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BIOMD0000000416 - Muraro2011_Cytokinin-Auxin_CrossRegulation

 

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Reference Publication
Publication ID: 21640126
Muraro D, Byrne H, King J, Voss U, Kieber J, Bennett M.
The influence of cytokinin-auxin cross-regulation on cell-fate determination in Arabidopsis thaliana root development.
J. Theor. Biol. 2011 Aug; 283(1): 152-167
Centre for Plant Integrative Biology, School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough LE12 5RD, UK. Daniele.Muraro@nottingham.ac.uk  [more]
Model
Original Model: BIOMD0000000416.xml.origin
Submitter: Daniele Muraro
Submission ID: MODEL1203080000
Submission Date: 08 Mar 2012 10:06:20 UTC
Last Modification Date: 22 May 2014 19:02:54 UTC
Creation Date: 10 Apr 2012 17:36:57 UTC
Encoders:  Vijayalakshmi Chelliah
   Daniele Muraro
set #1
bqbiol:hasPart Gene Ontology regulation of cytokinin-activated signaling pathway
Gene Ontology auxin-activated signaling pathway
set #2
bqbiol:hasProperty Mathematical Modelling Ontology MAMO_0000046
set #3
bqbiol:hasTaxon Taxonomy Arabidopsis thaliana
set #4
bqmodel:isDerivedFrom PubMed 20135237
Notes

This model is from the article:
The influence of cytokinin-auxin cross-regulation on cell-fate determination in Arabidopsis thaliana root development
Muraro D, Byrne H, King J, Voss U, Kieber J, Bennett M. J Theor Biol.2011 Aug 21;283(1):152-67. PMID: 21640126,
Abstract:
Root growth and development in Arabidopsis thaliana are sustained by a specialised zone termed the meristem, which contains a population of dividing and differentiating cells that are functionally analogous to a stem cell niche in animals. The hormones auxin and cytokinin control meristem size antagonistically. Local accumulation of auxin promotes cell division and the initiation of a lateral root primordium. By contrast, high cytokinin concentrations disrupt the regular pattern of divisions that characterises lateral root development, and promote differentiation. The way in which the hormones interact is controlled by a genetic regulatory network. In this paper, we propose a deterministic mathematical model to describe this network and present model simulations that reproduce the experimentally observed effects of cytokinin on the expression of auxin regulated genes. We show how auxin response genes and auxin efflux transporters may be affected by the presence of cytokinin. We also analyse and compare the responses of the hormones auxin and cytokinin to changes in their supply with the responses obtained by genetic mutations of SHY2, which encodes a protein that plays a key role in balancing cytokinin and auxin regulation of meristem size. We show that although shy2 mutations can qualitatively reproduce the effect of varying auxin and cytokinin supply on their response genes, some elements of the network respond differently to changes in hormonal supply and to genetic mutations, implying a different, general response of the network. We conclude that an analysis based on the ratio between these two hormones may be misleading and that a mathematical model can serve as a useful tool for stimulate further experimental work by predicting the response of the network to changes in hormone levels and to other genetic mutations.

Model
Publication ID: 21640126 Submission Date: 08 Mar 2012 10:06:20 UTC Last Modification Date: 22 May 2014 19:02:54 UTC Creation Date: 10 Apr 2012 17:36:57 UTC
Mathematical expressions
Reactions
r1 r2 r3 r4
r5 r6 r7 r8
r9 r10 r11 r12
r13 r14 r15 r16
r17 r18 r19 r20
Rules
Assignment Rule (variable: TIR1) Assignment Rule (variable: ARF) Assignment Rule (variable: ARRBp) Assignment Rule (variable: CkAHKph)
Assignment Rule (variable: CkAHK) Assignment Rule (variable: F1) Assignment Rule (variable: F2) Assignment Rule (variable: F3)
Assignment Rule (variable: F4) Assignment Rule (variable: F5a) Assignment Rule (variable: F5b) Assignment Rule (variable: F6)
Physical entities
Compartments Species
cell IAAm IAAp AuxTIR1
AuxTIAA IAAs ARFIAA
ARF2 Aux PINm
PINp ARm ARp
TIR1 ARF CRm
CRp AHKph Ck
ARRBph ARRAph ARRAm
ARRAp ARRBp CkAHKph
CkAHK F1 F2
F3 F4 F5a
F5b F6  
Global parameters
eps lambda1 lambda3 alphaAux
alphaTIR1 alphaARF phiIAAp phiARp
phiPINp deltaIAAp deltaARp deltaPINp
muAux muIAAs etaAuxTIR1 etaARFIAA
la ld pa pd
ka kd qa qd
thetaARF thetaARF2 thARFIAA thetaIAAp
thetaARp psiARFIAA psiARF alphaCk
alphaARRB alphaAHK alphaPH phiCRp
phiARRAp deltaCRp deltaARRAp muCk
etaAHKph etaCkPh ra rd
ua ud sa sd
thARRAph thARRBph    
Reactions (20)
 
