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Advances in molecular methods to alter chromosomes and genome in the yeast Saccharomyces cerevisiae

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Abstract

A fundamental issue in biotechnology is how to breed useful strains of microorganisms for efficient production of valuable biomaterials. On-going and more recent developments in gene manipulation technologies and chromosomal and genomic modifications in particular have facilitated important contributions in this area. “Chromosome manipulation technology” as an outgrowth of “gene manipulation technology” may provide opportunities for creating novel strains of organisms with a variety of genomic constitutions. A simple and rapid chromosome splitting technology called “PCR-mediated chromosome splitting” (PCS) that we recently developed has made it possible to manipulate chromosomes and genomes on a large scale in an industrially important microorganism, Saccharomyces cerevisiae. This paper focuses on recent advances in molecular methods for altering chromosomes and genome in S. cerevisiae featuring chromosome splitting technology. These advances in introducing large-scale genomic modifications are expected to accelerate the breeding of novel strains for biotechnological purposes, and to reveal functions of presently uncharacterized chromosomal regions in S. cerevisiae and other organisms.

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References

  • Alper H, Moxley J, Nevoigt E, Fink GR, Stephanopoulos G (2006) Engineering yeast transcription machinery for improved ethanol tolerance and production. Science 314:1565–1568

    Article  CAS  Google Scholar 

  • Giaever G, Chu AM, Ni L et al (2002) Functional profiling of the Saccharomyces cerevisiae genome. Nature 418:387–391

    Article  CAS  Google Scholar 

  • Giga-Hama Y, Tohda H, Takegawa K, Kumagai H (2007) Schizosaccharomyces pombe minimum genome factory. Biotechnol Appl Biochem 46:147–155

    Article  CAS  Google Scholar 

  • Güldener U, Heck S, Fiedler T, Beinhauer J, Hegemann JH (1996) A new efficient gene disruption cassette for repeated use in budding yeast. Nucleic Acids Res 24:2519–2524

    Article  Google Scholar 

  • Hirashima K, Iwaki T, Takegawa K, Giga-Hama Y, Tohda H (2006) A simple and effective chromosome modification method for large-scale deletion of genome sequences and identification of essential genes in fission yeast. Nucleic Acids Res 34:e11

    Article  Google Scholar 

  • Ito H, Fukuda Y, Murata K, Kimura A (1983) Transformation of intact yeast cells treated with alkali cations. J Bacteriol 153:163–168

    Article  CAS  Google Scholar 

  • Kawasaki H, Ouchi K (1994) A DNA construct useful for specific chromosome loss in Saccharomyces cerevisiae. J Ferment Bioeng 77:125–130

    Article  CAS  Google Scholar 

  • Kim YH, Kaneko Y, Fukui K, Kobayashi A, Harashima S (2005a) A yeast artificial chromosome-splitting vector designed for precise manipulation of specific plant chromosome region. J Biosci Bioeng 99:55–60

    Article  CAS  Google Scholar 

  • Kim YH, Ishikawa D, Ha HP, Sugiyama M, Kaneko Y, Harashima S (2006a) Chromosome XII context is important for rDNA function in yeast. Nucleic Acids Res 34:2914–2924

    Article  CAS  Google Scholar 

  • Kim YH, Sugiyama M, Kaneko Y, Fukui K, Kobayashi A, Harashima S (2006b) A polymerase chain reaction-mediated yeast artificial chromosome-splitting technology for generating targeted yeast artificial chromosomes subclones. Methods Mol Biol 349:103–115

    CAS  PubMed  Google Scholar 

  • Kim YH, Sugiyama M, Yamagishi K, Kaneko Y, Fukui K, Kobayashi A, Harashima S (2005b) A versatile and general splitting technology for generating targeted YAC subclones. Appl Microbiol Biotechnol 69:65–70

    Article  CAS  Google Scholar 

  • Kolisnychenko V, Plunkett G III, Herring CD, Feher T, Posfai J, Blattner FR, Posfai G (2002) Engineering a reduced Escherichia coli genome. Genome Res 12:640–647

