JWS Online

Model

Name

liu1

Notes

The SBML for this model was obtained from the BioModels database (BioModels ID: BIOMD0000000269) Biomodels notes: 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) JWS Online curation: This model was curated by reproducing the figures as described in the BioModels Notes. No additional changes were made.

Substance units

None

Time units

None

Volume units

None

Area units

None

Length units

None

Reaction extent units

None

Manuscript information

Modelling and experimental analysis of hormonal crosstalk in Arabidopsis.

Junli Liu
Saher Mehdi
Jennifer Topping
Petr Tarkowski
Keith Lindsey

Mol. Syst. Biol. 2010; 6 : 373

PubMed: 20531403
PubMed Central: PMC2913391
DOI: 10.1038/msb.2010.26
ISSN: 1744-4292
URL: https://ncbi.nlm.nih.gov/pubmed/20531403

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.

Unit definitions 5

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
—	1e-06 mole
—	1e-06 mole litre^(-1.0)
—	1.0 second
—	1.0 second^(-1.0)
—	1e-06 mole litre^(-1.0) second^(-1.0)

Compartments 2

Id	Name	Spatial dimensions	Size
compartment_1	cell	3.0	1.0
extra	extracellular	3.0	1.0

Species 18

Id	Name	Initial quantity	Compartment	Fixed
ACC	ACC	0.0	extra (extracellular)	✔
Auxin	Auxin	0.1	compartment_1 (cell)	✘
CK	CK	0.1	compartment_1 (cell)	✘
CK_ex	Cytokinin_ext	0.0	extra (extracellular)	✔
CTR1	CTR1	0.0	compartment_1 (cell)	✔
CTR1T	CTR1_total	0.3	compartment_1 (cell)	✔
CTR1_star	CTR1*	0.3	compartment_1 (cell)	✘
ET	ET	0.1	compartment_1 (cell)	✘
IAA	IAA	0.0	extra (extracellular)	✔
PLSm	PLSm	0.1	compartment_1 (cell)	✘
PLSp	PLSp	0.1	compartment_1 (cell)	✘
Ra	Ra	0.0	compartment_1 (cell)	✔
RaT	Ra_total	1.0	compartment_1 (cell)	✔
Ra_star	Ra*	1.0	compartment_1 (cell)	✘
Re	Re	0.0	compartment_1 (cell)	✔
ReT	Re_total	0.3	compartment_1 (cell)	✔
Re_star	Re*	0.3	compartment_1 (cell)	✘
X	X	0.1	compartment_1 (cell)	✘

