Fabrication of a Partial Genome Microarray of the Methylotrophic Yeast Hansenula polymorpha: Optimization and Evaluation of Transcript Profiling

  • OH , KWAN-SEOK (Laboratory of Metabolic Engineering, Korea Research Institute of Bioscience and Biotechnology) ;
  • KWON, OH-SUK (Laboratory of Metabolic Engineering, Korea Research Institute of Bioscience and Biotechnology) ;
  • OH, YUN-WI (Laboratory of Metabolic Engineering, Korea Research Institute of Bioscience and Biotechnology) ;
  • SOHN, MIN-JEONG (Laboratory of Metabolic Engineering, Korea Research Institute of Bioscience and Biotechnology) ;
  • JUNG, SOON-GEE (Laboratory of Metabolic Engineering, Korea Research Institute of Bioscience and Biotechnology) ;
  • KIM, YONG-KYUNG (Laboratory of Metabolic Engineering, Korea Research Institute of Bioscience and Biotechnology) ;
  • KIM, MIN-GON (Laboratory of Metabolic Engineering, Korea Research Institute of Bioscience and Biotechnology) ;
  • RHEE, SANG-KI (Laboratory of Metabolic Engineering, Korea Research Institute of Bioscience and Biotechnology) ;
  • GERD GELLISSEN, (Rhein Biotech GmbH) ;
  • KANG, HYUN-AH (Laboratory of Metabolic Engineering, Korea Research Institute of Bioscience and Biotechnology)
  • Published : 2004.12.01

Abstract

The methylotrophic yeast Hansenula polymorpha has been extensively studied as a model organism for methanol metabolism and peroxisome biogenesis. Recently, this yeast has also attracted attention as a promising host organism for recombinant protein production. Here, we describe the fabrication and evaluation of a DNA chip spotted with 382 open reading frames (ORFs) of H. polymorpha. Each ORF was PCR-amplified using gene-specific primer sets, of which the forward primers had 5'-aminolink. The PCR products were printed in duplicate onto the aldehyde-coated slide glasses to link only the coding strands to the surface of the slide via covalent coupling between amine and aldehyde groups. With the partial genome DNA chip, we compared efficiency of direct and indirect cDNA target labeling methods, and found that the indirect method, using fluorescent-labeled dendrimers, generated a higher hybridization signal-to-noise ratio than the direct method, using cDNA targets labeled by incorporation of fluorescence-labeled nucIeotides during reverse transcription. In addition, to assess the quality of this DNA chip, we analyzed the expression profiles of H. polymorpha cells grown on different carbon sources, such as glucose and methanol, and also those of cells treated with the superoxide­generating drug, menadione. The profiles obtained showed a high-level induction of a set of ORFs involved in methanol metabolism and oxidative stress response in the presence of methanol and menadione, respectively. The results demonstrate the sensitivity and reliability of our arrays to analyze global gene expression changes of H. polymorpha under defined environmental conditions.

