Metabolic analysis of effects of sucrose translocation on phenotypic traits of Arabidopsis thaliana (snapshot 9)

Sucrose translocation between plant tissues is crucial for growth, development and reproduction of plants. Systemic analysis of this metabolic process and underlying regulatory processes can help to achieve better understanding of carbon distribution within the plant and the formation of phenotypic traits. Sucrose translocation from ‘source’ tissues (e.g. mesophyll) to ‘sink’ tissues (e.g. root) is tightly bound to the proton gradient across the membranes. The plant sucrose transporters are grouped into efflux exporters (SWEET family) and proton-symport importers (SUC, STP families). To better understand the regulatory connections between sucrose export from source tissues and sucrose import into sink tissues, there is a need for a metabolic model that takes in account the tissue organisation of Arabidopsis thaliana with corresponding metabolic specificities of respective tissues in terms of sucrose and proton production/utilization. An ability of the model to operate under different light modes (‘light’ and ‘dark’) and correspondingly in different energy producing modes is additional validating feature.

DOI: 10.15490/seek.1.investigation.74.9

Created at: 4th Jun 2016 at 00:00

Contents

Analysis of central carbon and energy metabolisms of growing Arabidopsis thaliana in relation to sucrose translocation

we describe a multi-compartmental model consisting of a mesophyll cell with plastid and mitochondrion, a phloem cell, as well as a root cell with mitochondrion. In this model, the phloem was considered as a non-growing transport compartment, the mesophyll compartment was considered as both autotrophic (growing on CO2 under light) and heterotrophic (growing on starch in darkness), and the root was always considered as heterotrophic tissue completely dependent on sucrose supply from the mesophyll
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Flux Balance Analysis of multi-compartment metabolic model of growing Arabidopsis thaliana

The multi-compartmental metabolic network of Arabidopsis thaliana was reconstructed and optimized in order to explain growth stoichiometry of the plant both in light and in dark conditions. Balances and turnover of energy (ATP/ADP) and redox (NAD(P)H/NAD(P)) metabolites as well as proton in different compartments were estimated. The model showed that in light conditions, the plastid ATP balance depended on the relationship between fluxes through photorespiration and photosynthesis including both
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ZucAt: FBA constraints for light conditions

Flux Balance Analysis (FBA) constraints for light conditions

  • FBA_constraints_light.txt

ZucAt: FBA constraints for dark conditions

Flux Balance Analysis (FBA) constraints for dark conditions

  • FBA_constraints_dark.txt

ZucAt: FBA solution of the model under dark growth conditions

The solution of Flux Balance Analysis (FBA) represent metabolic flux distribution in the model under dark growth conditions (i.e. constraints)

  • 2016-05-30 FBA dark v4.0.txt

ZucAt: The stoichiometric matrix of the model

The stoichiometric matrix of the multi-compartment metabolic model of growing Arabidopsis thaliana

  • Arabidopsis_thaliana_model_stoichiometric_matrix.txt

ZucAt: The compound database

The database in ASCII format includes information on compounds and metabolites (trivial name, elemental composition, charge, external database referece, etc) used in the model

  • Arabidopsis_compounds.dat

ZucAt: The gene database

The database in ASCII format includes information on gene (gene models in ATG format, gene definition, catalyzed reactions in the model, external database refeneces, locus information, etc) used in the model

  • Arabidopsis_enzymes.dat

ZucAt: The transformers database

The database in ASCII format includes information on transformers [reactions, transport steps, polymerizations] (model's identifier, trivial name, EC number, stoichiometric equation, external database referece, activators, belonging to a pathway, etc) used in the model

  • Arabidopsis_transformers.dat

ZucAt: FBA solution of the model under light growth conditions (I)

The solution of Flux Balance Analysis (FBA) represents metabolic flux distribution in ZucAt model under light growth conditions. In this solution, (i) the ratio photorespiration / photosynthesis has been fixed to 0.25; (ii) and cyclic electron flow through FQR (ferredoxin-plastoquinone reductase) has been set to 0. Under this constraints, ATP formed by non-cyclic photophosphorylation is not sufficient to fulfill ATP/NADPH ratio for carbon fixation, therefore plastid imports ATP from cytoplasm.

