Large-scale reconstruction and phylogenetic analysis of metabolic environments.

ABSTRACT: The topology of metabolic networks may provide important insights not only into the metabolic capacity of species, but also into the habitats in which they evolved. Here we introduce the concept of a metabolic network's "seed set"--the set of compounds that, based on the network topology, are exogenously acquired--and provide a methodological framework to computationally infer the seed set of a given network. Such seed sets form ecological "interfaces" between metabolic networks and their surroundings, approximating the effective biochemical environment of each species. Analyzing the metabolic networks of 478 species and identifying the seed set of each species, we present a comprehensive large-scale reconstruction of such predicted metabolic environments. The seed sets' composition signif

SUBMITTER: Borenstein E 

PROVIDER: S-EPMC2567166 | biostudies-literature | 2008 Sep

REPOSITORIES: biostudies-literature