Challenges to be faced in the reconstruction of metabolic networks from public databases.

In the post-genomic era, the biochemical information for individual compounds, enzymes, reactions to be found within named organisms has become readily available. The well-known KEGG and BioCyc databases provide a comprehensive catalogue for this information and have thereby substantially aided the scientific community. Using these databases, the complement of enzymes present in a given organism can be determined and, in principle, used to reconstruct the metabolic network. However, such reconstructed networks contain numerous properties contradicting biological expectation. The metabolic networks for a number of organisms are reconstructed from KEGG and BioCyc databases, and features of these networks are related to properties of their originating database.

[1]  B. Palsson,et al.  Genome-scale reconstruction of the metabolic network in Staphylococcus aureus N315: an initial draft to the two-dimensional annotation , 2005, BMC Microbiology.

[2]  Andrew R. Dalby,et al.  Constructing an enzyme-centric view of metabolism , 2004, Bioinform..

[3]  Hiroyuki Ogata,et al.  KEGG: Kyoto Encyclopedia of Genes and Genomes , 1999, Nucleic Acids Res..

[4]  Steffen Klamt,et al.  Minimal cut sets in biochemical reaction networks , 2004, Bioinform..

[5]  Juan Carlos Nuño,et al.  METATOOL: for studying metabolic networks , 1999, Bioinform..

[6]  B. Palsson,et al.  Genome-scale reconstruction of the Saccharomyces cerevisiae metabolic network. , 2003, Genome research.

[7]  D. Fell,et al.  Detection of elementary flux modes in biochemical networks: a promising tool for pathway analysis and metabolic engineering. , 1999, Trends in biotechnology.

[8]  W. Malaisse,et al.  Delayed interconversion of D-glucose anomers in D2O. , 2004, International journal of molecular medicine.

[9]  M. Wildermuth,et al.  Metabolic control analysis: biological applications and insights , 2000, Genome Biology.

[10]  R. Heinrich,et al.  The Regulation of Cellular Systems , 1996, Springer US.

[11]  C. Schilling,et al.  Flux coupling analysis of genome-scale metabolic network reconstructions. , 2004, Genome research.

[12]  Peter D. Karp,et al.  The EcoCyc Database , 2002, Nucleic Acids Res..

[13]  Kiyoko F. Aoki-Kinoshita,et al.  From genomics to chemical genomics: new developments in KEGG , 2005, Nucleic Acids Res..

[14]  H. Kacser,et al.  The control of flux. , 1995, Biochemical Society transactions.

[15]  C. Ouzounis,et al.  Expansion of the BioCyc collection of pathway/genome databases to 160 genomes , 2005, Nucleic acids research.