Journal of Microbiology and Biotechnology

The Korean Society for Microbiology and Biotechnology (한국미생물·생명공학회)
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Elucidation of Copper and Asparagine Transport Systems in Saccharomyces cerevisiae KNU5377 Through Genome-Wide Transcriptional Analysis

  • KIM IL-SUP (Department of Microbiology, School of Life Sciences and Biotechnology, Kyungpook National University) ;
  • YUN HAE SUN (Department of Microbiology, School of Life Sciences and Biotechnology, Kyungpook National University) ;
  • SHIMISU HISAYO (International Patent Depositary, National Institute of Advanced Industrial Science and Technology) ;
  • KITAGAWA EMIKO (Human Stress Signal Research Center, National Institute of Advanced Industrial Science and Technology) ;
  • IWAHASHI HITOSHI (International Patent Depositary, Research Institute of Biological Resources, Human Stress Signal Research Center, National Institute of Advanced Industrial Science and Technology) ;
  • JIN INGNYOL (Department of Microbiology, School of Life Sciences and Biotechnology, Kyungpook National University)
  • Published : 2005.12.01
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Abstract

Saccharomyces cerevisiae KNU5377 has potential as an industrial strain that can ferment wasted paper for fuel ethanol at $40^{\circ}C$ [15, 16]. To understand the characteristics of the strain, genome-wide expression was performed using DNA microarray technology. We compared the homology of the DNA microarray between genomic DNAs of S. cerevisiae KNU5377 and a control strain, S. cerevisiae S288C. Approximately $97\%$ of the genes in S. cerevisiae KNU5377 were identified with those of the reference strain. YHR053c (CUP1), YLR155c (ASP3), and YDR038c (ENA5) showed lower homology than those of S. cerevisiae S288C. In particular, the differences in the regions of YHR053c and YLR155c were confirmed by Southern hybridization, but did not with that of the region of YDR038c. The expression level of mRNA in S. cerevisiae KNU5377 and S288C was also compared: the 550 ORFs of S. cerevisiae KNU5377 showed more than two-fold higher intensity than those of S. cerevisiae S288C. Among the 550 ORFs, 59 ORFs belonged to the groups of ribosomal proteins and mitochondrial ribosomal proteins, and 200 ORFs belonged to the group of cellular organization. DIP5 and GAP1 were the most highly expressed genes. These results suggest that upregulated DIP5 and GAP 1 might take the place of ASP3 and, additionally, the sensitivity against copper might be contributable to the lowest expression level of copper-binding metallothioneins encoded by CUP 1a (YHR053c) and CUP1b (YHR055c) in S. cerevisiae KNU5377.

