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The Activity Reaction Core and Plasticity of Metabolic Networks

Figure 2

The Metabolic Core of E. coli

All reactions that are found to be active in each of the 30,000 investigated external conditions are shown. Metabolites that contribute directly to biomass formation [8] are colored blue, while core reactions (links) catalyzed by essential (or nonessential) enzymes [13] are colored red (or green). (Black-colored links denote enzymes with unknown deletion phenotype.) The blue dashed lines indicate multiple appearances of a metabolite, while links with arrows denote unidirectional reactions. Note that 20 out of the 51 metabolites necessary for biomass synthesis are not present in the core, indicating that they are produced (or consumed) in a growth-condition-specific manner. See Protocol S1 and Table S1 for the abbreviations of metabolites and a list of core reactions for E. coli, H. pylori, and S. cerevisiae. The folate and peptidoglycan biosynthesis pathways are indicated by blue and brown shading, respectively, and the white numbered arrows denote current antibiotic targets inhibited by: (1) sulfonamides, (2) trimethoprim, (3) cycloserine, and (4) fosfomycin. Note that a few reactions appear disconnected since we have omitted the drawing of cofactors.

Figure 2

doi: https://doi.org/10.1371/journal.pcbi.0010068.g002