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On the Accessibility of Adaptive Phenotypes of a Bacterial Metabolic Network

Figure 1

An example of the interaction rules found in the E. coli metabolic network.

The protein products of the genes b0116, b0726, and b0727 combine to form a protein complex that catalyzes production of succinate coenzyme A (SUCCOA) from alpha-ketoglutarate (AKG) and coenzyme A, with the concomitant reduction of nicotinamide adenine dinucleotide (NAD) and release of carbon dioxide (CO2). A matrix S of the stoichiometries of the reactants, and a vector V of fluxes are shown. v, b1, b2, b3, b4, b5, and b6 denote the rates of the above reaction, the production of AKG, NAD, and COA, and the utilization of CO2, NADH, and SUCCOA, respectively (Note that this is a simplification of the way the reaction is actually represented in our model). At steady state SยทV = 0. In the event that one of the genes catalyzing the above reaction is turned off by mutation, the reaction flux v is set to 0. Abbreviations (gene/protein product): b0116/LpdA, dihydrolipoamide dehydrogenase; b0726/SucAec, alpha-ketoglutarate decarboxylase; b0727/SucBec, dihydrolipoamide acetyltransferase.

Figure 1

doi: https://doi.org/10.1371/journal.pcbi.1000472.g001