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BIOMD0000000269 - Liu2010_Hormonal_Crosstalk_Arabidopsis

 

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Reference Publication
Publication ID: 20531403
Liu J, Mehdi S, Topping J, Tarkowski P, Lindsey K.
Modelling and experimental analysis of hormonal crosstalk in Arabidopsis.
Mol. Syst. Biol. 2010 Jun; 6: 373
The Integrative Cell Biology Laboratory and The Biophysical Sciences Institute, School of Biological and Biomedical Sciences, Durham University, Durham, UK. junli.liu@durham.ac.uk  [more]
Model
Original Model: http://www.nature.com/msb/...
Submitter: Lukas Endler
Submission ID: MODEL1008260000
Submission Date: 26 Aug 2010 14:33:56 UTC
Last Modification Date: 08 Feb 2012 19:28:43 UTC
Creation Date: 20 Sep 2010 17:04:58 UTC
Encoders:  Lukas Endler
   Junli Liu
set #1
bqbiol:isVersionOf Gene Ontology ethylene-activated signaling pathway
Gene Ontology auxin-activated signaling pathway
Gene Ontology cytokinin-activated signaling pathway
set #2
bqbiol:occursIn Taxonomy Arabidopsis thaliana
Notes

This is the single cell model for analysis of hormonal crosstalk in Arabidopsis described in the article:
Modelling and experimental analysis of hormonal crosstalk in Arabidopsis.
Liu J, Mehdi S, Topping J, Tarkowski P and Lindsey K. Mol Syst Biol. 2010 Jun 8;6:373; PmID: 20531403 , DOI: 10.1038/msb.2010.26
Abstract:
An important question in plant biology is how genes influence the crosstalk between hormones to regulate growth. In this study, we model POLARIS (PLS) gene function and crosstalk between auxin, ethylene and cytokinin in Arabidopsis. Experimental evidence suggests that PLS acts on or close to the ethylene receptor ETR1, and a mathematical model describing possible PLS-ethylene pathway interactions is developed, and used to make quantitative predictions about PLS-hormone interactions. Modelling correctly predicts experimental results for the effect of the pls gene mutation on endogenous cytokinin concentration. Modelling also reveals a role for PLS in auxin biosynthesis in addition to a role in auxin transport. The model reproduces available mutants, and with new experimental data provides new insights into how PLS regulates auxin concentration, by controlling the relative contribution of auxin transport and biosynthesis and by integrating auxin, ethylene and cytokinin signalling. Modelling further reveals that a bell-shaped dose-response relationship between endogenous auxin and root length is established via PLS. This combined modelling and experimental analysis provides new insights into the integration of hormonal signals in plants.

This model was originally created using Copasi and taken from the supplementary materials of the MSB article. It uses equation 5 for the auxin biosynthesis and was altered to also contain the reactions for ACC, IAA and cytokinine import. Different from the supplementary material, the parameters for the auxin synthesis, v2, are set to k2c = 0.01 uM and k2=0.2 uM_per_sec and for the WT PLS transcription k6=0.3 . To obtain the model described in the first table of the supplementary materials, set k2c=k2=0 and k6=0.9 . For the pls and PLSox mutants, k6 should be set to 0 and 0.45, respectively.

This model originates from BioModels Database: A Database of Annotated Published Models. It is copyright (c) 2005-2010 The BioModels Team.
For more information see the terms of use .
To cite BioModels Database, please use Le Novère N., Bornstein B., Broicher A., Courtot M., Donizelli M., Dharuri H., Li L., Sauro H., Schilstra M., Shapiro B., Snoep J.L., Hucka M. (2006) BioModels Database: A Free, Centralized Database of Curated, Published, Quantitative Kinetic Models of Biochemical and Cellular Systems Nucleic Acids Res., 34: D689-D691.

Model
Publication ID: 20531403 Submission Date: 26 Aug 2010 14:33:56 UTC Last Modification Date: 08 Feb 2012 19:28:43 UTC Creation Date: 20 Sep 2010 17:04:58 UTC
Mathematical expressions
Reactions
v1: Auxin Transport to the cell v2: Auxin biosynthesis in the cell v3: Auxin removal from the cell v4: Conversion of auxin receptor from the inactivated form to the activated form
v5: Conversion of auxin receptor from the activated form to the inactivated form v6: Transcription of POLARIS gene v7: Decay of mRNA of POLARIS gene v8: Translation of POLARIS gene
v9: Decay of protein of POLARIS gene v10: Conversion of the inactivated form of ethylene receptor to its activated form by PLSp v11: Conversion of the activated form of ethylene receptor to its inactivated form v12: Ethylene biosynthesis
v13: Removal of ethylene v14: Conversion of the inactivated form of CTR1 protein to its activated form by Re* v15: Conversion of the activated form of CTR1 protein to its inactivated form v16: Activation of the downstream of ethylene signalling response is inhibited by CTR1*
v17: Removal of the unknown molecule X v18: Biosynthesis of cytokinin v19: removal of cytokinin vEthylene: Uptake rate of exogenous ACC (1-aminocyclopropane-1-carboxylic acid)
vAuxin: Uptake rate of exogenous auxin (indole-3-acetic acid, IAA) vCytokinin: Uptake rate of exogenous cytokinin    
Rules
Assignment Rule (variable: Ra) Assignment Rule (variable: Re) Assignment Rule (variable: CTR1)  
Physical entities
Compartments Species
cell Auxin X PLSp
Ra Ra* Ra_total
CK ET PLSm
Re Re_total Re*
CTR1 CTR1_total CTR1*
     
