Complete synthesis of designer eukaryotic genome, Sc2.0

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This project aims to complete the synthesis of the world's first synthetic eukaryotic genome project, Sc2.0, a human-designed genome powering growth of the model organism Saccharomyces cerevisiae. Rather than simply re-writing a known genome sequence, the extensive set of design features written into the Sc2.0 genome is intended to confer increased genomic stability and genetic flexibility while maintaining normal growth. The Sc2.0 genome is designed to enable unique experiments that will "teach us biology". The project involves teams of scientists from around the world working together towards a common goal. The Build A Genome course, initiated by this project, is a distinctive educational vehicle for teaching synthetic biology and genomics to undergraduate students. The Sc2.0 genome is also a platform for bio-manufacturing by increasing the production of biofuels, vaccines, specialty chemicals, pharmaceuticals, and biologics. The Sc2.0 project has also taken a lead role in generating a "statement of principles" for the project addressing bioethics, safety and related concerns of the public. The synthetic Saccharomyces genome is well on its way to being completed. A global group of scientists is building strains encoding individual synthetic chromosomes, with the ultimate goal of combining them into a single cell to construct the world's first designer, entirely synthetic eukaryotic genome. Five additional chromosomes have been completely designed, synthesized and assembled, sequenced, and evaluated for fitness under diverse conditions. This project will be critical to its completion. Teams in the Boeke lab are working to complete chromosomes 1, 4 and 8. Also, while there are essentially 16 teams around the world each producing one chromosome, an important series of final steps relates to combining the synthetic chromosomes into a single strain. An extensive set of design features written into the Sc2.0 genome is intended to confer increased genomic stability and genetic flexibility while maintaining the ability to grow at a normal rate. For instance, destabilizing elements such as repetitive sequences are deleted from Sc2.0 chromosomes while tRNA genes are re-located to a separate "neochromosome". Additionally, an inducible evolution or genome scrambling system (Dymond and Boeke, 2012), plus a watermarking system to distinguish synthetic and wild type DNA, provide unprecedented capacity to generate derivative genomes with novel structures and track synthetic DNA. All 16 synthetic chromosomes have been designed. The completion of the synthesis and assembly of one and a half synthetic chromosomes has been reported (Annaluru et al., 2014; Dymond et al., 2011). Debugging of various types was required in some of the synthetic chromosomes to produce a high fitness isolate, by restoring to the native sequence certain designer changes found to be deleterious to expression, etc. In the coming years work will focus on building a synthetic yeast mitochondrial DNA, and deletion of all introns and splicing machinery from the genome, and the power of genome scrambling will be evaluated in new ways.The Sc2.0 project, looking ahead, will answer many evolutionary questions never before approachable, such as how introns and transposons evolve and spread throughout host genomes. Additional questions include: How extensive is the universe of minimal eukaryotic gene sets? Do introns/splicing machinery play essential roles? Can one build transposon-free and/or intron-free genomes? Can one add a 21st amino acid to the genetic code? What happens when transposons are introduced into such genomes? How do engineered genomes perform in meiosis? Will synthetic and native yeast genomes make fertile hybrids? Can one build a new type of genetics based entirely on changing gene sets and gene dosage rather than base changes?