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Journal of microbiology and biotechnology v.14 no.6, 2004년, pp.1239 - 1248   피인용횟수: 2
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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  );
  • 초록

    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.

  • 주제어

    DNA micro array .   transcript profiling .   Hansenula polymorpha .   target labeling .   open reading frames.  

  • 참고문헌 (33)

    1. Bilban, M., L. K. Buehler, S. Head, G. Desoye, and V. Quaranta. 2002. Normalizing DNA microarray data. Curr. Issues Mol. Biol. 4: 57-64 
    2. Chen, D., W. M. Toone, J. Mata, R. Lyne, G. Burns, K. Kivinen, A. Brazma, N. Jone, and J. Bahler. 2003. Global transcriptional responses of fission yeast to environmental stress. Mol. Biol. Cell 14: 214-229 
    3. 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 
    4. 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 
    5. 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 
    6. Lyne, R., G. Burns, J. Mata, C. J. Penkett, G. Rustici, D. Chen, C. Langford, D. Vetrie, and J. Bahler. 2003. Wholegenome microarrays of fission yeast: Characteristics, accuracy, reproducibility, and processing of array data. BMC Genomics 4: 27 
    7. 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 
    8. 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 
    9. 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 
    10. 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 
    11. 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 
    12. 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 
    13. Gellissen, G. 2002. Hansenula polymorpha - Biology and Applications. Wiley-VCH, Weinheim 
    14. 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 
    15. 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 
    16. 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 
    17. 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 
    18. Avila, J., C. Gonzalez, 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 
    19. 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 
    20. 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 
    21. 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 
    22. 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 
    23. 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 
    24. 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 
    25. 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 
    26. 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 
    27. 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 
    28. 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 
    29. 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 
    30. 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 
    31. 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 
    32. 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 
    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 
  • 이 논문을 인용한 문헌 (2)

    1. 2006. "" Journal of microbiology and biotechnology, 16(4): 543~549     
    2. 2007. "" Journal of microbiology and biotechnology, 17(12): 1949~1954     

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