Keywords

References

  1. Avila, J., C. González, N. Brito, and J. M. Siverio. 1998. Clustering of the YNA1 gene encoding a Zn(II)$_2$Cys$_6$ transcriptional factor in the yeast Hansenula polymorpha with the nitrate assimilation genes YNT1, YNI1 and YNR1, and its involvement in their transcriptional activation. Biochem. J. 335: 647-652
  2. Bilban, M., L. K. Buehler, S. Head, G. Desoye, and V. Quaranta. 2002. Normalizing DNA microarray data. Curr. Issues Mol. Biol. 4: 57-64
  3. Blandin, G., B. Llorente, A. Malpertuy, P. Wincker, F. Artiguenave, and B. Dujon. 2000. Genomic exploration of the hemiascomycetous yeasts: 13. Pichia angusta. FEBS Lett. 487: 76-81 https://doi.org/10.1016/S0014-5793(00)02284-5
  4. Bystrykh, L. V., L. R. Aminova, and Y. A. Trotsenko. 1988. Methanol metabolism in mutants of the methylotrophic yeast Hansenula polymorpha. FEMS Microbiol. Lett. 51: 89-94 https://doi.org/10.1111/j.1574-6968.1988.tb02975.x
  5. Chen, D., W. M. Toone, J. Mata, R. Lyne, G. Burns, K. Kivinen, A. Brazma, N. Jone, and J. Bähler. 2003. Global transcriptional responses of fission yeast to environmental stress. Mol. Biol. Cell 14: 214-229
  6. Cowen, L., A. Nantel, M. S. Whiteway, D. Y. Thomas, D. C. Tessiler, L. M. Kohn, and J. B. Anderson. 2002. Population genomics of drug resistance in Candida albicans. Proc. Natl. Acad. Sci. USA 99: 9284-9289
  7. DeRisi, J. L., V. R. Iyer, and P. O. Brown. 1997. Exploring the metabolic and genetic control of gene expression on a genomic scale. Science 278: 680-686
  8. Eisen, M. B., P. T. Spellman, P. O. Brown, and D. Botstein. 1998. Cluster analysis and display of genome-wide expression patterns. Proc. Natl. Acad. Sci. USA 95: 14863-14868
  9. Elion, E. A. and J. R. Warner. 1984. The major promoter element of rRNA transcription in yeast lies 2 kb upstream. Cell 39: 663-673
  10. Erasmus, D. J., G. K. van der Merwe, and H. J. van Vuuren. 2003. Genome-wide expression analyses: Metabolic adaptation of Saccharomyces cerevisiae to high sugar stress. FEMS Yeast Res. 3: 375-399
  11. Gasch A. P., 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
  12. Gellissen G., C. P. Hollenberg, and Z. A. Janowicz. 1995. Gene expression in methylotrophic yeasts, pp. 195-239. In Smith, A. (ed.). Gene Expression in Recombinant Microorganisms. New York, Dekker, U.S.A
  13. Gellissen, G. 2002. Hansenula polymorpha - Biology and Applications. Wiley-VCH, Weinheim
  14. Goffeau, A., B. G. Barrell, H. Bussey, R. W. Davis, B. Dujon, H. Feldmann, F. Galibert, J. D. Hoheisel, C. Jacq, M. Johnston, E. J. Louis, H. W. Mewes, Y. Murakami, P. Philippsen, H. Tettelin, and S. G. Oliver. 1996. Life with 6000 genes. Science 274: 546-567
  15. Hegde, P., R. Qi, K. Abernathy, C. Gay, S. Dharap, R. Gaspard, J. E. Hughes, E. Snesrud, N. Lee, and J. Quackenbush. 2000 A concise guide to cDNA microarray analysis. Biotechniques 29: 548-550, 552-554, 556-562
  16. Holm, C., D. W. Meeks-Wagner, W. L. Fangman, and D. Botstein. 1986. A rapid, efficient method for isolating DNA from yeast. Gene 42:169-173
  17. Jeoung, D., J.-W. Kim, Y.-H. Lee, M. Baek, S. Lee, N.-I. Baek, and H. Y. Kim. 2002. cDNA microarray analysis of transcriptional response to hyperin in human gastric cancer cells. J. Microbiol. Biotechnol. 12: 664-668
  18. Kang, H. A., J. H. Sohn, E. S. Choi, B. H. Chung, M. H. Yu, and S. K. Rhee. 1998. Glycosylation of human $\alpha$1-antitrypsin in Saccharomyces cerevisiae and methylotrophic yeasts. Yeast 14: 371-381
