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A consensus yeast metabolic network reconstruction obtained from a community approach to systems biology

Nature Biotechnology volume 26, pages 1155–1160 (2008)Cite this article

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Abstract

Genomic data allow the large-scale manual or semi-automated assembly of metabolic network reconstructions, which provide highly curated organism-specific knowledge bases. Although several genome-scale network reconstructions describe Saccharomyces cerevisiae metabolism, they differ in scope and content, and use different terminologies to describe the same chemical entities. This makes comparisons between them difficult and underscores the desirability of a consolidated metabolic network that collects and formalizes the 'community knowledge' of yeast metabolism. We describe how we have produced a consensus metabolic network reconstruction for S. cerevisiae. In drafting it, we placed special emphasis on referencing molecules to persistent databases or using database-independent forms, such as SMILES or InChI strings, as this permits their chemical structure to be represented unambiguously and in a manner that permits automated reasoning. The reconstruction is readily available via a publicly accessible database and in the Systems Biology Markup Language (http://www.comp-sys-bio.org/yeastnet). It can be maintained as a resource that serves as a common denominator for studying the systems biology of yeast. Similar strategies should benefit communities studying genome-scale metabolic networks of other organisms.

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Figure 1: An example of the SBML annotation of a metabolite species using the example of ATP, as used in the reconstruction of the consensus network, illustrating its use of the Systems Biology Ontology (http://www.ebi.ac.uk/sbo/) and its MIRIAM compliance.
Figure 2: Degree distribution of the metabolic network.

Change history

  • 07 May 2012

    In the HTML version of this article initially published, Nils Blüthgen’s name was spelled as Büthgen. The error has been corrected in the HTML version of the article.

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Acknowledgements

The Manchester groups thank the UK Biotechnology and Biological Sciences Research Council (BBSRC) and the Engineering and Physical Sciences Research Council (EPSRC) for financial support including for the Manchester Centre for Integrative Systems Biology (http://www.mcisb.org/). The UCSD participants thank the National Institutes of Health for financial support (NIH R01 GM071808). We thank Diane Kelly, Sarah Keating and Norman Paton for many useful discussions. The Jamboree was held under the auspices and with the sponsorship of the Yeast Systems Biology Network (EC Contract: LSHG-CT-2005-018942).

Author information

Author notes

  1. Markus J Herrgård & Dina Petranovic

    Present address: Present addresses: Synthetic Genomics, Inc., 11149 N. Torrey Pines Rd., La Jolla, California 92037, USA (M.J.H.) and Department of Chemical and Biological Engineering, Chalmers University of Technology, SE-412 96 Gothenburg, Sweden (D.P.).,

  2. Markus J Herrgård and Neil Swainston: These authors contributed equally to this work.

Authors and Affiliations

  1. Department of Bioengineering, University of California, San Diego, 9500 Gilman Drive, La Jolla, 92093-0412, California, USA

    Markus J Herrgård, Monica L Mo & Bernhard Ø Palsson

  2. School of Computer Science, The University of Manchester, Oxford Rd., Manchester, M13 9PL, UK

    Neil Swainston, Peter Li, Stephen Pettifer, Irena Spasié & Pedro Mendes

  3. The Manchester Centre for Integrative Systems Biology, Manchester Interdisciplinary Biocentre, The University of Manchester, 131 Princess St., Manchester, M1 7DN, UK

    Neil Swainston, Paul Dobson, Warwick B Dunn, Nils Blüthgen, Peter Li, Stephen Pettifer, Evangelos Simeonidis, Kieran Smallbone, Irena Spasié, Dieter Weichart, David S Broomhead, Hans V Westerhoff, Stephen G Oliver, Pedro Mendes & Douglas B Kell

  4. School of Chemistry, The University of Manchester, Manchester, M13 9PL, UK

    Paul Dobson, Warwick B Dunn, Dieter Weichart & Douglas B Kell

  5. Department of Chemical Engineering, Boğaziçi University, Bebek 34342, Istanbul, Turkey

    K Yalçin Arga & Betül Kürdar

  6. VTT Biotechnology Espoo, PO Box 1500, FIN-02044, Finland

    Mikko Arvas & Merja Penttilä

  7. School of Chemical Engineering and Analytical Science, The University of Manchester, UK

    Nils Blüthgen, Evangelos Simeonidis & Hans V Westerhoff

  8. Max-Planck-Institut für Molekulare Genetik, Ihnestrasse 73, Berlin, 14195, Germany

    Simon Borger, Wolfram Liebermeister & Edda Klipp

  9. Institut für Molekulare Systembiologie, ETH Zurich Wolfgang-Pauli-Str. 16, Zürich, 8093, Switzerland

    Roeland Costenoble, Matthias Heinemann & Uwe Sauer

  10. Control and Dynamical Systems, California Institute of Technology, Pasadena, 91125, California, USA

    Michael Hucka

  11. Computational Neurobiology, EMBL-EBI, Wellcome-Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK

    Nicolas Le Novère

  12. Department of Systems Biology, Center for Microbial Biotechnology, Technical University of Denmark, Building 223, DK-2800 Kgs. Lyngby, Denmark

    Ana Paula Oliveira, Dina Petranovic & Jens Nielsen

  13. School of Mathematics, The University of Manchester, Manchester, M13 9PL, UK

    Kieran Smallbone & David S Broomhead

  14. The Molecular Sciences Institute, 2168 Shattuck Avenue, Berkeley, 94704, California, USA

    Roger Brent

  15. Department of Molecular Cell Physiology, Vrije Universiteit, de Boelelaan 1085, Amsterdam, 1081 HV, The Netherlands

    Hans V Westerhoff

  16. Department of Biochemistry, University of Cambridge, Sanger Building, 80 Tennis Court Road, Cambridge, CB2 1GA, UK

    Stephen G Oliver

  17. Virginia Bioinformatics Institute, Virginia Tech, Washington St. 0477, Blacksburg, 24061, Virginia, USA

    Pedro Mendes

  18. Department of Chemical and Biological Engineering, Chalmers University of Technology, Gothenburg, SE-412 96, Sweden

    Jens Nielsen

Authors
  1. Markus J Herrgård
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  34. Douglas B Kell
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Contributions

All authors conceived the idea of the consensus reconstruction, the majority were present during the jamboree itself and all contributed to the writing of, and approved, the manuscript.

Corresponding author

Correspondence to Douglas B Kell.

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Herrgård, M., Swainston, N., Dobson, P. et al. A consensus yeast metabolic network reconstruction obtained from a community approach to systems biology. Nat Biotechnol 26, 1155–1160 (2008). https://doi.org/10.1038/nbt1492

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