
To cite BioModels Database, please use: Li C, Donizelli M, Rodriguez N, Dharuri H, Endler L, Chelliah V, Li L, He E, Henry A, Stefan MI, Snoep JL, Hucka M, Le Novère N, Laibe C (2010) BioModels Database: An enhanced, curated and annotated resource for published quantitative kinetic models. BMC Syst Biol., 4:92.

Model
Publication ID: 21734647 Submission Date: 29 May 2011 14:26:46 UTC Last Modification Date: 23 Aug 2011 14:13:38 UTC Creation Date: 01 Apr 2011 10:17:29 UTC
Mathematical expressions
Reactions
reac_DIA reac_DII reac_degrI reac_degrA
reac_degrDIA reac_degrDII reac_DIAxA reac_DIIxI
reac_degrR reac_prodI reac_prodA reac_prodR
Rules
Assignment Rule (variable: auxin) Assignment Rule (variable: kprime_IA) Assignment Rule (variable: kprime_II) Assignment Rule (variable: aux_basal)
Physical entities
Compartments Species
c_1 Aux/IAA ARF Aux/IAA:Aux/IAA
Aux/IAA:ARF mRNA auxin
Global parameters
pi_I d_r d_A d_II
d_IA k_II k_IA B_d
f_A gamma_I K_aux K_II
K_IA f_c w_A w_I
w_D d_I pi_A k_Am
kprime_IA kprime_II aux_basal  
Reactions (12)
 
 reac_DIA [ARF] + [Aux/IAA] ↔ [Aux/IAA:ARF];  
 
 reac_DII [Aux/IAA] + [Aux/IAA] ↔ [Aux/IAA:Aux/IAA];  
 
 reac_degrI [Aux/IAA] → ;   {auxin}
 
 reac_degrA [ARF] → ;  
 
 reac_degrDIA [Aux/IAA:ARF] → ;  
 
 reac_degrDII [Aux/IAA:Aux/IAA] → ;  
 
 reac_DIAxA [Aux/IAA:ARF] → [ARF];   {auxin}
 
 reac_DIIxI [Aux/IAA:Aux/IAA] → [Aux/IAA];   {auxin}
 
 reac_degrR [mRNA] → ;  
 
 reac_prodI  → [Aux/IAA];   {mRNA}
 
 reac_prodA  → [ARF];  
 
 reac_prodR  → [mRNA];   {ARF} , {Aux/IAA:ARF} , {Aux/IAA}
 
Rules (4)
 
 Assignment Rule (name: aux) auxin = piecewise(5, time > 1000, 0)
 
 Assignment Rule (name: kprime_IA) kprime_IA = K_IA*k_IA
 
 Assignment Rule (name: kprime_II) kprime_II = K_II*k_II
 
 Assignment Rule (name: aux_basal) aux_basal = 1/(K_aux*(gamma_I-1))
 
 c_1 Spatial dimensions: 3.0  Compartment size: 1.0
 
 Aux/IAA
Compartment: c_1
Initial concentration: 10.0
 
 ARF
Compartment: c_1
Initial concentration: 10.0
 
 Aux/IAA:Aux/IAA
Compartment: c_1
Initial concentration: 10.0
 
 Aux/IAA:ARF
Compartment: c_1
Initial concentration: 10.0
 
 mRNA
Compartment: c_1
Initial concentration: 1.0
 
  auxin
Compartment: c_1
Initial concentration: 0.11
 
Global Parameters (23)
 
 pi_I
Value: 1.0
Constant
 
 d_r
Value: 0.0070
Constant
 
 d_A
Value: 0.0030
Constant
 
 d_II
Value: 0.0030
Constant
 
 d_IA
Value: 0.0030
Constant
 
 k_II
Value: 1.0
Constant
 
 k_IA
Value: 1.0
Constant
 
 B_d
Value: 100.0
Constant
 
 f_A
Value: 10.0
Constant
 
 gamma_I
Value: 10.0
Constant
 
 K_aux
Value: 1.0
Constant
 
 K_II
Value: 10.0
Constant
 
 K_IA
Value: 10.0
Constant
 
 f_c
Value: 10.0
Constant
 
 w_A
Value: 10.0
Constant
 
 w_I
Value: 10.0
Constant
 
 w_D
Value: 10.0
Constant
 
 d_I
Value: 0.05
Constant
 
 pi_A
Value: 1.0
Constant
 
 k_Am
Value: 10.0
Constant
 
  kprime_IA
Value: 10.0
 
  kprime_II
Value: 10.0
 
  aux_basal
Value: 0.11
 
Representative curation result(s)
Representative curation result(s) of BIOMD0000000351

Curator's comment: (updated: 11 Aug 2011 17:28:30 BST)

Figure 3 of the supplementary material of the reference article has been reproduced here. Time evolution of all the variables in the model are plotted, under the influence of a step input of auxin level (auxin=5, when time>1000; 0.11, otherwise). pi_A is varied between 0 and 2 by steps of 0.1.
The model was integrated simulated using Copasi v4.7 (Build 34). Data were obtained from Copasi and plotted using Gnuplot.

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