A workflow for mathematical modeling of subcellular metabolic pathways in leaf metabolism of Arabidopsis thaliana

During the last decade genome sequencing has experienced a rapid technological development resulting in numerous sequencing projects and applications in life science. In plant molecular biology, the availability of sequence data on whole genomes has enabled the reconstruction of metabolic networks....

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Main Authors:	Nägele, Thomas, Weckwerth, Wolfram
Format:	Online
Language:	English
Published:	Frontiers Media S.A. 2013
Online Access:	https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3872044/

id	pubmed-3872044
recordtype	oai_dc
spelling	pubmed-38720442014-01-07 A workflow for mathematical modeling of subcellular metabolic pathways in leaf metabolism of Arabidopsis thaliana Nägele, Thomas Weckwerth, Wolfram Plant Science During the last decade genome sequencing has experienced a rapid technological development resulting in numerous sequencing projects and applications in life science. In plant molecular biology, the availability of sequence data on whole genomes has enabled the reconstruction of metabolic networks. Enzymatic reactions are predicted by the sequence information. Pathways arise due to the participation of chemical compounds as substrates and products in these reactions. Although several of these comprehensive networks have been reconstructed for the genetic model plant Arabidopsis thaliana, the integration of experimental data is still challenging. Particularly the analysis of subcellular organization of plant cells limits the understanding of regulatory instances in these metabolic networks in vivo. In this study, we develop an approach for the functional integration of experimental high-throughput data into such large-scale networks. We present a subcellular metabolic network model comprising 524 metabolic intermediates and 548 metabolic interactions derived from a total of 2769 reactions. We demonstrate how to link the metabolite covariance matrix of different Arabidopsis thaliana accessions with the subcellular metabolic network model for the inverse calculation of the biochemical Jacobian, finally resulting in the calculation of a matrix which satisfies a Lyaponov equation. In this way, different strategies of metabolite compartmentation and involved reactions were identified in the accessions when exposed to low temperature. Frontiers Media S.A. 2013-12-24 /pmc/articles/PMC3872044/ /pubmed/24400018 http://dx.doi.org/10.3389/fpls.2013.00541 Text en Copyright © 2013 Nägele and Weckwerth. http://creativecommons.org/licenses/by/3.0/ This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) or licensor are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.
repository_type	Open Access Journal
institution_category	Foreign Institution
institution	US National Center for Biotechnology Information
building	NCBI PubMed
collection	Online Access
language	English
format	Online
author	Nägele, Thomas Weckwerth, Wolfram
spellingShingle	Nägele, Thomas Weckwerth, Wolfram A workflow for mathematical modeling of subcellular metabolic pathways in leaf metabolism of Arabidopsis thaliana
author_facet	Nägele, Thomas Weckwerth, Wolfram
author_sort	Nägele, Thomas
title	A workflow for mathematical modeling of subcellular metabolic pathways in leaf metabolism of Arabidopsis thaliana
title_short	A workflow for mathematical modeling of subcellular metabolic pathways in leaf metabolism of Arabidopsis thaliana
title_full	A workflow for mathematical modeling of subcellular metabolic pathways in leaf metabolism of Arabidopsis thaliana
title_fullStr	A workflow for mathematical modeling of subcellular metabolic pathways in leaf metabolism of Arabidopsis thaliana
title_full_unstemmed	A workflow for mathematical modeling of subcellular metabolic pathways in leaf metabolism of Arabidopsis thaliana
title_sort	workflow for mathematical modeling of subcellular metabolic pathways in leaf metabolism of arabidopsis thaliana
description	During the last decade genome sequencing has experienced a rapid technological development resulting in numerous sequencing projects and applications in life science. In plant molecular biology, the availability of sequence data on whole genomes has enabled the reconstruction of metabolic networks. Enzymatic reactions are predicted by the sequence information. Pathways arise due to the participation of chemical compounds as substrates and products in these reactions. Although several of these comprehensive networks have been reconstructed for the genetic model plant Arabidopsis thaliana, the integration of experimental data is still challenging. Particularly the analysis of subcellular organization of plant cells limits the understanding of regulatory instances in these metabolic networks in vivo. In this study, we develop an approach for the functional integration of experimental high-throughput data into such large-scale networks. We present a subcellular metabolic network model comprising 524 metabolic intermediates and 548 metabolic interactions derived from a total of 2769 reactions. We demonstrate how to link the metabolite covariance matrix of different Arabidopsis thaliana accessions with the subcellular metabolic network model for the inverse calculation of the biochemical Jacobian, finally resulting in the calculation of a matrix which satisfies a Lyaponov equation. In this way, different strategies of metabolite compartmentation and involved reactions were identified in the accessions when exposed to low temperature.
publisher	Frontiers Media S.A.
publishDate	2013
url	https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3872044/
_version_	1612041190435192832

A workflow for mathematical modeling of subcellular metabolic pathways in leaf metabolism of Arabidopsis thaliana

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