    Article  CAS  Google Scholar 

  • Kouprina N, Larionov V (2006) TAR cloning: insights into gene function, long-range hapolotypes and genome structure and evlolution. Nat Rev Genet 7:805–812

    Article  CAS  Google Scholar 

  • Kouprina N, Larionov V (2008) Selective isolation of genomic loci from complex genomes by transformation-associated recombination cloning in the yeast Saccharomyces cerevisiae. Nature Protocol 3:371–377

    Article  CAS  Google Scholar 

  • Kuyper M, Toirkens MJ, Diderich JA, Winkler AA, van Dijken JP, Pronk JT (2005) Evolutionary engineering of mixed-sugar utilization by a xylose-fermenting Saccharomyces cerevisiae strain. FEMS Yeast Res 5:925–934

    Article  CAS  Google Scholar 

  • Mizukami A, Nagamori E, Takakura Y, Matsunaga S, Kaneko Y, Kajiyama S, Harashima S, Kobayashi A, Fukui K (2003) Transformation of yeast using calcium alginate microbeads with surface-immobilized chromosomal DNA. Biotechniques 35:734–740

    Article  CAS  Google Scholar 

  • Murakami K, Tao E, Ito Y, Sugiyama M, Kaneko Y, Harashima S, Sumiya T, Nakamura A, Nishizawa M (2007) Large scale deletions in the Saccharomyces cerevisiae genome create strains with altered regulation of carbon metabolism. Appl Microbiol Biotechnol 75:589–597

    Article  CAS  Google Scholar 

  • Murray AW, Szostak JW (1983) Construction of artificial chromosomes in yeast. Nature 305(5931):189–193

    Article  CAS  Google Scholar 

  • Murray AW, Schultes NP, Szostak JW (1986) Chromosome length controls mitotic chromosome segregation in yeast. Cell 45:529–536

    Article  CAS  Google Scholar 

  • Murray AW, Claus TB, Szostak JW (1988) Characterization of two telomeric DNA processing reactions in Saccharomyces cerevisiae. Mol Cell Biol 8:4642–4650

    Article  CAS  Google Scholar 

  • Noël AJ, Wende W, Pingoud A (2004) DNA recognition by the homing endonuclease PI-SceI involves a divalent metal ion cofactor-induced conformational change. J Biol Chem 279:6794–6804

    Article  Google Scholar 

  • `Olson MV (1991) Genome structure and organization in Saccharomyces cerevisiae. In: Broach JR, Pringle JR, Jones EW (eds) The molecular and cellular biology of the yeast Saccharomyces, vol 1. Cold Spring Harbor Laboratory Press, New York, pp 1–39

    Google Scholar 

  • Pavan WJ, Hieter P, Sears D, Burkhoff A, Reeves RH (1991) High-efficiency yeast artificial chromosome fragmentation vectors. Gene 106:125–127

    Article  CAS  Google Scholar 

  • Riethman HC, Moyzis RK, Meyne J, Burke DT, Olson MV (1989) Cloning human telomeric DNA fragments into Saccharomyces cerevisiae using a yeast-artificial- chromosome vector. Proc Natl Acad Sci 86:6240–6244

    Article  CAS  Google Scholar 

  • Roy N, Runqe KW (1999) The ZDS1 and ZDS2 proteins require the Sir3p component of yeast silent chromatin to enhance the stability of short linear centromeric plasmids. Chromosoma 108:146–161

    Article  CAS  Google Scholar 

  • Shi DJ, Wang CL, Wang KM (2009) Genome shuffling to improve thermotolerance, ethanol tolerance and ethanol productivity of Saccharomyces cerevisiae. J Ind Microbiol Biotechnol 36:139–147

    Article  CAS  Google Scholar 

  • Sugiyama M, Ikushima S, Nakazawa T, Kaneko Y, Harashima S (2005) PCR-mediated repeated chromosome splitting in Saccharomyces cerevisiae. Biotechniques 38:909–914

