This project, funded by the Systems and Synthetic Biology Program in MCB and the Biotechnology, Biochemical and Biomass Engineering Program in CBET, is part of a larger ERASynBio funded collaborative. The researchers have previously developed the capability to design and synthesize entire yeast chromosomes, and have inserted into the chromosomes sites that make it easy to modify or recombine pieces of the chromosome. In this work, they leverage this capability to evolve yeast strains that will be particularly well suited for production of chemicals or fuels or other biomanufacturing tasks. In addition, they will collect data that will help them address questions about how chromosomes evolve in laboratory or manufacturing settings, and what characteristics give rise to more stable chromosomes and better growing yeast strains. At the same time, the researchers will develop on line courses to teach ethics related to the field of synthetic biology, and expand their laboratory classes that enable undergraduates to synthesize parts of the yeast chromosome and learn the tools needed to enter into this research field.
Induced Evolution of Synthetic Yeast genomes (IESY) will use the first synthetic eukaryote, Saccharomyces cerevisiae 2.0 (Sc2.0), as a platform for metabolic engineering and genome minimization, and more importantly for generating and understanding industrially high-value phenotypes. Synthetic chromosomes in Sc2.0 permit rapid and comprehensive genome evolution through synthetic chromosome rearrangement and modification by loxP-mediated evolution (SCRaMbLE). SCRaMbLE will be exploited here to evolve strains selected for high-value phenotypes for biofuels and biotechnology, using both chemostats and batch transfer methods in the USA and Europe. Technologies for neochromosomes and orthogonal SCRaMbLE of gene classes will be developed. Evolutionary trajectories will be analyzed to relate genome structure with genome function: DNA sequencing will reveal the genome sequence, rearrangements, and copy number changes in the evolved strains; chromosome conformation capture will show how massive rearrangements affect 3D structure; and deep sequencing technologies will relate sequence and structure to gene expression and isoform abundance. Computational analysis will identify the evolutionary drivers for high fitness, with the potential for further optimization. IESY builds on resources uniquely available from the international Sc2.0 consortium and will be an international resource for efficient evolution of high-value phenotypes. This project represents a new paradigm in synthetic biology in which a genome is pre-programmed to explore combinatorial diversity space to evolve new and useful function.