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References

  1. Audrey, P. G., P. T. Spellman, C. M. Kao, C. H. Orna, M. B. Eisen, G. Storz, D. Botstein, and P. O. Brown. 2000. Genomic expression programs in the response of yeast cells to environmental changes. Mol. Biol. Cell. 11: 4241-4257 https://doi.org/10.1091/mbc.11.12.4241
  2. Bengt, L. P., J. O. Lagerstedt, J. R. Pratt, P. G. Johanna, K. Lundh, S. Shokrollahzadeh, and F. Lundh. 2003. Regulation of phosphate acquisition in Saccharomyces cerevisiae. Curr. Genet. 225: 225-244
  3. Birgitte R., S. Holmberg, L. D. Olsen, and M. C. Kielland- Brandt. 1998. Dip5p mediates high-affinity and high-capacity transport of L-glutamate and L-aspartate in Saccharomyces cerevisiae. Curr. Genet. 33: 171-177 https://doi.org/10.1007/s002940050324
  4. Choowong, A., T. Homma, H. Tochio, M. Shirakawa, Y. Kaneko, and S. Harashima. 2004. Intracellular phosphate serves as a signal for the regulation of the PHO pathway in Saccharomyces cerevisiae. J. Biol. Chem. 279: 17289- 17294 https://doi.org/10.1074/jbc.M312202200
  5. Church, G. M. and W. Gilbert. 1984. Genomic sequencing. Proc. Natl. Acad. Sci. USA 81: 1991-1995
  6. David, G., T. Rushmore, and C. T. Caskey. 1999. DNA chips: Promising toys have become powerful tools. Trends Biochem. Sci. 24: 168-173 https://doi.org/10.1016/S0968-0004(99)01382-1
  7. Francisca, R. G., P. Sanz, and J. A. Prieto. 1999. Engineering baker's yeast: Room for improvement. Trends Biotechnol. 17: 237-244 https://doi.org/10.1016/S0167-7799(99)01318-9
  8. Frank, C. P. H., E. G. Jennings, J. J. Wyrick, T. I. Lee, C. J. Hengartner, M. R. Green, T. R. Golub, E. S. Lander, and R. A. Young. 1998. Dissecting the regulatory circuitry of a eukaryotic genome. Cell 95: 717-728 https://doi.org/10.1016/S0092-8674(00)81641-4
  9. Gasch, A. P. 2002. Yeast genomic expression studies using DNA microarrays. Methods Enzymol. 350: 393-414 https://doi.org/10.1016/S0076-6879(02)50976-9
  10. Gasch, A. P. and M. Werner-Washburne. 2002. The genomics of yeast responses to environmental stress and starvation. Funct. Integr. Genomics 2: 181-192 https://doi.org/10.1007/s10142-002-0058-2
  11. Gross, C. and K. Watson. 1996. Heat shock protein synthesis and trehalose accumulation are not required for induced thermotolerance in depressed Saccharomyces cerevisiae. Biochem. Biophys. Comm. 220: 766-772 https://doi.org/10.1006/bbrc.1996.0478
  12. Gross, C. and K. Watson. 1998. Application of mRNA differential display to investigate gene expression in thermotolerant cells of Saccharomyces cerevisiae. Yeast 14: 431-432 https://doi.org/10.1002/(SICI)1097-0061(19980330)14:5<431::AID-YEA242>3.0.CO;2-V
  13. Helen, C. C., B. Ren, S. S. Koh, C. T. Harbison, E. Kanin, E. G. Jennings, T. I. Lee, H. L. True, E. S. Lander, and R. A. Young. 2001. Remodeling of yeast genome expression in response to environmental changes. Mol. Biol. Cell. 12: 323-337 https://doi.org/10.1091/mbc.12.2.323
  14. Heo, S. Y., J. K. Kim, Y. M. Kim, and S. W. Nam. 2004. Xylan hydrolysis by treatment with endoxylanase and $\beta$- xylosidase expressed in yeast. J. Microbiol. Biotechnol. 14: 171-177
  15. Kim, J. W., I. N. Jin, and J. H. Seu. 1995. Isolation of Saccharomyces cerevisiae F38-1, a thermotolerant yeast for fuel alcohol production at high temperature. Kor. J. Appl. Microbiol. Biotechnol. 23: 617-623
  16. Kim, J. W., S. H. Kim, and I. N. Jin. 1995. The fermentation characteristics of Saccharomyces cerevisiae F38-1, a thermotolerant yeast isolated for fuel alcohol production at elevated temperature. Kor. J. Appl. Microbiol. Biotechnol. 23: 624-631
  17. Kosman, D. J. 2003. Molecular mechanisms of iron uptake in fungi. Mol. Microbiol. 47: 1185-1197 https://doi.org/10.1046/j.1365-2958.2003.03368.x
  18. Lim, Y. S., S. M. Bae, and K. Kim. 2005. Mass production of yeast spores from compressed yeast. J. Microbiol. Biotechnol. 15: 568-572
  19. Maria, M. P., S. Puig, and D. J. Thiele. 2000. Characterization of the Saccharomyces cerevisiae high affinity copper transporter Ctr3. J. Biol. Chem. 275: 33244-33251 https://doi.org/10.1074/jbc.M005392200
  20. Oh, K. S., S. K. Oh, Y. W. Oh, M. J. Sohn, S. G. Jung, Y. K. Kim, M. G. Kim, S. K. Rhee, G. Gellissen, and H. A. Kang. 2004. Fabrication of a partial genome microarray of the methylotrophic yeast Hansenula polymorpha: Optimization and evaluation of transcript profiling. J. Microbiol. Biotechnol. 14: 1239-1278
  21. Oshima, Y. 1997. The phosphatase system in Saccharomyces cerevisiae. Genes Genet. Syst. 72: 323-334 https://doi.org/10.1266/ggs.72.323
  22. Paik, S. K., H. S. Yun, H. Y. Sohn, and I. N. Jin. 2003. Effect of trehalose accumulation on the intrinsic and acquired thermotolerance in a natural isolate, Saccharomyces cerevisiae KNU5377. J. Microbiol. Biotechnol. 13: 85-89
  23. Pascale, D. L., J. M. Daran, P. Kotter, T. Petit, M. D. W. Piper, and J. T. Pronk. 2003. Comparative genotyping of the Saccharomyces cerevisiae laboratory strains S288C and CEN.PK 113-7D using oligonucleotide microarrays. FEMS Yeast Res. 4: 259-269 https://doi.org/10.1016/S1567-1356(03)00156-9
  24. Schmitt, M. E., T. A. Brown, and B. L. Trumpower. 1990. A rapid and simple method for preparation of RNA from Saccharomyces cerevisiae. Nucleic Acids Res. 18: 3091-3092 https://doi.org/10.1093/nar/18.10.3091
  25. Stefan, H. and W. H. Mager. 2003. Yeast Stress Response, pp. 201-240. 2nd Ed. Springer-Verlag Berlin Heidelberg, New York, U.S.A
  26. Strathern, J. N., E. W. Jones, and J. R. Bioach. 1982. The Molecular Biology of the Yeast Saccharomyces: Metabolism and Gene Expression, pp. 399-461. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, New York, U.S.A
  27. Vishwanath, R. I., C. Gross, M. Kellehers, P. O. Brown, and D. R. Winge. 2000. Identification of the copper regulon in Saccharomyces cerevisiae by DNA microarrays. J. Biol. Chem. 275: 32310-32316 https://doi.org/10.1074/jbc.M005946200
  28. Yun, H. S., S. K. Paik, I. S. Kim, I. K. Rhee, C. B. Yu, and I. Y. Jin. 2003. Stress response of a thermotolerant alcoholfermenting yeast strain, Saccahromyces cerevisiae KNU5377, against inorganic acids and its alcohol fermentation productivity under the presence of these acids. Kor. J. Life Sci. 13: 110-117 https://doi.org/10.5352/JLS.2003.13.1.110
  29. Yun, H. S., S. K. Paik, I. S. Kim, I. N. Jin, and H. Y. Shon. 2004. Direct evidence of intracellular alkalinization in Saccharomyces cerevisiae KNU5377 exposed to inorganic acid. J. Microbiol. Biotechnol. 14: 243-249