  • 2016-06-03 FBA light v4.0 (Photoresp=0.25, FQR=0).txt

ZucAt: FBA solution of the model under light growth conditions (II)

The solution of Flux Balance Analysis (FBA) represents metabolic flux distribution in ZucAt model under light growth conditions. In this solution, (i) the ratio photorespiration / photosynthesis has been fixed to 0.25; (ii) and ATP transport between plastid and cytoplasm has been set to 0. The last constraint allows finding the ratio between fluxes through FQR (ferredoxin-plastoquinone reductase) and FRN (ferredoxin-NADP oxidoreductase) under which the ATP balance in plastid becomes self-sufficient
...

  • 2016-06-03 FBA light v4.0 (Photoresp=0.25, T.ATP=0).txt

ZucAt: FBA solution of the model under light growth conditions (III)

The solution of Flux Balance Analysis (FBA) represents metabolic flux distribution in ZucAt model under light growth conditions. In this solution, (i) the ratio photorespiration / photosynthesis has been fixed to 0.25; and (ii) cyclic electron flow through FQR (ferredoxin-plastoquinone reductase) has been set 0.5 from non-cyclic flow through FRN (ferredoxin-NADP oxidoreductase). Under this constraints, ATP is over-produced in plastid and a surplus is exported to cytoplasm. Flux through FQR
...

  • 2016-06-03 FBA light v4.0 (Photoresp=0.25, FQR=0.5).txt

ZucAt: the model documentation

The ASCII file includes complete information on used transformers / compounds / genes and their inter-connection in the model. The Transformer information includes: Identifier name, Trivial name, Stoichiometric equation, Compartment, EC number, Pathway, Associated genes). The Compound information includes: Identifier name, Trivial name, Kegg ID, Compartment. The Gene information includes: ATG code of the genes whose products participate in transformations accounted in the model, Association with
...

  • Arabidopsis_thaliana_model_documentation.txt

ZucAt: FBA solution of the model under light growth conditions (IV)

The solution of Flux Balance Analysis (FBA) represents metabolic flux distribution in the model under light growth conditions. In this solution, (i) the photorespiration was set to 0; and (ii) cyclic electron flow through FQR (ferredoxin-plastoquinone reductase) has been set of 0.1 of flow through FRN (ferredoxin-NADP oxidoreductase). Under this constraints, ATP is under-produced in plastid and therefore is additionally imported to cytoplasm. Flux through FQR represents cyclic electron flow through
...

  • 2016-06-03 FBA light v4.0 (Photoresp=0, FQR=0.1).txt

ZucAt: FBA solution of the model under light growth conditions (V)

The solution of Flux Balance Analysis (FBA) represents metabolic flux distribution in ZucAt model under light growth conditions. In this solution, (i) the ratio photorespiration / photosynthesis has been fixed to 0.25; and (ii) cyclic electron flow through FQR (ferredoxin-plastoquinone reductase) has been set 0.1 from non-cyclic flow through FRN (ferredoxin-NADP oxidoreductase). Under this constraints, ATP formed by non-cyclic photophosphorylation is not sufficient to fulfill ATP/NADPH ratio for
...

  • 2016-06-03 FBA light v4.0 (Photoresp=0.25, FQR=0.1).txt

ZucAt: multi-compartment metabolic model of growing Arabidopsis thaliana

The model presents a multi-compartmental (mesophyll, phloem and root) metabolic model of growing Arabidopsis thaliana. The flux balance analysis (FBA) of the model quantifies: sugar metabolism, central carbon and nitrogen metabolism, energy and redox metabolism, proton turnover, sucrose translocation from mesophyll to root and biomass growth under both dark- and light-growth conditions with corresponding growth either on starch (in darkness) or on CO2 (under light). The FBA predicts that
...

  • Arabidopsis_thaliana_model.m
  • Arabidopsis_thaliana_model.xml
  • Arabidopsis_thaliana_model_image.jpg
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Citation
Zakhartsev, M., & Krebs, O. (2016). Metabolic analysis of effects of sucrose translocation on phenotypic traits of Arabidopsis thaliana. FAIRDOMHub. http://doi.org/10.15490/seek.1.investigation.74.9
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