Analysis of Yeast Metabolism to Overproduce Isobutanol and n-Butanol

Cells can synthesize cellular building blocks from different substrates using a large network of reactions. Metabolic engineering utilizes this reaction network to re-wire the cell to produce chemicals of interest. Traditionally, metabolic engineers made mutations in individual or competing pathways. Constraint-based modeling is a very powerful tool to understand and engineer metabolism. It provides a deep and systematic way to analyze the metabolic network and thus leads to rational strain designs that differ from those found using traditional approaches. SimOptStrain is a strain design algorithm that uses constraint-based models to suggest gene knockout and gene addition strategies to enhance biochemical production.

SimOptStrain was applied to a model of Saccharomyces cerevisiae to identify strategies that are predicted to increase isobutanol and n-butanol production with glucose or xylose as the substrate. We also computationally evaluated how different enzyme location (mitochondria or cytosol) and cofactor (NADH or NADPH) usage would impact the production rate. By analyzing the metabolic network, we provided gene knockout and gene addition strategies to enhance the biochemical production and insights into how these alterations would impact the metabolism in yeast. The proposed strategies are currently being tested experimentally.