Genome structure of a Saccharomyces cerevisiae strain widely used in bioethanol production

  1. Juan Lucas Argueso1,9,10,
  2. Marcelo F. Carazzolle3,9,
  3. Piotr A. Mieczkowski6,9,
  4. Fabiana M. Duarte3,
  5. Osmar V.C. Netto3,
  6. Silvia K. Missawa3,
  7. Felipe Galzerani3,
  8. Gustavo G.L. Costa3,
  9. Ramon O. Vidal3,
  10. Melline F. Noronha3,
  11. Margaret Dominska1,
  12. Maria G.S. Andrietta4,
  13. Sílvio R. Andrietta4,
  14. Anderson F. Cunha5,
  15. Luiz H. Gomes7,
  16. Flavio C.A. Tavares7,
  17. André R. Alcarde8,
  18. Fred S. Dietrich1,2,
  19. John H. McCusker1,
  20. Thomas D. Petes1 and
  21. Gonçalo A.G. Pereira3,10
  1. 1 Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, North Carolina 27710, USA;
  2. 2 Institute for Genome Sciences and Policy, Duke University Medical Center, Durham, North Carolina 27710, USA;
  3. 3 Laboratório de Genômica e Expressão, Departamento de Genética e Evolução, Instituto de Biologia, Universidade Estadual de Campinas, Campinas-São Paulo 13083-970, Brazil;
  4. 4 Laboratório de Biotecnologia e Bioprocessos, Centro Pluridisciplinar de Pesquisas Químicas e Biológicas, Universidade Estadual de Campinas, Campinas-São Paulo 13081-970, Brazil;
  5. 5 Departamento de Genética e Evolução, CCBS, Universidade Federal de São Carlos, São Carlos-São Paulo 13565-905, Brazil;
  6. 6 Department of Genetics, School of Medicine, University of North Carolina, Chapel Hill, North Carolina 27599, USA;
  7. 7 Departmento de Genética, Universidade de São Paulo, Piracicaba-São Paulo 13418-900, Brazil;
  8. 8 Departamento de Agroindústria, Alimentos e Nutrição, Escola Superior de Agricultura “Luiz de Queiroz,” Universidade de São Paulo, Piracicaba-São Paulo 13418-900, Brazil
    1. 9 These authors contributed equally to this work.

    Abstract

    Bioethanol is a biofuel produced mainly from the fermentation of carbohydrates derived from agricultural feedstocks by the yeast Saccharomyces cerevisiae. One of the most widely adopted strains is PE-2, a heterothallic diploid naturally adapted to the sugar cane fermentation process used in Brazil. Here we report the molecular genetic analysis of a PE-2 derived diploid (JAY270), and the complete genome sequence of a haploid derivative (JAY291). The JAY270 genome is highly heterozygous (∼2 SNPs/kb) and has several structural polymorphisms between homologous chromosomes. These chromosomal rearrangements are confined to the peripheral regions of the chromosomes, with breakpoints within repetitive DNA sequences. Despite its complex karyotype, this diploid, when sporulated, had a high frequency of viable spores. Hybrid diploids formed by outcrossing with the laboratory strain S288c also displayed good spore viability. Thus, the rearrangements that exist near the ends of chromosomes do not impair meiosis, as they do not span regions that contain essential genes. This observation is consistent with a model in which the peripheral regions of chromosomes represent plastic domains of the genome that are free to recombine ectopically and experiment with alternative structures. We also explored features of the JAY270 and JAY291 genomes that help explain their high adaptation to industrial environments, exhibiting desirable phenotypes such as high ethanol and cell mass production and high temperature and oxidative stress tolerance. The genomic manipulation of such strains could enable the creation of a new generation of industrial organisms, ideally suited for use as delivery vehicles for future bioenergy technologies.

    Footnotes

    • 10 Corresponding authors.

      E-mail lucas.argueso{at}duke.edu; fax (919) 684-6033.

      E-mail goncalo{at}unicamp.br; fax 55-19-3521-6235.

    • [Supplemental material is available online at http://www.genome.org. This whole-genome shotgun project has been deposited at DDBJ/EMBL/GenBank under accession no. ACFL00000000. The version described in this work is the first version, ACFL01000000. The microarray data from this study have been deposited at the NCBI Gene Expression Omnibus (http://www.ncbi.nlm.nih.gov/geo/) under accession nos. GSE14601 and GSE17578.]

    • Article published online before print. Article and publication date are at http://www.genome.org/cgi/doi/10.1101/gr.091777.109.

      • Received January 30, 2009.
      • Accepted August 18, 2009.

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