1887

Abstract

Within the field of functional genomics, DNA microarrays have become a very useful tool to study genome-wide gene-expression changes under diverse experimental conditions. Here, the design and production of a gene microarray, called the ‘yeast cell wall chip’, specifically tailored to investigate cell wall functions, is described. This array has been validated and shown to be useful to address gene involvement in the regulation of the response to cell wall damage in yeast. The advantages of this tailored gene microarray, which contains 390 genes, in terms of reproducibility, accuracy, versatility and ease of use are reported. Importantly, the microarray design permits the performance of a double hybridization process (two experiments) on the same slide. Cell wall stress leads to the transcriptional activation of a set of genes involved in cell wall remodelling. This response has been shown to be strongly controlled by the MAP kinase (MAPK) Slt2p, but other signalling pathways have also been suggested to be involved in this process. Here, using the tailored microarray, the role of the HOG1 pathway in the regulation of the transcriptional compensatory response to cell wall damage was evaluated by comparing the transcriptional profiles of a mutant and a wild-type strain in the presence of Congo red. Two genes, () and , were found to be dependent on the Hog1p MAPK for their induction, indicating that an additional level of regulation of cell wall functions is mediated by this MAPK.

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2005-07-01
2019-11-22
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References

  1. Agarwal, A. K., Rogers, P. D., Baerson, S. R., Jacob, M. R., Barker, K. S., Cleary, J. D., Walker, L. A., Nagle, D. G. & Clark, A. M. ( 2003; ). Genome-wide expression profiling of the response to polyene, pyrimidine, azole, and echinocandin antifungal agents in Saccharomyces cerevisiae. J Biol Chem 278, 34998–35015.[CrossRef]
    [Google Scholar]
  2. Alberola, T. M., García-Martínez, J., Antúnez, O., Viladevall, L., Barceló, A., Ariño, J. & Pérez-Ortín, J. E. ( 2004; ). A new set of DNA macrochips for the yeast Saccharomyces cerevisiae: features and uses. Int Microbiol 7, 199–206.
    [Google Scholar]
  3. Baetz, K., Moffat, J., Haynes, J., Chang, M. & Andrews, B. ( 2001; ). Transcriptional coregulation by the cell integrity mitogen-activated protein kinase Slt2 and the cell cycle regulator Swi4. Mol Cell Biol 21, 6515–6528.[CrossRef]
    [Google Scholar]
  4. Boorsma, A., De Nobel, H., ter Riet, B., Bargmann, B., Brul, S., Hellingwerf, K. J. & Klis, F. M. ( 2004; ). Characterization of the transcriptional response to cell wall stress in Saccharomyces cerevisiae. Yeast 21, 413–427.[CrossRef]
    [Google Scholar]
  5. Cid, V. J., Duran, A., del Rey, F., Snyder, M. P., Nombela, C. & Sanchez, M. ( 1995; ). Molecular basis of cell integrity and morphogenesis in Saccharomyces cerevisiae. Microbiol Rev 59, 345–386.
    [Google Scholar]
  6. De Groot, P. W., Ruiz, C., Vazquez de Aldana, C. R. & 14 other authors ( 2001; ). A genomic approach for the identification and classification of genes involved in cell wall formation and its regulation in Saccharomyces cerevisiae. Comp Funct Genom 2, 124–142.[CrossRef]
    [Google Scholar]
  7. De Nobel, H., Ruiz, C., Martin, H., Morris, W., Brul, S., Molina, M. & Klis, F. M. ( 2000; ). Cell wall perturbation in yeast results in dual phosphorylation of the Slt2/Mpk1 MAP kinase and in an Slt2-mediated increase in FKS2lacZ expression, glucanase resistance and thermotolerance. Microbiology 146, 2121–2132.
    [Google Scholar]
  8. Dodou, E. & Treisman, R. ( 1997; ). The Saccharomyces cerevisiae MADS-box transcription factor Rlm1 is a target for the Mpk1 mitogen-activated protein kinase pathway. Mol Cell Biol 17, 1848–1859.
