Cargando…

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

BACKGROUND: 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 pheno...

Descripción completa

Detalles Bibliográficos
Autores principales: Zakhartsev, Maksim, Medvedeva, Irina, Orlov, Yury, Akberdin, Ilya, Krebs, Olga, Schulze, Waltraud X.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: BioMed Central 2016
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5192601/
https://www.ncbi.nlm.nih.gov/pubmed/28031032
http://dx.doi.org/10.1186/s12870-016-0868-3
_version_ 1782487810065825792
author Zakhartsev, Maksim
Medvedeva, Irina
Orlov, Yury
Akberdin, Ilya
Krebs, Olga
Schulze, Waltraud X.
author_facet Zakhartsev, Maksim
Medvedeva, Irina
Orlov, Yury
Akberdin, Ilya
Krebs, Olga
Schulze, Waltraud X.
author_sort Zakhartsev, Maksim
collection PubMed
description BACKGROUND: 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. RESULTS: 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 CO(2) under 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. CONCLUSIONS: 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. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/s12870-016-0868-3) contains supplementary material, which is available to authorized users.
format Online
Article
Text
id pubmed-5192601
institution National Center for Biotechnology Information
language English
publishDate 2016
publisher BioMed Central
record_format MEDLINE/PubMed
spelling pubmed-51926012016-12-29 Metabolic model of central carbon and energy metabolisms of growing Arabidopsis thaliana in relation to sucrose translocation Zakhartsev, Maksim Medvedeva, Irina Orlov, Yury Akberdin, Ilya Krebs, Olga Schulze, Waltraud X. BMC Plant Biol Research Article BACKGROUND: 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. RESULTS: 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 CO(2) under 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. CONCLUSIONS: 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. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/s12870-016-0868-3) contains supplementary material, which is available to authorized users. BioMed Central 2016-12-28 /pmc/articles/PMC5192601/ /pubmed/28031032 http://dx.doi.org/10.1186/s12870-016-0868-3 Text en © The Author(s). 2016 Open AccessThis article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.
spellingShingle Research Article
Zakhartsev, Maksim
Medvedeva, Irina
Orlov, Yury
Akberdin, Ilya
Krebs, Olga
Schulze, Waltraud X.
Metabolic model of central carbon and energy metabolisms of growing Arabidopsis thaliana in relation to sucrose translocation
title Metabolic model of central carbon and energy metabolisms of growing Arabidopsis thaliana in relation to sucrose translocation
title_full Metabolic model of central carbon and energy metabolisms of growing Arabidopsis thaliana in relation to sucrose translocation
title_fullStr Metabolic model of central carbon and energy metabolisms of growing Arabidopsis thaliana in relation to sucrose translocation
title_full_unstemmed Metabolic model of central carbon and energy metabolisms of growing Arabidopsis thaliana in relation to sucrose translocation
title_short Metabolic model of central carbon and energy metabolisms of growing Arabidopsis thaliana in relation to sucrose translocation
title_sort metabolic model of central carbon and energy metabolisms of growing arabidopsis thaliana in relation to sucrose translocation
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5192601/
https://www.ncbi.nlm.nih.gov/pubmed/28031032
http://dx.doi.org/10.1186/s12870-016-0868-3
work_keys_str_mv AT zakhartsevmaksim metabolicmodelofcentralcarbonandenergymetabolismsofgrowingarabidopsisthalianainrelationtosucrosetranslocation
AT medvedevairina metabolicmodelofcentralcarbonandenergymetabolismsofgrowingarabidopsisthalianainrelationtosucrosetranslocation
AT orlovyury metabolicmodelofcentralcarbonandenergymetabolismsofgrowingarabidopsisthalianainrelationtosucrosetranslocation
AT akberdinilya metabolicmodelofcentralcarbonandenergymetabolismsofgrowingarabidopsisthalianainrelationtosucrosetranslocation
AT krebsolga metabolicmodelofcentralcarbonandenergymetabolismsofgrowingarabidopsisthalianainrelationtosucrosetranslocation
AT schulzewaltraudx metabolicmodelofcentralcarbonandenergymetabolismsofgrowingarabidopsisthalianainrelationtosucrosetranslocation