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Open Access Research article

A network perspective on the topological importance of enzymes and their phylogenetic conservation

Wei-chung Liu1*, Wen-hsien Lin1, Andrew J Davis2, Ferenc Jordán34, Hsih-te Yang1 and Ming-jing Hwang1

Author Affiliations

1 Institute of Biomedical Sciences, Academia Sinica, Taipei 115, Taiwan

2 Biochemistry Section, Max Planck Institute for Chemical Ecology, Hans-Knoell-Strasse 8, 07745 Jena, Germany

3 Collegium Budapest, Institute for Advanced Study, Szentháromság utca 2, H-1014, Budapest, Hungary

4 Animal Ecology Research Group, HAS, Hungarian Natural History Museum, Ludovika t. 2., H-1083, Budapest, Hungary

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BMC Bioinformatics 2007, 8:121  doi:10.1186/1471-2105-8-121

Published: 11 April 2007

Abstract

Background

A metabolic network is the sum of all chemical transformations or reactions in the cell, with the metabolites being interconnected by enzyme-catalyzed reactions. Many enzymes exist in numerous species while others occur only in a few. We ask if there are relationships between the phylogenetic profile of an enzyme, or the number of different bacterial species that contain it, and its topological importance in the metabolic network. Our null hypothesis is that phylogenetic profile is independent of topological importance. To test our null hypothesis we constructed an enzyme network from the KEGG (Kyoto Encyclopedia of Genes and Genomes) database. We calculated three network indices of topological importance: the degree or the number of connections of a network node; closeness centrality, which measures how close a node is to others; and betweenness centrality measuring how frequently a node appears on all shortest paths between two other nodes.

Results

Enzyme phylogenetic profile correlates best with betweenness centrality and also quite closely with degree, but poorly with closeness centrality. Both betweenness and closeness centralities are non-local measures of topological importance and it is intriguing that they have contrasting power of predicting phylogenetic profile in bacterial species. We speculate that redundancy in an enzyme network may be reflected by betweenness centrality but not by closeness centrality. We also discuss factors influencing the correlation between phylogenetic profile and topological importance.

Conclusion

Our analysis falsifies the hypothesis that phylogenetic profile of enzymes is independent of enzyme network importance. Our results show that phylogenetic profile correlates better with degree and betweenness centrality, but less so with closeness centrality. Enzymes that occur in many bacterial species tend to be those that have high network importance. We speculate that this phenomenon originates in mechanisms driving network evolution. Closeness centrality reflects phylogenetic profile poorly. This is because metabolic networks often consist of distinct functional modules and some are not in the centre of the network. Enzymes in these peripheral parts of a network might be important for cell survival and should therefore occur in many bacterial species. They are, however, distant from other enzymes in the same network.