    [Google Scholar]
  9. Duran, A. & Nombela, C. ( 2004; ). Fungal cell wall biogenesis: building a dynamic interface with the environment. Microbiology 150, 3099–3103.[CrossRef]
    [Google Scholar]
  10. Evans, A. L., Sharkey, A. S., Saidi, S. A., Print, C. G., Catalano, R. D., Smith, S. K. & Charnock-Jones, D. S. ( 2003; ). Generation and use of a tailored gene array to investigate vascular biology. Angiogenesis 6, 93–104.[CrossRef]
    [Google Scholar]
  11. Firon, A., Lesage, G. & Bussey, H. ( 2004; ). Integrative studies put cell wall synthesis on the yeast functional map. Curr Opin Microbiol 7, 617–623.[CrossRef]
    [Google Scholar]
  12. García, R., Bermejo, C., Grau, C., Perez, R., Rodriguez-Peña, J. M., Francois, J., Nombela, C. & Arroyo, J. ( 2004; ). The global transcriptional response to transient cell wall damage in Saccharomyces cerevisiae and its regulation by the cell integrity signaling pathway. J Biol Chem 279, 15183–15195.[CrossRef]
    [Google Scholar]
  13. García-Rodriguez, L. J., Duran, A. & Roncero, C. ( 2000; ). Calcofluor antifungal action depends on chitin and a functional high-osmolarity glycerol response (HOG) pathway: evidence for a physiological role of the Saccharomyces cerevisiae HOG pathway under non inducing conditions. J Bacteriol 182, 2428–2437.[CrossRef]
    [Google Scholar]
  14. Guimond, C., Trudel, N., Brochu, C. & 11 other authors ( 2003; ). Modulation of gene expression in Leishmania drug resistant mutants as determined by targeted DNA microarrays. Nucleic Acids Res 31, 5886–5896.[CrossRef]
    [Google Scholar]
  15. Gustin, M. C., Albertyn, J., Alexander, M. & Davenport, K. ( 1998; ). MAP kinase pathways in the yeast Saccharomyces cerevisiae. Microbiol Mol Biol Rev 62, 1264–1300.
    [Google Scholar]
  16. Haas, S., Vingron, M., Poustka, A. & Wiemann, S. ( 1998; ). Primer design for large scale sequencing. Nucleic Acids Res 26, 3006–3012.[CrossRef]
    [Google Scholar]
  17. Hayashi, S. ( 2004; ). Prediction of hormone sensitivity by DNA microarray. Biomed Pharmacother 58, 1–9.[CrossRef]
    [Google Scholar]
  18. Igual, J. C., Johnson, A. L. & Johnston, L. H. ( 1996; ). Coordinated regulation of gene expression by the cell cycle transcription factor Swi4 and the protein kinase C MAP kinase pathway for yeast cell integrity. EMBO J 15, 5001–5013.
    [Google Scholar]
  19. Jung, U. S. & Levin, D. E. ( 1999; ). Genome-wide analysis of gene expression regulated by the yeast cell wall integrity signalling pathway. Mol Microbiol 34, 1049–1057.[CrossRef]
    [Google Scholar]
  20. Kapteyn, J. C., ter Riet, B., Vink, E., Blad, S., De Nobel, H., Van Den, E. H. & Klis, F. M. ( 2001; ). Low external pH induces HOG1-dependent changes in the organization of the Saccharomyces cerevisiae cell wall. Mol Microbiol 39, 469–479.[CrossRef]
    [Google Scholar]
  21. Ketela, T., Green, R. & Bussey, H. ( 1999; ). Saccharomyces cerevisiae mid2p is a potential cell wall stress sensor and upstream activator of the PKC1-MPK1 cell integrity pathway. J Bacteriol 181, 3330–3340.
    [Google Scholar]
  22. Klis, F. M., Mol, P., Hellingwerf, K. & Brul, S. ( 2002; ). Dynamics of cell wall structure in Saccharomyces cerevisiae. FEMS Microbiol Rev 26, 239–256.[CrossRef]
    [Google Scholar]
  23. Kopecka, M. & Gabriel, M. ( 1992; ). The influence of Congo red on the cell wall and (1,3)-β-d-glucan microfibril biogenesis in Saccharomyces cerevisiae. Arch Microbiol 158, 115–126.[CrossRef]
    [Google Scholar]
  24. Lagorce, A., Hauser, N. C., Labourdette, D., Rodriguez, C., Martin-Yken, H., Arroyo, J., Hoheisel, J. D. & Francois, J. ( 2003; ). Genome-wide analysis of the response to cell wall mutations in the yeast Saccharomyces cerevisiae. J Biol Chem 278, 20345–20357.[CrossRef]
    [Google Scholar]
  25. Lee, B. N. & Elion, E. A. ( 1999; ). The MAPKKK Ste11 regulates vegetative growth through a kinase cascade of shared signaling components. Proc Natl Acad Sci U S A 96, 12679–12684.[CrossRef]
    [Google Scholar]
  26. Livak, K. J. & Schmittgen, T. D. ( 2001; ). Analysis of relative gene expression data using real-time quantitative PCR and the 2−ΔΔCt Method. Methods 25, 402–408.[CrossRef]
    [Google Scholar]
  27. Lorenz, M. G., Cortes, L. M., Lorenz, J. J. & Liu, E. T. ( 2003; ). Strategy for the design of custom cDNA microarrays. Biotechniques 34, 1264–1270.
