Chapter 9 - Reconstruction of Metabolic Networks from Genome Information and Its Structural and Functional Analysis

Abstract

This chapter illustrates the major approaches and available databases for the reconstruction of genome-scale metabolic networks. An important step in the reconstruction of organism-specific metabolic networks from genome information is to obtain the gene-enzyme and enzyme-reaction relationships. Enzymes are the key players that link a gene with a specific metabolic reaction. The International Union of Biochemistry and Molecular Biology (IUBMB) assigns an Enzyme Commission classification number to each enzyme. For information on a newly sequenced organism that has not yet been included in the enzyme databases, one can obtain an enzyme list for it directly from its genome annotation information. A proper mathematical representation of the large number of reactions obtained for a specific organism is necessary for any structural analysis of metabolic networks. The uncovering of the bow-tie structure of metabolic networks has important implications for biotechnology and biomedicine. For example, understanding and manipulating the distribution and control of metabolic fluxes over the metabolic network are key steps in metabolic engineering of organisms and therapy of certain metabolic diseases.