title: Large-scale genome reorganization in Saccharomyces cerevisiae through combinatorial loss of mini-chromosomes.
abstract: A highly efficient technique, termed PCR-mediated chromosome splitting (PCS), was used to create cells containing a variety of genomic constitutions in a haploid strain of Saccharomyces cerevisiae. Using PCS, we constructed two haploid strains, ZN92 and SH6484, that carry multiple mini-chromosomes. In strain ZN92, chromosomes IV and XI were split into 16 derivative chromosomes, seven of which had no known essential genes. Strain SH6484 was constructed to have 14 mini-chromosomes carrying only non-essential genes by splitting chromosomes I, II, III, VIII, XI, XIII, XIV, XV, and XVI. Both strains were cultured under defined nutrient conditions and analyzed for combinatorial loss of mini-chromosomes. During culture, cells with various combinations of mini-chromosomes arose, indicating that genomic reorganization could be achieved by splitting chromosomes to generate mini-chromosomes followed by their combinatorial loss. We found that although non-essential mini-chromosomes were lost in various combinations in ZN92, one mini-chromosome (18kb) that harbored 12 genes was not lost. This finding suggests that the loss of some combination of these 12 non-essential genes might result in synthetic lethality. We also found examples of genome-wide amplifications induced by mini-chromosome loss. In SH6484, the mitochondrial genome, as well as the copy number of genomic regions not contained in the mini-chromosomes, was specifically amplified. We conclude that PCS allows for genomic reorganization, in terms of both combinations of mini-chromosomes and gene dosage, and we suggest that PCS could be useful for the efficient production of desired compounds by generating yeast strains with optimized genomic constitutions.
authors.affiliation: New Projects Development Division, Toray Industries, Inc., 10-1 Tebiro 6-chome, Kamakura, Kanagawa 248-8555, Japan. Yoji_ueda@nts.toray.co.jp
authors.forename: Youji
authors.initials: Y
authors.lastname: Ueda
authors.forename: Shigehito
authors.initials: S
authors.lastname: Ikushima
authors.forename: Minetaka
authors.initials: M
authors.lastname: Sugiyama
authors.forename: Ryo
authors.initials: R
authors.lastname: Matoba
authors.forename: Yoshinobu
authors.initials: Y
authors.lastname: Kaneko
authors.forename: Kenichi
authors.initials: K
authors.lastname: Matsubara
authors.forename: Satoshi
authors.initials: S
authors.lastname: Harashima
mesh_terms: D057005:Bioengineering; D002872:Chromosome Deletion; D015825:Chromosomes, Fungal / Q000235:genetics*; D016681:Genome, Fungal; D006238:Haploidy; D016133:Polymerase Chain Reaction / Q000379:methods; D012441:Saccharomyces cerevisiae / Q000235:genetics* / Q000648:ultrastructure