Automated Metabolic Engineering of Yeast Cells Using a Biological Foundry

Given the complexity of biological systems, cellular reprogramming requires both identification of genetic targets on a genome scale and optimization of their expression in a concerted manner.  Here we report the use of automated genome engineering to improve glycerol utilization and acetic acid tolerance phenotypes in Saccharomyces cerevisiae.  Strains harboring multiplex genetic mutations, including both overexpression and knockdown modifications, were constructed and screened using the iBioFab (Illinois Biological Foundry for Advanced Biomanufacturing) platform.  The evolutionary trajectories of improved mutants were also analyzed using next-generation sequencing.  Our technology represents a prototype of industrialized biomanufacturing, where the design-build-test cycle is rapidly executed by a fully integrated robotic system.