TABLE 3.
Simulation analyses of the metabolic network
| Organism | Proportion (%) of: |
|||
|---|---|---|---|---|
| Essential metabolic genes (gene essentialitya ) in: |
Reactions (flux variabilityb
) |
|||
| Glucose medium | Protein-rich environment |
Varying | Bidirectional | |
| E. coli | 15 | 12 | 60 | 4 |
| R. solanacearum | 15 | 13 | 48 | 3 |
| B. pertussis | No growth | 40 | ||
| X. fastidiosa | 54 | 51 | 32 | 1 |
Proportion of essential metabolic genes according to metabolic modeling, in glucose medium and a protein-rich environment. As B. pertussis cannot grow on glucose, the gene essentiality value is given only for a simulated protein-rich growth environment (12). Data for B. pertussis and E. coli (growth on glucose) were extracted from the work of Fyson et al. (12) and Orth et al. (67). Values for R. solanacearum and X. fastidiosa in both environments and for E. coli in a protein-rich environment were computed for this study. The detailed results are available in Data Set S4.
Assessment of flux variability. The proportion of varying reactions represents the number of reactions with non-null flux variation divided by the total number of metabolic reactions in the network. Bidirectional reactions are reversible reactions that can carry out both positive and negative flux to sustain an optimal growth. The proportion was equally determined by calculating the ratio of these reactions divided by the total number of metabolic reactions in the network. The detailed results are available in Data Set S2.