Larbat2016.3 - Modeling the diversion of primary carbon flux into secondary metabolism under variable nitrate and light or dark conditions (Light Dark Cycles with Minimum Starch Adaption)

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Model Identifier
BIOMD0000000859
Short description 
This is a global mathematical model describing metabolic partitioning of carbon resources in plants between growth and defense, as a function of nitrate fertilization. The model hinges on the dynamics of sucrose inflow/outflow properties. The model also accounts for variations in photosynthetic activity as dictated by a daily light/dark cycle. Furthermore, the adaptive changes in starch metabolism that occur with changing light durations (short days vs long days) are also investigated.
Format
SBML (L2V4)
Related Publication
  • Modeling the diversion of primary carbon flux into secondary metabolism under variable nitrate and light/dark conditions.
  • Larbat R, Robin C, Lillo C, Drengstig T, Ruoff P
  • Journal of theoretical biology , 8/ 2016 , Volume 402 , pages: 144-157 , PubMed ID: 27164436
  • INRA UMR 1121, Agronomie & Environnement Nancy-Colmar, TSA 40602, 54518 Vandoeuvre Cedex, France; Université de Lorraine UMR 1121, Agronomie & Environnement Nancy-Colmar, TSA 40602, 54518 Vandoeuvre Cedex, France. Electronic address: romain.larbat@univ-lorraine.fr.
  • In plants, the partitioning of carbon resources between growth and defense is detrimental for their development. From a metabolic viewpoint, growth is mainly related to primary metabolism including protein, amino acid and lipid synthesis, whereas defense is based notably on the biosynthesis of a myriad of secondary metabolites. Environmental factors, such as nitrate fertilization, impact the partitioning of carbon resources between growth and defense. Indeed, experimental data showed that a shortage in the nitrate fertilization resulted in a reduction of the plant growth, whereas some secondary metabolites involved in plant defense, such as phenolic compounds, accumulated. Interestingly, sucrose, a key molecule involved in the transport and partitioning of carbon resources, appeared to be under homeostatic control. Based on the inflow/outflow properties of sucrose homeostatic regulation we propose a global model on how the diversion of the primary carbon flux into the secondary phenolic pathways occurs at low nitrate concentrations. The model can account for the accumulation of starch during the light phase and the sucrose remobilization by starch degradation during the night. Day-length sensing mechanisms for variable light-dark regimes are discussed, showing that growth is proportional to the length of the light phase. The model can describe the complete starch consumption during the night for plants adapted to a certain light/dark regime when grown on sufficient nitrate and can account for an increased accumulation of starch observed under nitrate limitation.
Contributors
Submitter of the first revision: Johannes Meyer
Submitter of this revision: Johannes Meyer
Modellers: Johannes Meyer

Metadata information

hasProperty (3 statements)
Mathematical Modelling Ontology Ordinary differential equation model
Gene Ontology sucrose metabolic process
Gene Ontology starch metabolic process

Curation status
Curated
Modelling approach(es)
ordinary differential equation model
Tags

Connected external resources

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Name Description Size Actions

Model files
Larbat2016.3.xml SBML L2V4 Representation of Larbat2016.3 - Modeling the diversion of primary carbon flux into secondary metabolism under variable nitrate and light or dark conditions (Light Dark Cycles with Minimum Starch Adaption) 119.17 KB Preview | Download

Additional files
Larbat2016.3.cps COPASI file of Larbat2016.3 - Modeling the diversion of primary carbon flux into secondary metabolism under variable nitrate and light or dark conditions (Light Dark Cycles with Minimum Starch Adaption) 185.07 KB Preview | Download
Larbat2016.3.sedml SED-ML file of Larbat2016.3 - Modeling the diversion of primary carbon flux into secondary metabolism under variable nitrate and light or dark conditions (Light Dark Cycles with Minimum Starch Adaption) 4.38 KB Preview | Download

  • Model originally submitted by : Johannes Meyer
  • Submitted: Nov 13, 2019 4:56:20 PM
  • Last Modified: Nov 13, 2019 4:56:20 PM
Revisions
  • Version: 2 public model Download this version
    • Submitted on: Nov 13, 2019 4:56:20 PM
    • Submitted by: Johannes Meyer
    • With comment: Automatically added model identifier BIOMD0000000859
Legends
: Variable used inside SBML models


Species
Species Initial Concentration/Amount
N

nitrate 		5.0 mmol
trioseP

CHEBI:27137 ; phosphorylated 		0.0 mmol
ETP

C49887 		0.0 mmol
M1

0000568 ; C63905 		0.0 mmol
M2

0000568 ; C61366 		3.342 mmol
Estarch

C49887 ; starch 		55.574 mmol
sucr

sucrose 		5.14E-5 mmol
EtrioseP

C49887 ; CHEBI:27137 		6.012 mmol
Enitrate

nitrate ; C49887 		18.75 mmol
Reactions
Reactions Rate Parameters
N => compartment*k12*N k12 = 15.0
=> trioseP; ECO2 compartment*k29*f_act_trioseP*ECO2 k29 = 10.1; f_act_trioseP = 0.999999999998
=> ETP; starch compartment*k53*starch k53 = 2.5E-4
M1 => M2 compartment*k44*K_I_L*M1/(K_I_L+k29) k29 = 10.1; k44 = 1000.0; K_I_L = 1.0E-4
M2 => compartment*k29*k40*M2/(K_M_M2+M2) K_M_M2 = 1.0E-6; k29 = 10.1; k40 = 0.0568
ETP => compartment*k54*ETP/(k55+ETP) k54 = 0.00625; k55 = 1.0E-4
=> Estarch compartment*k34 k34 = 9.8
sucr => compartment*k5*sucr*f_act_pcf f_act_pcf = 0.833333333333333; k5 = 2.492
EtrioseP => ; sucr compartment*k2*sucr*EtrioseP/(k3+EtrioseP) k3 = 1.0E-5; k2 = 1.0
Enitrate => ; N compartment*k27*N*Enitrate/(k28+Enitrate) k27 = 0.1; k28 = 1.0E-6
Curator's comment:
(added: 13 Nov 2019, 16:55:56, updated: 13 Nov 2019, 16:55:56)
Reproduced plot of Figure 7(c)(Short Days) in the original publication. Model simulated and plot produced using COPASI 4.24 (Build 197).