 r1  → [IAAm];   {F1} , {F2} , {F3}
 
 r2  → [IAAp];   {IAAm} , {AuxTIR1} , {AuxTIAA} , {ARFIAA} , {ARF}
 
 r3  → [AuxTIR1];   {Aux} , {TIR1} , {AuxTIAA} , {IAAp}
 
 r4  → [AuxTIAA];   {AuxTIAA} , {IAAp} , {AuxTIR1}
 
 r5  → [IAAs];   {AuxTIAA}
 
 r6  → [ARFIAA];   {ARF} , {IAAp}
 
 r7  → [ARF2];   {ARF}
 
 r8  → [Aux];   {TIR1} , {AuxTIR1}
 
 r9  → [PINm];   {F5a} , {F5b}
 
 r10  → [PINp];   {PINm}
 
 r11  → [ARm];   {F5a} , {F5b}
 
 r12  → [ARp];   {ARm}
 
 r13  → [CRm];   {F4}
 
 r14  → [CRp];   {CRm}
 
 r15  → [AHKph];   {CkAHKph} , {Ck}
 
 r16  → [Ck];   {AHKph} , {CkAHKph}
 
 r17  → [ARRBph];   {CkAHKph} , {CkAHK} , {ARRBp}
 
 r18  → [ARRAph];   {CkAHKph} , {ARRAp} , {CkAHK} , {ARRAph}
 
 r19  → [ARRAm];   {F6}
 
 r20  → [ARRAp];   {ARRAm} , {CkAHK} , {ARRAph} , {CkAHKph}
 
Rules (12)
 
 Assignment Rule (name: TIR1) TIR1 = alphaTIR1-AuxTIR1-AuxTIAA
 
 Assignment Rule (name: ARF) ARF = alphaARF-2*ARF2-ARFIAA
 
 Assignment Rule (name: ARRBp) ARRBp = alphaARRB-etaAHKph*ARRBph
 
 Assignment Rule (name: CkAHKph) CkAHKph = alphaPH-AHKph-ARRAph-ARRBph
 
 Assignment Rule (name: CkAHK) CkAHK = alphaAHK-etaAHKph*(AHKph+CkAHKph)
 
 Assignment Rule (name: F1) F1 = ARF/thetaARF/(1+ARF/thetaARF+ARF2/thetaARF2+ARFIAA/thARFIAA+ARF*IAAp/psiARFIAA+ARF^2/psiARF+ARRBph/thARRBph)
 
 Assignment Rule (name: F2) F2 = (ARF2/thetaARF2+ARF^2/psiARF)/(1+ARF/thetaARF+ARF2/thetaARF2+ARFIAA/thARFIAA+ARF*IAAp/psiARFIAA+ARF^2/psiARF+ARRBph/thARRBph)
 
 Assignment Rule (name: F3) F3 = ARRBph/thARRBph/(1+ARF/thetaARF+ARF2/thetaARF2+ARFIAA/thARFIAA+ARF*IAAp/psiARFIAA+ARF^2/psiARF+ARRBph/thARRBph)
 
 Assignment Rule (name: F4) F4 = ARRBph/thARRBph/(1+ARRAph/thARRAph+ARRBph/thARRBph)
 
 Assignment Rule (name: F5a) F5a = ARF/thetaARF/(1+ARF/thetaARF+ARF2/thetaARF2+ARFIAA/thARFIAA+ARF*IAAp/psiARFIAA+ARF^2/psiARF)
 
 Assignment Rule (name: F5b) F5b = (ARF2/thetaARF2+ARF^2/psiARF)/(1+ARF/thetaARF+ARF2/thetaARF2+ARFIAA/thARFIAA+ARF*IAAp/psiARFIAA+ARF^2/psiARF)
 
 Assignment Rule (name: F6) F6 = ARp/thetaARp/(1+ARp/thetaARp)
 
