Genomatica has established a revolutionary, proprietary, integrated suite of computational and experimental technologies to design, create, and optimize novel high-producing organisms and bioprocesses. Genomatica first uses the speed and power of its industry leading in silico modeling and simulation technology to identify and optimize an unparalleled range of cellular design strategies. The most promising designs are then brought to life with high-throughput cell engineering, applied evolution and fermentation capabilities. This patented Integrated Metabolic Engineering Platform enables Genomatica to generate proprietary organisms with superior performance characteristics, in less time and at a lower cost compared to current approaches in the industry. Here we present as an example the use of our platform to design, construct, and optimize E. coli strains for the production of the industrial chemical 1,4-butanediol (BDO) from glucose and sucrose. BDO is a four carbon diol that currently is manufactured exclusively through various petrochemical routes. It is part of a large volume family of solvents and polymer intermediates that includes gamma-butyrolactone (GBL), tetrahydrofuran (THF), pyrrolidone, N-methylpyrrolidone, and N-vinyl-pyrrolidone, with an overall market opportunity exceeding $4.0B. Therefore, this product represents an opportunity to make a significant impact on the replacement of traditional petrochemical processes with benign bioprocesses using renewable feedstocks.

This presentation will cover the application of this integrated technology platform to computationally design, experimentally engineer, and evolve a high-performing microorganism capable of producing this chemical from a carbohydrate for the first time. The major considerations in engineering strains for chemical production are the biochemical pathway that produces the compound of interest from native metabolites, and the host central metabolism, which must direct cellular resources to this pathway. The Biopathway Predictor algorithm was employed to elucidate all possible routes to BDO from central metabolites, and the most favorable pathway chosen by various criteria. To engineer host strain metabolism, we utilized the OptKnock methodology to identify a set of gene deletions designed to couple product formation to growth. In other words, the cell must produce the compound of interest in order to grow efficiently. Evolutionary engineering is a complementary experimental approach that uses controlled selection pressure to optimize strain fitness and growth rate following genetic manipulations. Due to the growth-coupled nature of the product, cells evolved for improved growth have superior product yield. The host was also evolved to tolerate the concentrations of BDO necessary for successful commercialization of the process. After constructing the host and pathway based on the design, our models facilitated the analysis of laboratory data to evaluate performance, thus finding targets for further rounds of strain engineering.

The results presented will demonstrate commercialization potential of this breakthrough biochemical process. More generally, it will demonstrate that our combined computational and experimental approach is significantly expediting the successful metabolic engineering of superior industrial organisms for low-cost chemical and fuel production.

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