Achievement

IGERT trainee David Byrne (graduated May, 2012) in Byrne D, Dumitriu A, and Segre D, Comparative multi-goal tradeoffs in systems engineering of microbial metabolism, submitted to BMC Systems Biology. Metabolic engineering design seeks to achieve simultaneous goals such as maximizing productivity while minimizing raw material costs. Here, we use constraint-based modeling to design combinations of medium compositions and gene-deletion strains for three microorganisms (E. coli, S. cerevisiae, and S. oneidensis) and six industrially important byproducts (acetate, D-lactate, hydrogen, ethanol, formate, and succinate). We evaluate over 435 million simulated conditions and 36 engineering traits, including rates, costs, yields and product purity. The resulting phenotypes can be classified into dominant clusters for each organism, which illustrate phenotypic variation and sensitivities, trade-offs associated with multiple goals, and fundamental differences in organism-specific capabilities.