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

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 p...

• Type: Journal
• Year: 2007
• Where: BMCBI
• Authors: Wei-chung Liu, Wen-hsien Lin, Andrew J. Davis, Ferenc Jordán, Hsih-te Yang, Ming-jing Hwang
• Keywords: BMCBI 2007, Enzymes, Phylogenetic Profile, Topological Importance