title: Synthetic chromosome arms function in yeast and generate phenotypic diversity by design.
abstract: Recent advances in DNA synthesis technology have enabled the construction of novel genetic pathways and genomic elements, furthering our understanding of system-level phenomena. The ability to synthesize large segments of DNA allows the engineering of pathways and genomes according to arbitrary sets of design principles. Here we describe a synthetic yeast genome project, Sc2.0, and the first partially synthetic eukaryotic chromosomes, Saccharomyces cerevisiae chromosome synIXR, and semi-synVIL. We defined three design principles for a synthetic genome as follows: first, it should result in a (near) wild-type phenotype and fitness; second, it should lack destabilizing elements such as tRNA genes or transposons; and third, it should have genetic flexibility to facilitate future studies. The synthetic genome features several systemic modifications complying with the design principles, including an inducible evolution system, SCRaMbLE (synthetic chromosome rearrangement and modification by loxP-mediated evolution). We show the utility of SCRaMbLE as a novel method of combinatorial mutagenesis, capable of generating complex genotypes and a broad variety of phenotypes. When complete, the fully synthetic genome will allow massive restructuring of the yeast genome, and may open the door to a new type of combinatorial genetics based entirely on variations in gene content and copy number.
authors.affiliation: High Throughput Biology Center, Johns Hopkins University School of Medicine, 733 North Broadway, Baltimore, Maryland 21205, USA.
authors.forename: Jessica S
authors.initials: JS
authors.lastname: Dymond
authors.forename: Sarah M
authors.initials: SM
authors.lastname: Richardson
authors.forename: Candice E
authors.initials: CE
authors.lastname: Coombes
authors.forename: Timothy
authors.initials: T
authors.lastname: Babatz
authors.forename: Héloïse
authors.initials: H
authors.lastname: Muller
authors.forename: Narayana
authors.initials: N
authors.lastname: Annaluru
authors.forename: William J
authors.initials: WJ
authors.lastname: Blake
authors.forename: Joy W
authors.initials: JW
authors.lastname: Schwerzmann
authors.forename: Junbiao
authors.initials: J
authors.lastname: Dai
authors.forename: Derek L
authors.initials: DL
authors.lastname: Lindstrom
authors.forename: Annabel C
authors.initials: AC
authors.lastname: Boeke
authors.forename: Daniel E
authors.initials: DE
authors.lastname: Gottschling
authors.forename: Srinivasan
authors.initials: S
authors.lastname: Chandrasegaran
authors.forename: Joel S
authors.initials: JS
authors.lastname: Bader
authors.forename: Jef D
authors.initials: JD
authors.lastname: Boeke
mesh_terms: D001287:Attachment Sites, Microbiological / Q000235:genetics; D018244:Chromosomes, Artificial, Yeast / Q000235:genetics*; D019020:Directed Molecular Evolution / Q000379:methods; D018628:Gene Dosage / Q000235:genetics; D020869:Gene Expression Profiling; D015966:Gene Expression Regulation, Fungal; D005818:Genetic Engineering / Q000379:methods*; D056084:Genetic Fitness / Q000235:genetics; D016681:Genome, Fungal / Q000235:genetics; D005838:Genotype; D006238:Haploidy; D008969:Molecular Sequence Data; D016296:Mutagenesis / Q000235:genetics; D010641:Phenotype; D012331:RNA, Fungal / Q000032:analysis / Q000235:genetics; D012441:Saccharomyces cerevisiae / Q000145:classification / Q000235:genetics*; D058615:Synthetic Biology / Q000379:methods*
chemical_list: D012331:RNA, Fungal