Metabolic and physiological responses to genetic perturbations are of fundamental interest to systems biology and metabolic engineering. They reveal underlying information about network structure including kinetics, regulation, and the presence of otherwise “hidden” reactions. Quantitative prediction of these responses is essential for rational strain design, but has been a persistent challenge in the field. There has been much work done to develop in silico predictive models of metabolism, most notably the constraint-based models. Progress in this area has been limited, however, by a lack of high-quality reproducible experimental metabolic flux (fluxomic) data of genetically perturbed strains. In this study, 13C metabolic flux analysis (13C-MFA) was applied to 50 Escherichia coli knockout strains spanning the major pathways of central carbon metabolism (glycolysis, pentose phosphate pathway, TCA cycle). Moreover, a full physiological characterization of each strain was performed, including detailed biomass composition analysis. The flux and physiological responses of these strains collectively provide important new insights into the robustness of central carbon metabolic pathways, as well as areas of likely kinetic limitation. Severely growth-impaired knockout strains helped to point out the most important enzymes in central metabolism. Particularly surprising flux responses, including identification of novel enzymatic activities, will be emphasized in this presentation. Next, we used this comprehensive flux data set, combined with complementary transcriptomic and metabolomic data, to parametize a genome-scale kinetic model of E. coli metabolism. In addition to having significant value in advancing fundamental biological knowledge, this model provides a valuable new toolkit for industrial biotechnology.

From genotype to 13C-fluxome to a comprehensive kinetic model of Escherichia coli

Macromolecular Chemistry: The Second Century

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ACS Spring 2020 National Meeting & Expo

The official archive and repository for all ACS Meetings & Expositions abstracts and select posters or presentations.