Integrated knowledge-based reverse engineering of metabolic pathways

A framework for reverse engineering of metabolic pathways is proposed. It is driven by the knowledge of the reaction stoichiometry and constraints from flux balance analysis. For a desired product, the framework predicts the theoretical yield of the product. and generates all the possible reaction network topologies capable of producing the maximal theoretical yield. Two rules are used to select the most useful pathways. The first one is ATP yield. The pathways with higher ATP production are valued because they are energetically favorable. The second rule is calculating the number of gene knockouts. which indicates the cost of engineering the organism. Based on these two criteria, this framework can generate several pathway candidates for the metabolic engineer to enhance the yield of the product secreted by an organism. We illustrate the entire procedure for ethanol production.