  Spatial dimensions: 3.0  Compartment size: 1.0
 
 IAAm
Compartment: cell
Initial concentration: 0.0
 
 IAAp
Compartment: cell
Initial concentration: 0.0
 
 AuxTIR1
Compartment: cell
Initial concentration: 0.0
 
 AuxTIAA
Compartment: cell
Initial concentration: 0.0
 
 IAAs
Compartment: cell
Initial concentration: 0.0
 
 ARFIAA
Compartment: cell
Initial concentration: 0.0
 
 ARF2
Compartment: cell
Initial concentration: 0.0
 
 Aux
Compartment: cell
Initial concentration: 1.0
 
 PINm
Compartment: cell
Initial concentration: 0.0
 
 PINp
Compartment: cell
Initial concentration: 0.0
 
 ARm
Compartment: cell
Initial concentration: 0.0
 
 ARp
Compartment: cell
Initial concentration: 0.0
 
  TIR1
Compartment: cell
Initial concentration: 0.0
 
  ARF
Compartment: cell
Initial concentration: 0.0
 
 CRm
Compartment: cell
Initial concentration: 0.0
 
 CRp
Compartment: cell
Initial concentration: 0.0
 
 AHKph
Compartment: cell
Initial concentration: 1.0
 
 Ck
Compartment: cell
Initial concentration: 1.0
 
 ARRBph
Compartment: cell
Initial concentration: 0.0
 
 ARRAph
Compartment: cell
Initial concentration: 0.0
 
 ARRAm
Compartment: cell
Initial concentration: 0.0
 
 ARRAp
Compartment: cell
Initial concentration: 0.0
 
  ARRBp
Compartment: cell
Initial concentration: 0.0
 
  CkAHKph
Compartment: cell
Initial concentration: 0.0
 
  CkAHK
Compartment: cell
Initial concentration: 0.0
 
   F1
Compartment: cell
Initial concentration: 0.0
 
   F2
Compartment: cell
Initial concentration: 0.0
 
   F3
Compartment: cell
Initial concentration: 0.0
 
   F4
Compartment: cell
Initial concentration: 0.0
 
   F5a
Compartment: cell
Initial concentration: 0.0
 
   F5b
Compartment: cell
Initial concentration: 0.0
 
   F6
Compartment: cell
Initial concentration: 0.0
 
Global Parameters (50)
 
   eps
Value: 0.01
Constant
 
   lambda1
Value: 0.1
Constant
 
   lambda3
Value: 0.02
Constant
 
   alphaAux
Value: 1.0
Constant
 
   alphaTIR1
Value: 1.0
Constant
 
   alphaARF
Value: 1.0
Constant
 
   phiIAAp
Value: 100.0
Constant
 
   phiARp
Value: 2.0
Constant
 
   phiPINp
Value: 100.0
Constant
 
   deltaIAAp
Value: 1.0
Constant
 
   deltaARp
Value: 1.0
Constant
 
   deltaPINp
Value: 1.0
Constant
 
   muAux
Value: 0.1
Constant
 
   muIAAs
Value: 1.0
Constant
 
   etaAuxTIR1
Value: 10.0
Constant
 
   etaARFIAA
Value: 1.0
Constant
 
   la
Value: 0.5
Constant
 
   ld
Value: 0.1
Constant
 
   pa
Value: 10.0
Constant
 
   pd
Value: 10.0
Constant
 
   ka
Value: 100.0
Constant
 
   kd
Value: 1.0
Constant
 
   qa
Value: 1.0
Constant
 
   qd
Value: 1.0
Constant
 
   thetaARF
Value: 0.1
Constant
 
   thetaARF2
Value: 0.01
Constant
 
   thARFIAA
Value: 0.1
Constant
 
   thetaIAAp
Value: 0.1
Constant
 
   thetaARp
Value: 0.1
Constant
 
   psiARFIAA
Value: 0.1
Constant
 
   psiARF
Value: 0.1
Constant
 
   alphaCk
Value: 1.0
Constant
 
   alphaARRB
Value: 2.0
Constant
 
   alphaAHK
Value: 1.0
Constant
 
   alphaPH
Value: 1.0
Constant
 
   phiCRp
Value: 2.0
Constant
 
   phiARRAp
Value: 100.0
Constant
 
   deltaCRp
Value: 1.0
Constant
 
   deltaARRAp
Value: 1.0
Constant
 
   muCk
Value: 0.1
Constant
 
   etaAHKph
Value: 1.0
Constant
 
   etaCkPh
Value: 1.0
Constant
 
   ra
Value: 1.0
Constant
 
   rd
Value: 1.0
Constant
 
   ua
Value: 1.0
Constant
 
   ud
Value: 1.0
Constant
 
   sa
Value: 1.0
Constant
 
   sd
Value: 1.0
Constant
 
   thARRAph
Value: 0.1
Constant
 
   thARRBph
Value: 0.1
Constant
 
Representative curation result(s)
Representative curation result(s) of BIOMD0000000416

Curator's comment: (updated: 10 Apr 2012 18:36:41 BST)

Figure 7 of the reference publication has been reproduced here. The parameter values of alphaARRB and alphaCk has to set to the values mentioned in the curation figure, to get the appropriate plots. The model was simulated using Copasi v4.7 (Build 34).

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