Study of the Effects of Alternative Fluxes on the Metabolic Control Analysis of Optimally Grown E. coli

The intracellular metabolite and flux states have a significant impact on the responses to metabolic networks to changes in their enzyme activities and environmental conditions. Therefore, it is important to characterize systematically all possible intracellular flux states, and analyze their properties. Although abundant fluxomics data are nowadays available, the size and complexity of metabolic networks does not allow determination of the exact intracellular metabolic flux values. As a result, there exist multiple alternative flux profiles that are able to describe the same physiology.

In this work, we employed the ORACLE (Optimization and Risk Analysis of Complex Living Entities) framework to characterize all the alternative intracellular flux profiles that are consistent with the studied physiology. ORACLE consists of a set of successive computational procedures wherein we integrate biological data from several sources, metabolomics, fluxomics, thermodynamics and data about kinetic properties of enzymes, and we construct a population of kinetic models of cellular metabolism. We enumerated all the flux profiles that are thermodynamically consistent and consistent with the physiology of a wild-type E. coli grown under optimal aerobic condition. Then, for each flux profile: (i) we characterized the thermodynamic displacement of reactions from equilibrium; (ii) we quantified the flexibility of metabolite concentration levels and metabolic fluxes; (iii) we built the populations of the corresponding kinetic models; and (iv) we computed the control coefficients and characterized the metabolic responses to changes in enzyme activities. We used these results to quantify the differences between different flux profiles, and we also determined the common features of these profiles that are not affected by alternative intracellular flux profiles. This analysis shows the importance of exact determination of intracellular flux profiles and how alternative flux profiles could lead to distinct and different conclusions about the metabolic design strategies.