Accelerating the reconstruction of genome-scale metabolic networks

被引:116
作者
Notebaart, Richard A.
Van Enckevort, Frank H. J.
Francke, Christof
Siezen, Roland J.
Teusink, Bas
机构
[1] Radboud Univ Nijmegen, Ctr Mol & Biomol Informat, NL-6500 GL Nijmegen, Netherlands
[2] Wageningen Ctr Food Sci, NL-6700 AN Wageningen, Netherlands
[3] NIZO Food Res, NL-6710 BA Ede, Netherlands
关键词
D O I
10.1186/1471-2105-7-296
中图分类号
Q5 [生物化学];
学科分类号
071010 ; 081704 ;
摘要
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. Conclusion: 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.
引用
收藏
页数:10
相关论文
共 45 条
[1]  
[Anonymous], PYTHON PROGRAMMING L
[2]   Protein sequence databases [J].
Apweiler, R ;
Bairoch, A ;
Wu, CH .
CURRENT OPINION IN CHEMICAL BIOLOGY, 2004, 8 (01) :76-80
[3]   The ENZYME database in 2000 [J].
Bairoch, A .
NUCLEIC ACIDS RESEARCH, 2000, 28 (01) :304-305
[4]   Genome-scale reconstruction of the metabolic network in Staphylococcus aureus N315: an initial draft to the two-dimensional annotation [J].
Becker, SA ;
Palsson, BO .
BMC MICROBIOLOGY, 2005, 5 (1)
[5]   The complete genome sequence of the lactic acid bacterium Lactococcus lactis ssp lactis IL1403 [J].
Bolotin, A ;
Wincker, P ;
Mauger, S ;
Jaillon, O ;
Malarme, K ;
Weissenbach, J ;
Ehrlich, SD ;
Sorokin, A .
GENOME RESEARCH, 2001, 11 (05) :731-753
[6]   GenMAPP, a new tool for viewing and analyzing microarray data on biological pathways [J].
Dahlquist, KD ;
Salomonis, N ;
Vranizan, K ;
Lawlor, SC ;
Conklin, BR .
NATURE GENETICS, 2002, 31 (01) :19-20
[7]   A method for classifying metabolites in topological pathway analyses based on minimization of pathway number [J].
Dandekar, T ;
Moldenhauer, F ;
Bulik, S ;
Bertram, H ;
Schuster, S .
BIOSYSTEMS, 2003, 70 (03) :255-270
[8]   The Escherichia coli MG1655 in silico metabolic genotype:: Its definition, characteristics, and capabilities [J].
Edwards, JS ;
Palsson, BO .
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 2000, 97 (10) :5528-5533
[9]   In silico predictions of Escherichia coli metabolic capabilities are consistent with experimental data [J].
Edwards, JS ;
Ibarra, RU ;
Palsson, BO .
NATURE BIOTECHNOLOGY, 2001, 19 (02) :125-130
[10]   Genome-scale reconstruction of the Saccharomyces cerevisiae metabolic network [J].
Förster, J ;
Famili, I ;
Fu, P ;
Palsson, BO ;
Nielsen, J .
GENOME RESEARCH, 2003, 13 (02) :244-253