2006 Volume 17 Issue 1 Pages 230-239
Recent evidence points to the existence of scale-free properties in many biological networks.By topological analysis, several models including preferential attachment and hierarchical moduleshave been proposed to explain how these networks are organized. On the other hand, analyses usingdynamics have suggested that gene expression and metabolic networks have been organized withthe scale-free property by the other models such as “rich-travel-more” and “log-normal dynamics.” Because most of these approaches are based on comparative genomics of extant species, and didnot consider evolutionary events such as horizontal gene transfer, gene loss and gene gain, wehave analyzed transition of metabolic networks from the vertical point of view of evolution. First, to identify metabolic networks of common ancestors, we applied a parsimony algorithm for theenzymatic reaction set. Then by comparing the estimated metabolic networks among commonancestors, we investigated the transition of metabolic networks along the evolutionary process.As a result, we estimated enzymatic reaction contents of 227 common ancestors from 228 extantspecies, and found that links of several specific metabolites have frequently changed during the course of evolution.