An optimization framework for identifying reaction activation/inhibition or elimination candidates for overproduction in microbial systems

We introduce a computational framework termed OptReg that determines the optimal reaction activations/inhibitions and eliminations for targeted biochemical production. A reaction is deemed up- or downregulated if it is constrained to assume flux values significantly above or below its steady-state before the genetic manipulations. The developed framework is demonstrated by studying the overproduction of ethanol in Escherichia coli. Computational results reveal the existence of synergism between reaction deletions and modulations implying that the simultaneous application of both types of genetic manipulations yields the most promising results. For example, the downregulation of phosphoglucomutase in conjunction with the deletion of oxygen uptake and pyruvate formate lyase yields 99.8% of the maximum theoretical ethanol yield. Conceptually, the proposed strategies redirect both the carbon flux as well as the cofactors to enhance ethanol production in the network. The OptReg framework is a versatile tool for strain design which allows for a broad array of genetic manipulations.