Initial assignments 0

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

Reactions 22

Id	Name	Reaction Equation and Kinetic Law
reaction_1	v1: Auxin Transport to the cell	∅ > Auxin compartment_1 * function_2(k1a, X, k1)
reaction_10	v10: Conversion of the inactivated form of ethylene receptor to its activated form by PLSp	Re > Re_star compartment_1 * function_10(k10, PLSp, k10a, Re)
reaction_11	v11: Conversion of the activated form of ethylene receptor to its inactivated form	Re_star > Re compartment_1 * function_12(Re_star, ET, k11)
reaction_12	v12: Ethylene biosynthesis	∅ > ET compartment_1 * function_13(Auxin, CK, k12, k12a)
reaction_13	v13: Removal of ethylene	ET > ∅ compartment_1 * function_15(ET, k13)
reaction_14	v14: Conversion of the inactivated form of CTR1 protein to its activated form by Re*	CTR1 > CTR1_star compartment_1 * function_16(Re_star, k14, CTR1)
reaction_15	v15: Conversion of the activated form of CTR1 protein to its inactivated form	CTR1_star > CTR1 compartment_1 * function_17(CTR1_star, k15)
reaction_16	v16: Activation of the downstream of ethylene signalling response is inhibited by CTR1*	∅ > X compartment_1 * function_18(CTR1_star, k16, k16a)
reaction_17	v17: Removal of the unknown molecule X	X > ∅ compartment_1 * function_19(X, k17)
reaction_18	v18: Biosynthesis of cytokinin	∅ > CK compartment_1 * function_20(Auxin, k18a, k18)
reaction_19	v19: removal of cytokinin	CK > ∅ compartment_1 * function_21(CK, k19)
reaction_2	v2: Auxin biosynthesis in the cell	∅ > Auxin compartment_1 * function_3(k2, k2a, ET, CK, k2b, PLSp, k2c)
reaction_3	v3: Auxin removal from the cell	Auxin > ∅ compartment_1 * function_1(k3, k3a, X, Auxin)
reaction_4	v4: Conversion of auxin receptor from the inactivated form to the activated form	Ra > Ra_star compartment_1 * function_4(k4, Auxin, Ra)
reaction_5	v5: Conversion of auxin receptor from the activated form to the inactivated form	Ra_star > Ra compartment_1 * k5 * Ra_star
reaction_6	v6: Transcription of POLARIS gene	∅ > PLSm compartment_1 * function_6(k6, Ra_star, ET, k6a)
reaction_7	v7: Decay of mRNA of POLARIS gene	PLSm > ∅ compartment_1 * function_7(k7, PLSm)
reaction_8	v8: Translation of POLARIS gene	∅ > PLSp compartment_1 * function_8(k8, PLSm)
reaction_9	v9: Decay of protein of POLARIS gene	PLSp > ∅ compartment_1 * function_9(k9, PLSp)
v_Auxin	vAuxin: Uptake rate of exogenous auxin (indole-3-acetic acid, IAA)	IAA > Auxin compartment_1 * k_auxin * IAA
v_Cytokinin	vCytokinin: Uptake rate of exogenous cytokinin	CK_ex > CK compartment_1 * k_cytokinin * CK_ex
v_Ethylene	vEthylene: Uptake rate of exogenous ACC (1-aminocyclopropane-1-carboxylic acid)	ACC > ET compartment_1 * k_ethylene * ACC

Parameters 0 32

Global parameters

Id	Value
k1	1.0 uM
k10	0.0003
k10a	0.5
k11	5.0
k12	0.1
k12a	0.1
k13	1.0
k14	3.0
k15	0.085
k16	0.3
k16a	1.0
k17	0.1
k18	0.1 uM
k18a	1.0
k19	1.0
k1a	1.0
k2	0.2
k2a	2.8
k2b	1.0 uM
k2c	0.01 uM
k3	2.0
k3a	0.45
k4	1.0
k5	1.0
k6	0.3
k6a	0.2 uM
k7	1.0
k8	1.0
k9	1.0
k_auxin	70.0
k_cytokinin	10.0
k_ethylene	0.5

Local parameters

Id	Value	Reaction

Rules 0 0 3

Assignment rules

Definition
CTR1 = CTR1T - CTR1_star
Re = ReT - Re_star
Ra = RaT - Ra_star

Rate rules

Definition

Algebraic rules

Definition

Function definitions 18

Definition
function_16(Re_star, k14, CTR1) = k14 * Re_star * CTR1
function_15(ET, k13) = k13 * ET
function_3(k2, k2a, ET, CK, k2b, PLSp, k2c) = k2 + k2a * (ET / (1 + CK / k2b)) * (PLSp / (k2c + PLSp))
function_2(k1a, X, k1) = k1a / (1 + X / k1)
function_1(k3, k3a, X, Auxin) = (k3 + k3a * X) * Auxin
function_21(CK, k19) = k19 * CK
function_19(X, k17) = k17 * X
function_18(CTR1_star, k16, k16a) = k16 - k16a * CTR1_star
function_20(Auxin, k18a, k18) = k18a / (1 + Auxin / k18)
function_17(CTR1_star, k15) = k15 * CTR1_star
function_13(Auxin, CK, k12, k12a) = k12 + k12a * Auxin * CK
function_12(Re_star, ET, k11) = k11 * Re_star * ET
function_10(k10, PLSp, k10a, Re) = (k10 + k10a * PLSp) * Re
function_9(k9, PLSp) = k9 * PLSp
function_8(k8, PLSm) = k8 * PLSm
function_7(k7, PLSm) = k7 * PLSm
function_6(k6, Ra_star, ET, k6a) = k6 * Ra_star / (1 + ET / k6a)
function_4(k4, Auxin, Ra) = k4 * Auxin * Ra

Events 0

Trigger	Assignments