    Article  CAS  Google Scholar 

  • Sugiyama M, Yamamoto E, Mukai Y, Kaneko Y, Nishizawa M, Harashima S (2006) Chromosome-shuffling technique for selected chromosomal segments in Saccharomyces cerevisiae. Appl Microbiol Biotechnol 72:947–952

    Article  CAS  Google Scholar 

  • Sugiyama M, Nishizawa M, Hayashi K, Kaneko Y, Fukui K, Kobayashi A, Harashima S (2003) Repeated chromosome splitting targeted to delta sequences in Saccharomyces cerevisiae. J Biosci Bioeng 96:397–400

    Article  CAS  Google Scholar 

  • Sugiyama M, Nakazawa T, Murakami K, Sumiya T, Nakamura A, Kaneko Y, Nishizawa M, Harashima S (2008) PCR-mediated one-step deletion of targeted chromosomal regions in haploid Saccharomyces cerevisiae. Appl Microbiol Biotechnol 80:545–553

    Article  CAS  Google Scholar 

  • Surosky RT, Neqlon CS, Tye BK (1986) The mitotic stability of deletion derivatives of chromosome III in yeast. Proc Natl Acad Sci USA 83:414–418

    Article  CAS  Google Scholar 

  • Widianto D, Yamamoto E, Mukai Y, Oshima Y, Harashima S (1997) A method for fusing chromosomes in Saccharomyces cerevisiae. J Ferment Bioeng 83:125–131

    Article  CAS  Google Scholar 

  • Widianto D, Yamamoto E, Sugiyama M, Mukai Y, Kaneko Y, Oshima Y, Nishizawa M, Harashima S (2003) Creating a Saccharomyces cerevisiae haploid strain having 21 chromosomes. J Biosci Bioeng 95:89–94

    Article  CAS  Google Scholar 

  • Yamagishi K, Sugiyama M, Kaneko Y, Harashima S (2008a) Conditional chromosome splitting in Saccharomyces cerevisiae using the homing endonuclease PI-SceI. Appl Microbiol Biotechnol 79:699–706

    Article  CAS  Google Scholar 

  • Yamagishi K, Sugiyama M, Kaneko Y, Nishizawa M, Harashima S (2008b) Construction and characterization of single-gene chromosomes in Saccharomyces cerevisiae. J Biosci Bioeng 106:563–567

    Article  CAS  Google Scholar 

  • Yu BJ, Sung BH, Koob MD, Lee CH, Lee JH, Lee WS, Kim MS, Kim SC (2002) Minimization of the Escherichia coli genome using a Tn5-targeted Cre/loxP excision system. Nat Biotechnol 20:1018–1023

    Article  CAS  Google Scholar 

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Author notes

  1. Yeon-Hee Kim

    Present address: Department of Biotechnology and Bioengineering, Dong-Eui University, 995 Eomgwangno, Busanjin-gu, Busan, 614-714, Korea

Authors and Affiliations

  1. Department of Biotechnology, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita-shi, Osaka, 565-0871, Japan

    Minetaka Sugiyama, Kazuo Yamagishi, Yeon-Hee Kim, Yoshinobu Kaneko & Satoshi Harashima

  2. Department of Microbiology and Immunology, Keio University School of Medicine, 35 Shinanomachi, Shinjuku, Tokyo, 160-8582, Japan

    Masafumi Nishizawa

Authors
  1. Minetaka Sugiyama
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  2. Kazuo Yamagishi
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  3. Yeon-Hee Kim
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  4. Yoshinobu Kaneko
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  5. Masafumi Nishizawa
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  6. Satoshi Harashima
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Corresponding author

Correspondence to Satoshi Harashima.

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Sugiyama, M., Yamagishi, K., Kim, YH. et al. Advances in molecular methods to alter chromosomes and genome in the yeast Saccharomyces cerevisiae . Appl Microbiol Biotechnol 84, 1045–1052 (2009). https://doi.org/10.1007/s00253-009-2144-z

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  • DOI: https://doi.org/10.1007/s00253-009-2144-z

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