band1

The SBML for this model was obtained from the BioModels database (BioModels ID: BIOMD0000000413) Biomodels notes: 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). JWS Online curation: This model was curated by reproducing the Figure S15A.

None

None

None

None

None

None

Root gravitropism is regulated by a transient lateral auxin gradient controlled by a tipping-point mechanism.

  • Leah R Band
  • Darren M Wells
  • Antoine Larrieu
  • Jianyong Sun
  • Alistair M Middleton
  • Andrew P French
  • Géraldine Brunoud
  • Ethel Mendocilla Sato
  • Michael H Wilson
  • Benjamin Péret
  • Marina Oliva
  • Ranjan Swarup
  • Ilkka Sairanen
  • Geraint Parry
  • Karin Ljung
  • Tom Beeckman
  • Jonathan M Garibaldi
  • Mark Estelle
  • Markus R Owen
  • Kris Vissenberg
  • T Charlie Hodgman
  • Tony P Pridmore
  • John R King
  • Teva Vernoux
  • Malcolm J Bennett
Proc. Natl. Acad. Sci. U.S.A. 2012; 109 (12): 4668-4673
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.

Unit definitions have no effect on the numerical analysis of the model. It remains the responsibility of the modeler to ensure the internal numerical consistency of the model. If units are provided, however, the consistency of the model units will be checked.

Name Definition
Id Name Spatial dimensions Size
cell 3.0 1.0
Id Name Initial quantity Compartment Fixed
TIR1 15.4 cell
VENUS 40.4 cell
auxin 7.38 cell
auxinTIR1 0.28 cell
auxinTIR1VENUS 2.78 cell

Initial assignments are expressions that are evaluated at time=0. It is not recommended to create initial assignments for all model entities. Restrict the use of initial assignments to cases where a value is expressed in terms of values or sizes of other model entities. Note that it is not permitted to have both an initial assignment and an assignment rule for a single model entity.

Definition
Id Name Objective coefficient Reaction Equation and Kinetic Law Flux bounds
VENUSphotobleachingdecay VENUS > ∅

lambda * VENUS
VENUSproduction ∅ > VENUS

delta
auxin_TIR1_VENUSassociation auxinTIR1 + VENUS > auxinTIR1VENUS

la * auxinTIR1 * VENUS
auxin_TIR1_VENUSdissociation auxinTIR1VENUS > auxinTIR1 + VENUS

ld * auxinTIR1VENUS
auxin_TIR1_VENUSdissociationleadingtoubiquitination auxinTIR1VENUS > auxinTIR1

lm * auxinTIR1VENUS
auxin_TIR1association auxin + TIR1 > auxinTIR1

ka * auxin * TIR1
auxin_TIR1dissociation auxinTIR1 > auxin + TIR1

kd * auxinTIR1
auxindecay auxin > ∅

mu * auxin
auxinproduction ∅ > auxin

alpha_tr

Global parameters

Id Value
TIR1T 18.5
alpha_tr 30.5
delta 0.486
ka 0.000822
kd 0.334
la 1.15
lambda 0.00316
ld 4.49
lm 0.175
mu 0.79

Local parameters

Id Value Reaction

Assignment rules

Definition

Rate rules

Definition

Algebraic rules

Definition
Trigger Assignments