Figure 3

Organization of metabolic genotype space. The figure shows the genotype networks of potential metabolisms containing 23, 24 and 25 reactions. Each filled circle corresponds to a genotype. Two genotypes are connected by an edge (curved line) if they are neighbors. Red circles correspond to minimal metabolisms of a given number of reactions n. (A) The genotype network of size 23 is fragmented, with component A containing two adjacent genotypes, while component B contains one genotype. (B) Structure of the genotype network at size n = 24 reactions. Addition of one reaction to the two genotypes in component A results in genotypes of size 24 which belong to component A’ (green), and addition of one reaction to the genotype in component B yields genotypes of size 24 which belong to component B’ (orange). At size n = 24 reactions, eight minimal metabolisms (red circles) also arise, of which three genotypes belong to component A’, and five to component B’. Note that genotypes in components A’ and B’ remain disconnected. (C) Structure of the genotype network at size n = 25 reactions. Adding one reaction to all genotypes in component A’ yields genotypes (green) in subgraph A”, while adding one reaction to all genotypes in component B’ yields the genotypes (orange) of subgraph B”. There are 23 minimal metabolisms of size 25 (red), of which 4 genotypes form a disconnected component C (blue, bottom center). Note that genotypes of size 25 in subgraphs A” and B” are connected either directly or through minimal metabolisms. The size of each circle corresponds to its number of neighboring genotypes, which increases as metabolism size increases. Graphs were drawn using the graph visualization software Gephi [46].