Microorganisms have been increasingly designed by metabolic engineering to produce biofuels and chemicals. Most of these engineering efforts have focused on model organisms such as baker's yeasts. However, many other microbes offer unique advantages for biomanufacturing valuable products. Moreover, traditional metabolic engineering studies require substantial time and effort because only a limited number of genes can be explored and manipulated at a time. The goal of the Genome Scale Engineering (GSE) Center is to overcome these limitations by developing genome-scale design and engineering tools that will allow rapid engineering of new organisms for the production of industrial compounds. These tools will be integrated with advanced metabolic analyses and computational modeling to engineer two emerging yeast model systems to produce high-levels of lipid- and organic acids-derived fuels and chemicals. The resulting technology platform will accelerate the microorganism "design-build-test" cycle to elevate both yeast species to a production chassis status and will facilitate the development of new microbial organisms relevant to DOE's mission in renewable energy.