Genome Engineering Technologies, Strategies and Applications

The era of genome engineering well underway. DNA synthesis and sequencing technologies have now advanced to the point that they are no longer the rate limiting step in pathway to genome scale engineering projects. These technologies were used in the creation of the first synthetic genome. Such genome-construction technology was first applied to the copying of existing genomes. Current and future applications seek to design genomes that require increasingly sophisticated design capabilities, with a focus on engineering industrially relevant functions; such as production of biofuels, commodity or speciality chemicals, pharmaceuticals, industrial enzymes, etc. Such applications will require that we are able to not only identify genes encoding functions that enable such applications but also combinations of such genes, and combinations of such combinations, that together result in optimal organism performance. We are developing a range of new technologies for designing genomes based upon the i) construction and use of “ideal” chassis strains, ii) efficient identification of gene-to-phenotype design rules, iii) automated “rational” combinatorial mutation library generation, and iv) parallel interrogation of such libraries to identify combinatorial design rules. This presentation will describe the first generation of such technologies, the current state of next-generation approaches, and the most recent application of such tools to design and construct microbial genomes relevant to sustainable fuels and chemicals production.