extracellular IAA ACC Cytokinin_ext
Global parameters
k1a k1 k2 k2a
k2b k2c k3 k3a
k4 k5 k6 k6a
k7 k8 k9 k10
k10a k11 k12 k12a
k13 k14 k15 k16
k16a k17 k18a k18
k19 k_ethylene k_auxin k_cytokinin
Reactions (22)
 
 v1: Auxin Transport to the cell  → [Auxin];   {X}
 
 v2: Auxin biosynthesis in the cell  → [Auxin];   {ET} , {CK} , {PLSp}
 
 v3: Auxin removal from the cell [Auxin] → ;   {X}
 
 v4: Conversion of auxin receptor from the inactivated form to the activated form [Ra] → [Ra*];   {Auxin}
 
 v5: Conversion of auxin receptor from the activated form to the inactivated form [Ra*] → [Ra];  
 
 v6: Transcription of POLARIS gene  → [PLSm];   {Ra*} , {ET}
 
 v7: Decay of mRNA of POLARIS gene [PLSm] → ;  
 
 v8: Translation of POLARIS gene  → [PLSp];   {PLSm}
 
 v9: Decay of protein of POLARIS gene [PLSp] → ;  
 
 v10: Conversion of the inactivated form of ethylene receptor to its activated form by PLSp [Re] → [Re*];   {PLSp}
 
 v11: Conversion of the activated form of ethylene receptor to its inactivated form [Re*] → [Re];   {ET}
 
 v12: Ethylene biosynthesis  → [ET];   {Auxin} , {CK}
 
 v13: Removal of ethylene [ET] → ;  
 
 v14: Conversion of the inactivated form of CTR1 protein to its activated form by Re* [CTR1] → [CTR1*];   {Re*}
 
 v15: Conversion of the activated form of CTR1 protein to its inactivated form [CTR1*] → [CTR1];  
 
 v16: Activation of the downstream of ethylene signalling response is inhibited by CTR1*  → [X];   {CTR1*}
 
 v17: Removal of the unknown molecule X [X] → ;  
 
 v18: Biosynthesis of cytokinin  → [CK];   {Auxin}
 
 v19: removal of cytokinin [CK] → ;  
 
 vEthylene: Uptake rate of exogenous ACC (1-aminocyclopropane-1-carboxylic acid) [ACC] → [ET];  
 
 vAuxin: Uptake rate of exogenous auxin (indole-3-acetic acid, IAA) [IAA] → [Auxin];  
 
 vCytokinin: Uptake rate of exogenous cytokinin [Cytokinin_ext] → [CK];  
 
Rules (3)
 
 Assignment Rule (name: Ra) Ra = RaT-Ra_star
 
 Assignment Rule (name: Re) Re = ReT-Re_star
 
 Assignment Rule (name: CTR1) CTR1 = CTR1T-CTR1_star
 
Functions (18)
 
 Rate law for v3: Auxin removal from the cell lambda(k3, k3a, X, Auxin, (k3+k3a*X)*Auxin)
 
 Rate law for v1: Auxin Transport to the cell lambda(k1a, X, k1, k1a/(1+X/k1))
 
 Rate law for v2: Auxin biosynthesis in the cell lambda(k2, k2a, ET, CK, k2b, PLSp, k2c, k2+k2a*ET/(1+CK/k2b)*PLSp/(k2c+PLSp))
 
 Rate law for v4: Conversion of auxin receptor from the inactivated form to the activated form lambda(k4, Auxin, Ra, k4*Auxin*Ra)
 
 Rate law for v6: Transcription of POLARIS gene lambda(k6, Ra_star, ET, k6a, k6*Ra_star/(1+ET/k6a))
 
 Rate law for v7: Decay of mRNA of POLARIS gene lambda(k7, PLSm, k7*PLSm)
 
 Rate law for v8: Translation of POLARIS gene lambda(k8, PLSm, k8*PLSm)
 
 Rate law for v9: Decay of protein of POLARIS gene lambda(k9, PLSp, k9*PLSp)
 
 Rate law for v10: Conversion of the inactivated form of ethylene receptor to its activated form by PLSp lambda(k10, PLSp, k10a, Re, (k10+k10a*PLSp)*Re)
 
 Rate law for v11: Conversion of the activated form of ethylene receptor to its inactivated form lambda(Re_star, ET, k11, k11*Re_star*ET)
 
 Rate law for v12: Ethylene biosynthesis lambda(Auxin, CK, k12, k12a, k12+k12a*Auxin*CK)
 
 Rate law for v13: Removal of ethylene lambda(ET, k13, k13*ET)
 
