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Open Access Methodology article

Integrated pathway modules using time-course metabolic profiles and EST data from Milnesium tardigradum

Daniela Beisser1, Markus A Grohme2, Joachim Kopka3, Marcus Frohme2, Ralph O Schill4, Steffen Hengherr4, Thomas Dandekar1, Gunnar W Klau56, Marcus Dittrich1* and Tobias Müller1*

Author Affiliations

1 Department of Bioinformatics, Biocenter, University of Würzburg, Am Hubland, Würzburg 97074, Germany

2 Molecular Biotechnology and Functional Genomics, Technical University of Applied Sciences Wildau, Bahnhofstraße 1, Wildau 15745, Germany

3 Department of Molecular Physiology, Max-Planck-Institute of Molecular Plant Physiology, Potsdam-Golm, Brandenburg, Germany

4 Department of Zoology, Biological Institute, University of Stuttgart, Pfaffenwaldring 57, Stuttgart 70569, Germany

5 Life Sciences group, CWI, Science Park 123, Amsterdam 1098 XG, the Netherlands

6 , Netherlands Institute for Systems Biology, Amsterdam, the Netherlands

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BMC Systems Biology 2012, 6:72  doi:10.1186/1752-0509-6-72

Published: 19 June 2012

Abstract

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.

Keywords:
Integrated network analysis; Functional modules; Metabolic profiles; Metabolic pathways; Trend test