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LeishCyc: A Guide to Building a Metabolic Pathway Database and Visualization of Metabolomic Data

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Microbial Systems Biology

Part of the book series: Methods in Molecular Biology ((MIMB,volume 881))

Abstract

The complexity of the metabolic networks in even the simplest organisms has raised new challenges in organizing metabolic information. To address this, specialized computer frameworks have been developed to capture, manage, and visualize metabolic knowledge. The leading databases of metabolic information are those organized under the umbrella of the BioCyc project, which consists of the reference database MetaCyc, and a number of pathway/genome databases (PGDBs) each focussed on a specific organism. A number of PGDBs have been developed for bacterial, fungal, and protozoan pathogens, greatly facilitating dissection of the metabolic potential of these organisms and the identification of new drug targets. Leishmania are protozoan parasites belonging to the family Trypanosomatidae that cause a broad spectrum of diseases in humans. In this work we use the LeishCyc database, the BioCyc database for Leishmania major, to describe how to build a BioCyc database from genomic sequences and associated annotations. By using metabolomic data generated in our group, we show how such databases can be utilized to elucidate specific changes in parasite metabolism.

Equal first author contribution.

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Acknowledgments

This work is supported by the grant DP0878227 from the Australian Research Council. We thank David P. de Souza for assistance in the preparation and analysis of metabolite extracts by GC-MS. We thank Peter D. Karp for valuable comments on the manuscript.

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Authors and Affiliations

  1. Department of Biochemistry and Molecular Biology, University of Melbourne, Parkville, VIC, Australia

    Eleanor C. Saunders, James I. MacRae, Thomas Naderer, Milica Ng & Malcolm J. McConville

  2. Bio21 Institute of Molecular Science and Biotechnology, University of Melbourne, Parkville, VIC, Australia

    Eleanor C. Saunders, James I. MacRae, Thomas Naderer, Milica Ng, Malcolm J. McConville & Vladimir A. Likić

Authors
  1. Eleanor C. Saunders
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  2. James I. MacRae
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  3. Thomas Naderer
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  4. Milica Ng
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  5. Malcolm J. McConville
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  6. Vladimir A. Likić
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Corresponding author

Correspondence to Vladimir A. Likić .

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Editors and Affiliations

  1. Physics & Life Sciences Directorate, Biosciences & Biotechnology Div., Lawrence Livermore National Laboratory, East Avenue 7000, Livermore, 94551, California, USA

    Ali Navid

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Saunders, E.C., MacRae, J.I., Naderer, T., Ng, M., McConville, M.J., Likić, V.A. (2012). LeishCyc: A Guide to Building a Metabolic Pathway Database and Visualization of Metabolomic Data. In: Navid, A. (eds) Microbial Systems Biology. Methods in Molecular Biology, vol 881. Humana Press, Totowa, NJ. https://doi.org/10.1007/978-1-61779-827-6_17

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  • DOI: https://doi.org/10.1007/978-1-61779-827-6_17

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  • Publisher Name: Humana Press, Totowa, NJ

  • Print ISBN: 978-1-61779-826-9

  • Online ISBN: 978-1-61779-827-6

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