Biosynthetic potentials from species-specific metabolic networks

Genome Inform. 2008;20:135-48.


Studies of genome-scale metabolic networks allow for qualitative and quantitative descriptions of an organism's capability to convert nutrients into products. The set of synthesizable products strongly depends on the provided nutrients as well as on the structure of the metabolic network. Here, we apply the method of network expansion and the concept of scopes, describing the synthesizing capacities of an organism when certain nutrients are provided. We analyze the biosynthetic properties of four species: Arabidopsis thaliana, Saccharomyces cerevisiae, Buchnera aphidicola, and Escherichia coli. Matthäus et al. have recently developed a method to identify clusters of scopes, reflecting specific biological functions and exhibiting a hierarchical arrangement, using the network comprising all reactions in KEGG. We extend this method by considering random sets of nutrients on well-curated networks of the investigated species from BioCyc. We identify structural properties of the networks that allow to differentiate their biosynthetic capabilities. Furthermore, we evaluate the quality of the clustering of scopes applied to the species-specific networks. Our study provides a novel assessment of the biosynthetic properties of different species.

MeSH terms

  • Algorithms
  • Arabidopsis / genetics*
  • Arabidopsis / metabolism
  • Buchnera / genetics*
  • Buchnera / metabolism
  • Cluster Analysis
  • Databases, Genetic
  • Escherichia coli / genetics*
  • Escherichia coli / metabolism
  • Genome, Bacterial*
  • Genome, Fungal*
  • Genome, Plant*
  • Models, Genetic*
  • Saccharomyces cerevisiae / genetics*
  • Saccharomyces cerevisiae / metabolism