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BIOMD0000000413 - Band2012_DII-Venus_FullModel

 

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Reference Publication
Publication ID: 22393022
Band LR, Wells DM, Larrieu A, Sun J, Middleton AM, French AP, Brunoud G, Sato EM, Wilson MH, Péret B, Oliva M, Swarup R, Sairanen I, Parry G, Ljung K, Beeckman T, Garibaldi JM, Estelle M, Owen MR, Vissenberg K, Hodgman TC, Pridmore TP, King JR, Vernoux T, Bennett MJ.
Root gravitropism is regulated by a transient lateral auxin gradient controlled by a tipping-point mechanism.
Proc. Natl. Acad. Sci. U.S.A. 2012 Mar; 109(12): 4668-4673
Centre for Plant Integrative Biology, University of Nottingham, Sutton Bonington LE12 5RD, United Kingdom.  [more]
Model
Original Model: BIOMD0000000413.origin
Submitter: Leah Band
Submission ID: MODEL1203230002
Submission Date: 23 Mar 2012 14:47:51 UTC
Last Modification Date: 02 Apr 2014 00:25:31 UTC
Creation Date: 05 Apr 2012 14:38:40 UTC
Encoders:  Vijayalakshmi Chelliah
   Leah Band
set #1
bqbiol:hasProperty Mathematical Modelling Ontology MAMO_0000046
set #2
bqbiol:isVersionOf Gene Ontology positive gravitropism
Gene Ontology regulation of auxin metabolic process
set #3
bqbiol:hasTaxon Taxonomy Arabidopsis
Notes

This model is from the article:
Root gravitropism is regulated by a transient lateral auxin gradient controlled by a tipping-point mechanism.
Band LR, Wells DM, Larrieu A, Sun J, Middleton AM, French AP, Brunoud G, Sato EM, Wilson MH, Péret B, Oliva M, Swarup R, Sairanen I, Parry G, Ljung K, Beeckman T, Garibaldi JM, Estelle M, Owen MR, Vissenberg K, Hodgman TC, Pridmore TP, King JR, Vernoux T, Bennett MJ. Proc Natl Acad Sci U S A.2012 Mar 20;109(12):4668-73 22393022,
Abstract:
Gravity profoundly influences plant growth and development. Plants respond to changes in orientation by using gravitropic responses to modify their growth. Cholodny and Went hypothesized over 80 years ago that plants bend in response to a gravity stimulus by generating a lateral gradient of a growth regulator at an organ's apex, later found to be auxin. Auxin regulates root growth by targeting Aux/IAA repressor proteins for degradation. We used an Aux/IAA-based reporter, domain II (DII)-VENUS, in conjunction with a mathematical model to quantify auxin redistribution following a gravity stimulus. Our multidisciplinary approach revealed that auxin is rapidly redistributed to the lower side of the root within minutes of a 90° gravity stimulus. Unexpectedly, auxin asymmetry was rapidly lost as bending root tips reached an angle of 40° to the horizontal. We hypothesize roots use a "tipping point" mechanism that operates to reverse the asymmetric auxin flow at the midpoint of root bending. These mechanistic insights illustrate the scientific value of developing quantitative reporters such as DII-VENUS in conjunction with parameterized mathematical models to provide high-resolution kinetics of hormone redistribution.

This model corresponds to the full model described in the article.

Model
Publication ID: 22393022 Submission Date: 23 Mar 2012 14:47:51 UTC Last Modification Date: 02 Apr 2014 00:25:31 UTC Creation Date: 05 Apr 2012 14:38:40 UTC
Mathematical expressions
Reactions
auxin_TIR1association auxin_TIR1dissociation auxin_TIR1_VENUSassociation auxin_TIR1_VENUSdissociation
auxin_TIR1_VENUSdissociationleadingtoubiquitination auxinproduction auxindecay VENUSproduction
VENUSphotobleachingdecay      
Physical entities
Compartments Species
cell auxin TIR1 auxinTIR1
auxinTIR1VENUS VENUS  
Global parameters
kd ka mu ld
lm la delta lambda
TIR1T alpha_tr    
Reactions (9)
 
 auxin_TIR1association [auxin] + [TIR1] → [auxinTIR1];  
 
 auxin_TIR1dissociation [auxinTIR1] → [auxin] + [TIR1];  
 
 auxin_TIR1_VENUSassociation [auxinTIR1] + [VENUS] → [auxinTIR1VENUS];  
 
 auxin_TIR1_VENUSdissociation [auxinTIR1VENUS] → [auxinTIR1] + [VENUS];  
 
 auxin_TIR1_VENUSdissociationleadingtoubiquitination [auxinTIR1VENUS] → [auxinTIR1];  
 
 auxinproduction  → [auxin];  
 
 auxindecay [auxin] → ;  
 
 VENUSproduction  → [VENUS];  
 
 VENUSphotobleachingdecay [VENUS] → ;  
 
  Spatial dimensions: 3.0  Compartment size: 1.0
 
 auxin
Compartment: cell
Initial concentration: 7.38
 
 TIR1
Compartment: cell
Initial concentration: 15.4
 
 auxinTIR1
Compartment: cell
Initial concentration: 0.28
 
 auxinTIR1VENUS
Compartment: cell
Initial concentration: 2.78
 
 VENUS
Compartment: cell
Initial concentration: 40.4
 
Global Parameters (10)
 
   kd
Value: 0.334
Constant
 
   ka
Value: 8.22E-4
Constant
 
   mu
Value: 0.79
Constant
 
   ld
Value: 4.49
Constant
 
   lm
Value: 0.175
Constant
 
   la
Value: 1.15
Constant
 
   delta
Value: 0.486
Constant
 
   lambda
Value: 0.00316
Constant
 
   TIR1T
Value: 18.5
Constant
 
   alpha_tr
Value: 30.5
Constant
 
Representative curation result(s)
Representative curation result(s) of BIOMD0000000413

Curator's comment: (updated: 05 Apr 2012 15:34:39 BST)

Figure s15 in the supplementary material of the reference publication has been reproduced here. Figure E in the curation figure also corresponds to Figure 2A of the reference publication. The model as such corresponds to the auxin dose of 10nM (cyan line in the plot). Different auxin doses are incorporated in the model using the parameter, alpha_tr.
alpha_tr = 5.83 (no auxin)
alpha_tr = 7.44 (1nM)
alpha_tr = 19.96 (5nM)
alpha_tr = 30.50 (10nM)
alpha_tr = 132.82 (100nM)
alpha_tr = 270.52 (1000nM).

The model was simulated using Copasi v4.8 (Build 35).

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