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Cell Syst. 2016 May 25;2(5):312-22. doi: 10.1016/j.cels.2016.04.017. Epub 2016 May 19.

A Genome-Scale Database and Reconstruction of Caenorhabditis elegans Metabolism.

Author information

1
Research Group Theoretical Systems Biology, Friedrich Schiller-University (FSU) Jena, 07745 Jena, Germany; Department of Bioinformatics, Friedrich Schiller-University (FSU) Jena, 07743 Jena, Germany.
2
Research Group Theoretical Systems Biology, Friedrich Schiller-University (FSU) Jena, 07745 Jena, Germany.
3
Department of Human Nutrition, Friedrich Schiller-University Jena (FSU), 07743 Jena, Germany; Energy Metabolism Laboratory, Swiss Federal Institute of Technology (ETH) Zürich, 8003 Zürich, Switzerland.
4
Department of Human Nutrition, Friedrich Schiller-University Jena (FSU), 07743 Jena, Germany.
5
Research Group Theoretical Systems Biology, Friedrich Schiller-University (FSU) Jena, 07745 Jena, Germany; Research Group Medical Systems Biology, Christian-Albrechts-University Kiel, 24105 Kiel, Germany.
6
Department of Bioinformatics, Friedrich Schiller-University (FSU) Jena, 07743 Jena, Germany; Applied Systems Biology, Leibniz Institute for Natural Product Research and Infection Biology, Hans Knöll Institute, 07745Jena, Germany.
7
Department of Bioinformatics, Friedrich Schiller-University (FSU) Jena, 07743 Jena, Germany.
8
Institute of Molecular Systems Biology, Swiss Federal Institute of Technology (ETH) Zürich, 8093 Zürich, Switzerland.
9
Research Group Theoretical Systems Biology, Friedrich Schiller-University (FSU) Jena, 07745 Jena, Germany; Jena University Language and Information Engineering Lab, Friedrich Schiller-University (FSU) Jena, 07743 Jena, Germany.
10
Research Group Medical Systems Biology, Christian-Albrechts-University Kiel, 24105 Kiel, Germany; Research Group Theoretical Systems Biology, Friedrich Schiller-University (FSU) Jena, 07745 Jena, Germany. Electronic address: c.kaleta@iem.uni-kiel.de.

Abstract

We present a genome-scale model of Caenorhabditis elegans metabolism along with the public database ElegCyc (http://elegcyc.bioinf.uni-jena.de:1100), which represents a reference for metabolic pathways in the worm and allows for the visualization as well as analysis of omics datasets. Our model reflects the metabolic peculiarities of C. elegans that make it distinct from other higher eukaryotes and mammals, including mice and humans. We experimentally verify one of these peculiarities by showing that the lifespan-extending effect of L-tryptophan supplementation is dose dependent (hormetic). Finally, we show the utility of our model for analyzing omics datasets through predicting changes in amino acid concentrations after genetic perturbations and analyzing metabolic changes during normal aging as well as during two distinct, reactive oxygen species (ROS)-related lifespan-extending treatments. Our analyses reveal a notable similarity in metabolic adaptation between distinct lifespan-extending interventions and point to key pathways affecting lifespan in nematodes.

PMID:
27211858
DOI:
10.1016/j.cels.2016.04.017
[Indexed for MEDLINE]
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