 Rate law for v14: Conversion of the inactivated form of CTR1 protein to its activated form by Re* lambda(Re_star, k14, CTR1, k14*Re_star*CTR1)
 
 Rate law for v15: Conversion of the activated form of CTR1 protein to its inactivated form lambda(CTR1_star, k15, k15*CTR1_star)
 
 Rate law for v18: Biosynthesis of cytokinin lambda(Auxin, k18a, k18, k18a/(1+Auxin/k18))
 
 Rate law for v16: Activation of the downstream of ethylene signalling response is inhibited by CTR1* lambda(CTR1_star, k16, k16a, k16-k16a*CTR1_star)
 
 Rate law for v17: Removal of the unknown molecule X lambda(X, k17, k17*X)
 
 Rate law for v19: removal of cytokinin lambda(CK, k19, k19*CK)
 
 cell Spatial dimensions: 3.0  Compartment size: 1.0
 
 Auxin
Compartment: cell
Initial concentration: 0.1
 
 X
Compartment: cell
Initial concentration: 0.1
 
 PLSp
Compartment: cell
Initial concentration: 0.1
 
  Ra
Compartment: cell
Initial concentration: 0.0
 
 Ra*
Compartment: cell
Initial concentration: 1.0
 
 Ra_total
Compartment: cell
Initial concentration: 1.0
 
 CK
Compartment: cell
Initial concentration: 0.1
 
 ET
Compartment: cell
Initial concentration: 0.1
 
 PLSm
Compartment: cell
Initial concentration: 0.1
 
  Re
Compartment: cell
Initial concentration: 0.0
 
 Re_total
Compartment: cell
Initial concentration: 0.3
 
 Re*
Compartment: cell
Initial concentration: 0.3
 
  CTR1
Compartment: cell
Initial concentration: 0.0
 
 CTR1_total
Compartment: cell
Initial concentration: 0.3
 
 CTR1*
Compartment: cell
Initial concentration: 0.3
 
 extracellular Spatial dimensions: 3.0  Compartment size: 1.0
 
 IAA
Compartment: extracellular
Initial concentration: 0.0
 
 ACC
Compartment: extracellular
Initial concentration: 0.0
 
 Cytokinin_ext
Compartment: extracellular
Initial concentration: 0.0
 
Global Parameters (32)
 
 k1a
Value: 1.0   (Units: per_uM_per_sec)
Constant
 
 k1
Value: 1.0   (Units: uM)
Constant
 
 k2
Value: 0.2   (Units: per_uM_per_sec)
Constant
 
 k2a
Value: 2.8   (Units: per_sec)
Constant
 
 k2b
Value: 1.0   (Units: uM)
Constant
 
 k2c
Value: 0.01   (Units: uM)
Constant
 
 k3
Value: 2.0   (Units: per_sec)
Constant
 
 k3a
Value: 0.45   (Units: per_uM_per_sec)
Constant
 
 k4
Value: 1.0   (Units: per_uM_per_sec)
Constant
 
 k5
Value: 1.0   (Units: per_sec)
Constant
 
 k6
Value: 0.3   (Units: per_sec)
Constant
 
 k6a
Value: 0.2   (Units: uM)
Constant
 
 k7
Value: 1.0   (Units: per_sec)
Constant
 
 k8
Value: 1.0   (Units: per_sec)
Constant
 
 k9
Value: 1.0   (Units: per_sec)
Constant
 
 k10
Value: 3.0E-4   (Units: per_sec)
Constant
 
 k10a
Value: 0.5   (Units: per_uM_per_sec)
Constant
 
 k11
Value: 5.0   (Units: per_uM_per_sec)
Constant
 
 k12
Value: 0.1   (Units: per_uM_per_sec)
Constant
 
 k12a
Value: 0.1   (Units: per_uM_per_sec)
Constant
 
 k13
Value: 1.0   (Units: per_sec)
Constant
 
 k14
Value: 3.0   (Units: per_uM_per_sec)
Constant
 
 k15
Value: 0.085   (Units: per_sec)
Constant
 
 k16
Value: 0.3   (Units: per_uM_per_sec)
Constant
 
 k16a
Value: 1.0   (Units: per_sec)
Constant
 
 k17
Value: 0.1   (Units: per_sec)
Constant
 
 k18a
Value: 1.0   (Units: per_uM_per_sec)
Constant
 
 k18
Value: 0.1   (Units: uM)
Constant
 
 k19
Value: 1.0   (Units: per_sec)
Constant
 
 k_ethylene
Value: 0.5   (Units: per_sec)
Constant
 
 k_auxin
Value: 70.0   (Units: per_sec)
Constant
 
 k_cytokinin
Value: 10.0   (Units: per_sec)
Constant
 
Representative curation result(s)
Representative curation result(s) of BIOMD0000000269

Curator's comment: (updated: 20 Sep 2010 18:04:44 BST)

Reproduction of figure 7 of the original publication using SBML ODESolver. Simulation were performed until a steady state was reached or until 1e4 time units (options: --time 1e4 -s --printstep 1)

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