Spontaneous Reaction Silencing in Metabolic Optimization
Figure 3
Portions of E. coli metabolic network under maximum growth condition.
(A) P1, P2, and P3 are alternative pathways for glucose transport and utilization. The most efficient pathway, P1, is active under maximum growth in glucose minimal medium. P2 and P3 are inactive, but if P1 is knocked out, P2 becomes active, and if both P1 and P2 are knocked out, P3 becomes active. In both knockout scenarios, the growth is predicted to be suboptimal. (B) Isocitrate lyase reaction in the pathway bypassing the tricarboxylic acid (TCA) cycle is predicted to be inactive under maximum growth due to its irreversibility. If it were to operate in the opposite direction, it would serve as a transverse pathway which redirects metabolic flow to growth-limiting reactions, increasing the maximum biomass production rate slightly. In both panels, single and double arrows are used to indicate irreversible and reversible reactions, respectively, and colors indicate the behavior of the reactions under maximum growth: active (red), inactive due to the irreversibility (green), and inactive due to cascading (yellow).