title: Metabolic model of central carbon and energy metabolisms of growing Arabidopsis thaliana in relation to sucrose translocation.
abstract: Sucrose translocation between plant tissues is crucial for growth, development and reproduction of plants. Systemic analysis of these metabolic and underlying regulatory processes allow a detailed understanding of carbon distribution within the plant and the formation of associated 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 regulation of 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 particularly important in understanding regulatory modules.
  
  
  
  Here, 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 CO2under light) and heterotrophic (growing on starch in darkness), and the root was always considered as heterotrophic tissue dependent on sucrose supply from the mesophyll compartment. In total, the model includes 413 balanced compounds interconnected by 400 transformers. The structured metabolic model accounts for central carbon metabolism, photosynthesis, photorespiration, carbohydrate metabolism, energy and redox metabolisms, proton metabolism, biomass growth, nutrients uptake, proton gradient generation and sucrose translocation between tissues. Biochemical processes in the model were associated with gene-products (742 ORFs). Flux Balance Analysis (FBA) of the model resulted in balanced carbon, nitrogen, proton, energy and redox states under both light and dark conditions. The main H+-fluxes were reconstructed and their directions matched with proton-dependent sucrose translocation from 'source' to 'sink' under any light condition.
  
  
  
  The model quantified the translocation of sucrose between plant tissues in association with an integral balance of protons, which in turn is defined by operational modes of the energy metabolism.
authors.affiliation: Department of Plant Systems Biology, University of Hohenheim, Fruwirthstraße 12, 70599, Stuttgart, Germany.
authors.forename: Maksim
authors.initials: M
authors.lastname: Zakhartsev
authors.affiliation: Novosibirsk State University, Pirogova 2, 630090, Novosibirsk, Russia.
authors.forename: Irina
authors.initials: I
authors.lastname: Medvedeva
authors.affiliation: The Federal Research Center Institute of Cytology and Genetics, Russian Academy of Sciences, Lavrentyeva 10, 630090, Novosibirsk, Russia.
authors.forename: Yury
authors.initials: Y
authors.lastname: Orlov
authors.affiliation: The Federal Research Center Institute of Cytology and Genetics, Russian Academy of Sciences, Lavrentyeva 10, 630090, Novosibirsk, Russia.|Biology Department, San Diego State University, San Diego, CA, 92182-4614, USA.
authors.forename: Ilya
authors.initials: I
authors.lastname: Akberdin
authors.affiliation: Heidelberg Institute of Theoretical Sciences, Schloss-Wolfsbrunnenweg 35, 69118, Heidelberg, Germany.
authors.forename: Olga
authors.initials: O
authors.lastname: Krebs
authors.affiliation: Department of Plant Systems Biology, University of Hohenheim, Fruwirthstraße 12, 70599, Stuttgart, Germany. wschulze@uni-hohenheim.de.
authors.forename: Waltraud X
authors.initials: WX
authors.lastname: Schulze
mesh_terms: D017360:Arabidopsis / Q000235:genetics / Q000254:growth & development / Q000378:metabolism* / Q000528:radiation effects; D029681:Arabidopsis Proteins / Q000235:genetics / Q000378:metabolism; D001692:Biological Transport; D002244:Carbon / Q000378:metabolism; D004734:Energy Metabolism; D018506:Gene Expression Regulation, Plant / Q000528:radiation effects; D008027:Light; D008954:Models, Biological; D052585:Phloem / Q000235:genetics / Q000378:metabolism; D010788:Photosynthesis; D013213:Starch / Q000378:metabolism; D013395:Sucrose / Q000378:metabolism*
chemical_list: D029681:Arabidopsis Proteins; D013395:Sucrose; D002244:Carbon; D013213:Starch
keywords: Central carbon metabolism; Diurnal growth; Energy metabolism; Flux balance analysis; Multi-compartment metabolic model; Sucrose metabolism; Sucrose transport