Metabolic flux analysis of Escherichia coli knockouts: lessons from the Keio collection and future outlook

• Methods for measuring and predicting fluxes in Escherichia coli knockouts are reviewed.
• Keio collection of E. coli KOs facilitates systemic study of regulation and metabolism.
• Recent advances in 13C-MFA permit highly precise and accurate flux measurements.
• Knockout flux results are currently difficult to compare and generalize.
• A high-resolution set of flux data for large number of Keio knockouts would be valuable.

Cellular metabolic and regulatory systems are of fundamental interest to biologists and engineers. Incomplete understanding of these complex systems remains an obstacle to progress in biotechnology and metabolic engineering. An established method for obtaining new information on network structure, regulation and dynamics is to study the cellular system following a perturbation such as a genetic knockout. The Keio collection of all viable Escherichia coli single-gene knockouts is facilitating a systematic investigation of the regulation and metabolism of E. coli. Of all omics measurements available, the metabolic flux profile (the fluxome) provides the most direct and relevant representation of the cellular phenotype. Recent advances in 13C-metabolic flux analysis are now permitting highly precise and accurate flux measurements for investigating cellular systems and guiding metabolic engineering efforts.

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