    [Google Scholar]
  28. Martinez-Pastor, M. T., Marchler, G., Schuller, C., Marchler-Bauer, A., Ruis, H. & Estruch, F. ( 1996; ). The Saccharomyces cerevisiae zinc finger proteins Msn2p and Msn4p are required for transcriptional induction through the stress response element (STRE). EMBO J 15, 2227–2235.
    [Google Scholar]
  29. Martzen, M. R., McCraith, S. M., Spinelli, S. L., Torres, F. M., Fields, S., Grayhack, E. J. & Phizicky, E. M. ( 1999; ). A biochemical genomics approach for identifying genes by the activity of their products. Science 286, 1153–1155.[CrossRef]
    [Google Scholar]
  30. Molina, M., Gil, C., Pla, J., Arroyo, J. & Nombela, C. ( 2000; ). Protein localisation approaches for understanding yeast cell wall biogenesis. Microsc Res Tech 51, 601–612.[CrossRef]
    [Google Scholar]
  31. O'Rourke, S. M. & Herskowitz, I. ( 2004; ). Unique and redundant roles for HOG MAPK pathway components as revealed by whole-genome expression analysis. Mol Biol Cell 15, 532–542.
    [Google Scholar]
  32. Popolo, L., Gualtieri, T. & Ragni, E. ( 2001; ). The yeast cell-wall salvage pathway. Med Mycol 39 (Supplement 1), 111–121.[CrossRef]
    [Google Scholar]
  33. Proft, M. & Struhl, K. ( 2002; ). Hog1 kinase converts the Sko1-Cyc8-Tup1 repressor complex into an activator that recruits SAGA and SWI/SNF in response to osmotic stress. Mol Cell 9, 1307–1317.[CrossRef]
    [Google Scholar]
  34. Quackenbush, J. ( 2002; ). Microarray data normalization and transformation. Nat Genet 32, 496–501.[CrossRef]
    [Google Scholar]
  35. Rae, M. T., Niven, D., Ross, A., Forster, T., Lathe, R., Critchley, H. O., Ghazal, P. & Hillier, S. G. ( 2004; ). Steroid signalling in human ovarian surface epithelial cells: the response to interleukin-1α determined by microarray analysis. J Endocrinol 183, 19–28.[CrossRef]
    [Google Scholar]
  36. Reinhold, W. C., Kouros-Mehr, H., Kohn, K. W. & 12 other authors ( 2003; ). Apoptotic susceptibility of cancer cells selected for camptothecin resistance: gene expression profiling, functional analysis, and molecular interaction mapping. Cancer Res 63, 1000–1011.
    [Google Scholar]
  37. Schwartz, M. A. & Madhani, H. D. ( 2004; ). Principles of MAP kinase signaling specificity in Saccharomyces cerevisiae. Annu Rev Genet 38, 725–748.[CrossRef]
    [Google Scholar]
  38. Smits, G. J., Kapteyn, J. C., Van Den, E. H. & Klis, F. M. ( 1999; ). Cell wall dynamics in yeast. Curr Opin Microbiol 2, 348–352.[CrossRef]
    [Google Scholar]
  39. Smits, G. J., Van Den, E. H. & Klis, F. M. ( 2001; ). Differential regulation of cell wall biogenesis during growth and development in yeast. Microbiology 147, 781–794.
    [Google Scholar]
  40. Sorger, P. K. ( 1991; ). Heat shock factor and the heat shock response. Cell 65, 363–366.[CrossRef]
    [Google Scholar]
  41. Tomas-Cobos, L., Casadome, L., Mas, G., Sanz, P. & Posas, F. ( 2004; ). Expression of the HXT1 low affinity glucose transporter requires the coordinated activities of the HOG and glucose signalling pathways. J Biol Chem 279, 22010–22019.[CrossRef]
    [Google Scholar]
  42. van Helden, J. ( 2003; ). Regulatory sequence analysis tools. Nucleic Acids Res 31, 3593–3596.[CrossRef]
    [Google Scholar]
  43. Yoshimoto, H., Saltsman, K., Gasch, A. P., Li, H. X., Ogawa, N., Botstein, D., Brown, P. O. & Cyert, M. S. ( 2002; ). Genome-wide analysis of gene expression regulated by the calcineurin/Crz1p signaling pathway in Saccharomyces cerevisiae. J Biol Chem 277, 31079–31088.[CrossRef]
    [Google Scholar]
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