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Integrated pathway modules using time-course metabolic profiles and EST data from Milnesium tardigradum
BACKGROUND: Tardigrades are multicellular organisms, resistant to extreme environmental changes such as heat, drought, radiation and freezing. They outlast these conditions in an inactive form (tun) to escape damage to cellular structures and cell death. Tardigrades are apparently able to prevent or...
Autores principales: | , , , , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
BioMed Central
2012
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3534414/ https://www.ncbi.nlm.nih.gov/pubmed/22713133 http://dx.doi.org/10.1186/1752-0509-6-72 |
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author | Beisser, Daniela Grohme, Markus A Kopka, Joachim Frohme, Marcus Schill, Ralph O Hengherr, Steffen Dandekar, Thomas Klau, Gunnar W Dittrich, Marcus Müller, Tobias |
author_facet | Beisser, Daniela Grohme, Markus A Kopka, Joachim Frohme, Marcus Schill, Ralph O Hengherr, Steffen Dandekar, Thomas Klau, Gunnar W Dittrich, Marcus Müller, Tobias |
author_sort | Beisser, Daniela |
collection | PubMed |
description | BACKGROUND: Tardigrades are multicellular organisms, resistant to extreme environmental changes such as heat, drought, radiation and freezing. They outlast these conditions in an inactive form (tun) to escape damage to cellular structures and cell death. Tardigrades are apparently able to prevent or repair such damage and are therefore a crucial model organism for stress tolerance. Cultures of the tardigrade Milnesium tardigradum were dehydrated by removing the surrounding water to induce tun formation. During this process and the subsequent rehydration, metabolites were measured in a time series by GC-MS. Additionally expressed sequence tags are available, especially libraries generated from the active and inactive state. The aim of this integrated analysis is to trace changes in tardigrade metabolism and identify pathways responsible for their extreme resistance against physical stress. RESULTS: In this study we propose a novel integrative approach for the analysis of metabolic networks to identify modules of joint shifts on the transcriptomic and metabolic levels. We derive a tardigrade-specific metabolic network represented as an undirected graph with 3,658 nodes (metabolites) and 4,378 edges (reactions). Time course metabolite profiles are used to score the network nodes showing a significant change over time. The edges are scored according to information on enzymes from the EST data. Using this combined information, we identify a key subnetwork (functional module) of concerted changes in metabolic pathways, specific for de- and rehydration. The module is enriched in reactions showing significant changes in metabolite levels and enzyme abundance during the transition. It resembles the cessation of a measurable metabolism (e.g. glycolysis and amino acid anabolism) during the tun formation, the production of storage metabolites and bioprotectants, such as DNA stabilizers, and the generation of amino acids and cellular components from monosaccharides as carbon and energy source during rehydration. CONCLUSIONS: The functional module identifies relationships among changed metabolites (e.g. spermidine) and reactions and provides first insights into important altered metabolic pathways. With sparse and diverse data available, the presented integrated metabolite network approach is suitable to integrate all existing data and analyse it in a combined manner. |
format | Online Article Text |
id | pubmed-3534414 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2012 |
publisher | BioMed Central |
record_format | MEDLINE/PubMed |
spelling | pubmed-35344142013-01-03 Integrated pathway modules using time-course metabolic profiles and EST data from Milnesium tardigradum Beisser, Daniela Grohme, Markus A Kopka, Joachim Frohme, Marcus Schill, Ralph O Hengherr, Steffen Dandekar, Thomas Klau, Gunnar W Dittrich, Marcus Müller, Tobias BMC Syst Biol Methodology Article BACKGROUND: Tardigrades are multicellular organisms, resistant to extreme environmental changes such as heat, drought, radiation and freezing. They outlast these conditions in an inactive form (tun) to escape damage to cellular structures and cell death. Tardigrades are apparently able to prevent or repair such damage and are therefore a crucial model organism for stress tolerance. Cultures of the tardigrade Milnesium tardigradum were dehydrated by removing the surrounding water to induce tun formation. During this process and the subsequent rehydration, metabolites were measured in a time series by GC-MS. Additionally expressed sequence tags are available, especially libraries generated from the active and inactive state. The aim of this integrated analysis is to trace changes in tardigrade metabolism and identify pathways responsible for their extreme resistance against physical stress. RESULTS: In this study we propose a novel integrative approach for the analysis of metabolic networks to identify modules of joint shifts on the transcriptomic and metabolic levels. We derive a tardigrade-specific metabolic network represented as an undirected graph with 3,658 nodes (metabolites) and 4,378 edges (reactions). Time course metabolite profiles are used to score the network nodes showing a significant change over time. The edges are scored according to information on enzymes from the EST data. Using this combined information, we identify a key subnetwork (functional module) of concerted changes in metabolic pathways, specific for de- and rehydration. The module is enriched in reactions showing significant changes in metabolite levels and enzyme abundance during the transition. It resembles the cessation of a measurable metabolism (e.g. glycolysis and amino acid anabolism) during the tun formation, the production of storage metabolites and bioprotectants, such as DNA stabilizers, and the generation of amino acids and cellular components from monosaccharides as carbon and energy source during rehydration. CONCLUSIONS: The functional module identifies relationships among changed metabolites (e.g. spermidine) and reactions and provides first insights into important altered metabolic pathways. With sparse and diverse data available, the presented integrated metabolite network approach is suitable to integrate all existing data and analyse it in a combined manner. BioMed Central 2012-06-19 /pmc/articles/PMC3534414/ /pubmed/22713133 http://dx.doi.org/10.1186/1752-0509-6-72 Text en Copyright ©2012 Beisser et al.; licensee BioMed Central Ltd. http://creativecommons.org/licenses/by/2.0 This is an Open Access article distributed under the terms of the Creative Commons Attribution License(http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. |
spellingShingle | Methodology Article Beisser, Daniela Grohme, Markus A Kopka, Joachim Frohme, Marcus Schill, Ralph O Hengherr, Steffen Dandekar, Thomas Klau, Gunnar W Dittrich, Marcus Müller, Tobias Integrated pathway modules using time-course metabolic profiles and EST data from Milnesium tardigradum |
title | Integrated pathway modules using time-course metabolic profiles and EST data from Milnesium tardigradum |
title_full | Integrated pathway modules using time-course metabolic profiles and EST data from Milnesium tardigradum |
title_fullStr | Integrated pathway modules using time-course metabolic profiles and EST data from Milnesium tardigradum |
title_full_unstemmed | Integrated pathway modules using time-course metabolic profiles and EST data from Milnesium tardigradum |
title_short | Integrated pathway modules using time-course metabolic profiles and EST data from Milnesium tardigradum |
title_sort | integrated pathway modules using time-course metabolic profiles and est data from milnesium tardigradum |
topic | Methodology Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3534414/ https://www.ncbi.nlm.nih.gov/pubmed/22713133 http://dx.doi.org/10.1186/1752-0509-6-72 |
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