title: Accelerating the reconstruction of genome-scale metabolic networks.
abstract: BACKGROUND
  The genomic information of a species allows for the genome-scale reconstruction of its metabolic capacity. Such a metabolic reconstruction gives support to metabolic engineering, but also to integrative bioinformatics and visualization. Sequence-based automatic reconstructions require extensive manual curation, which can be very time-consuming. Therefore, we present a method to accelerate the time-consuming process of network reconstruction for a query species. The method exploits the availability of well-curated metabolic networks and uses high-resolution predictions of gene equivalency between species, allowing the transfer of gene-reaction associations from curated networks.
  
  
  RESULTS
  We have evaluated the method using Lactococcus lactis IL1403, for which a genome-scale metabolic network was published recently. We recovered most of the gene-reaction associations (i.e. 74 - 85%) which are incorporated in the published network. Moreover, we predicted over 200 additional genes to be associated to reactions, including genes with unknown function, genes for transporters and genes with specific metabolic reactions, which are good candidates for an extension to the previously published network. In a comparison of our developed method with the well-established approach Pathologic, we predicted 186 additional genes to be associated to reactions. We also predicted a relatively high number of complete conserved protein complexes, which are derived from curated metabolic networks, illustrating the potential predictive power of our method for protein complexes.
  
  
  CONCLUSIONS
  We show that our methodology can be applied to accelerate the reconstruction of genome-scale metabolic networks by taking optimal advantage of existing, manually curated networks. As orthology detection is the first step in the method, only the translated open reading frames (ORFs) of a newly sequenced genome are necessary to reconstruct a metabolic network. When more manually curated metabolic networks will become available in the near future, the usefulness of our method in network prediction is likely to increase.
authors.affiliation: Center for Molecular and Biomolecular Informatics, Radboud University Nijmegen, The Netherlands. R.notebaart@cmbi.ru.nl
authors.forename: Richard A
authors.initials: RA
authors.lastname: Notebaart
authors.forename: Frank H J
authors.initials: FH
authors.lastname: van Enckevort
authors.forename: Christof
authors.initials: C
authors.lastname: Francke
authors.forename: Roland J
authors.initials: RJ
authors.lastname: Siezen
authors.forename: Bas
authors.initials: B
authors.lastname: Teusink
mesh_terms: D001412:Bacillus subtilis / Q000235:genetics / Q000378:metabolism; D001426:Bacterial Proteins / Q000235:genetics / Q000378:metabolism*; D019295:Computational Biology; D003198:Computer Simulation; D030541:Databases, Genetic; D004798:Enzymes / Q000235:genetics / Q000378:metabolism*; D048168:Escherichia coli K12 / Q000235:genetics / Q000378:metabolism; D016680:Genome, Bacterial; D048191:Lactiplantibacillus plantarum / Q000235:genetics / Q000378:metabolism; D013294:Lactococcus lactis / Q000235:genetics* / Q000378:metabolism*; D008957:Models, Genetic; D025941:Protein Interaction Mapping / Q000379:methods; D012986:Software Validation
chemical_list: D001426:Bacterial Proteins; D004798:Enzymes