  19. Kim, K. A., J. Y. Lee, K. S. Park, M. J. Kim, and J. H. Chung. 1996. Mechanism of menadione-induced cytotoxicity in rat platelets. Toxicol. Appl. Pharmacol. 138: 12-19
  20. Kim, S. Y., J. H. Sohn, Y. R. Pyun, and E. S. Choi. 2002. A cell surface display system using novel GPI-anchored proteins in Hansenula polymorpha. Yeast 19: 1153-1163
  21. Kim, T. W., S. G. Min, D. H. Choi, J. S. Jo, and H. Y. Kim. 2000. Rapid identification of Lactobacillus plantarum in Kimchi using polymerase chain reaction. J. Microbiol. Biotechnol. 10: 881-884
  22. Lyne, R., G. Burns, J. Mata, C. J. Penkett, G. Rustici, D. Chen, C. Langford, D. Vetrie, and J. Bähler. 2003. Wholegenome microarrays of fission yeast: Characteristics, accuracy, reproducibility, and processing of array data. BMC Genomics 4: 27
  23. Murad, A. M. A., C. dEnfert, C. Gaillardin, H. Tournu, F. Tekaia, D. Talibi, D. Marechal, V. Marchais, J. Cottin, and A. J. P. Brown. 2001. Transcript profiling in Candida albicans reveals new cellular functions for the transcriptional repressors CaTup1, CaMig1 and CaNrg1. Mol. Microbiol. 42: 981- 993
  24. Perez-Ortin, J. E., J. Garcia-Martinez, and T. M. Alberola. 2002. DNA chips for yeast biotechnology. The case of wine yeasts. J. Biotechnol. 98: 227-241
  25. Ramezani-Rad, M., C. P. Hollenberg, J. Lauber, H. Wedler, E. Griess, C. Wagner, K. Albermann, J. Hani, M. Piontek, U. Dahlems, and G. Gellissen. 2003. The Hansenula polymorpha (strain CBS4732) genome sequencing and analysis. FEMS Yeast Res. 4: 207-215
  26. Roberts, C. J., B. Nelson, M. J. Marton, R. Stoughton, M. R. Meyer, H. A. Bennett, Y. D. He, H. Dai, W. L. Walker, T. R. Hughes, M. Tyers, C. Boone, and S. H. Friend. 2000. Signaling and circuitry of multiple MAPK pathways revealed by a matrix of global gene expression profiles. Science 287: 873-880
  27. Stare, J., J. Stare, F. E. Jr. Harrell, and H. Heinzl. 2001. BJ: An S-Plus program to fit linear regression models to censored data using the Buckley-James method. Computer Methods Programs Biomed. 64: 45-52
  28. Titorenko, V. I., H. R. Waterham, J. M. Cregg, W. Harder, and M. Veenhuis. 1993. A complex set of interacting genes controls peroxisome biogenesis in Hansenula polymorpha. Proc. Natl. Acad. Sci. USA 90: 7470-7474
  29. van Dijk, R., K. N. Faber, J. A. K. W. Kiel, M. Veenhuis, and I. van der Klei. 2000. The methylotrophic yeast Hansenula polymorpha: A versatile cell factory. Enzyme Microbiol. Technol. 26: 793-800
  30. Veale, R. A., M. L. Giuseppin, H. M. van Eijk, P. E. Sudbery, and C. T. Verrips. 1992. Development of a strain of Hansenula polymorpha for the efficient expression of guar alpha-galactosidase. Yeast 8: 361-372
  31. Yang, Y. H., S. Dudoit, P. Luu, D. M. Lin, V. Peng, J. Ngal, and T. P. Speed. 2002. Normalization for cDNA microarray data: A robust composite method addressing single and multiple slide systematic variation. Nucleic Acids Res. 30: e15
  32. Yurimoto, H., T. Komeda, C. R. Lim, T. Nakagawa, K. Kondo, N. Kato, and Y. Sakai. 2000. Regulation and evaluation of five methanol-inducible promoters in the methylotrophic yeast Candida boidii. Biochim. Biophys. Acta 1493: 56-63
  33. Zammatteo N., L. Jeanmart, S. Hamels, S. Courtois, P. Louette, L. Hevesi, and J. Remacle. 2000. Comparison between different strategies of covalent attachment of DNA to glass surfaces to build DNA microarrays. Anal. Biochem. 280: 143-150