Damage recovery pathways in Saccharomyces cerevisiae revealed by genomic phenotyping and interactome mapping

Molecular Cancer Research

Volumn 1, Issue 2, 2002, Pages 103-112

  Begley, Thomas J ^a   Rosenbach, Ari S ^a   Ideker, Trey ^b   Samson, Leona D ^a  

^a Massachusetts Institute of Technology Cambridge   (United States)

^b WHITEHEAD INSTITUTE FOR BIOMEDICAL RESEARCH   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

4 NITROQUINOLINE 1 OXIDE; MESYLIC ACID METHYL ESTER; MUTAGENIC AGENT; TERT BUTYL HYDROPEROXIDE;

ARTICLE; CELL CYCLE; DATA BASE; DNA DAMAGE; DNA METABOLISM; DNA REPAIR; GENE DELETION; GENE MAPPING; GENETIC TRANSCRIPTION; NONHUMAN; PHENOTYPE; PRIORITY JOURNAL; PROTEIN DNA INTERACTION; PROTEIN PROTEIN INTERACTION; SACCHAROMYCES CEREVISIAE; ULTRAVIOLET RADIATION;

CELL DIVISION; CHROMOSOME MAPPING; DATABASES; DNA; DNA DAMAGE; DNA REPAIR; GENE LIBRARY; GENETIC TECHNIQUES; GENOME, FUNGAL; LIPID METABOLISM; MUTAGENS; PHENOTYPE; PLASMIDS; SACCHAROMYCES CEREVISIAE; SOFTWARE; TRANSCRIPTION, GENETIC;

SACCHAROMYCES; SACCHAROMYCES CEREVISIAE;

EID: 0036923370     PISSN: 15417786     EISSN: None     Source Type: Journal    
DOI: None     Document Type: Article

References (36)

1. Friedberg, E. C., Walker, G. C., and Siede, W. DNA Repair and Mutagenesis. Washington, DC: American Society for Microbiology Press, 1995.
2. Wahl, G. M. and Carr, A. M. The evolution of diverse biological responses to DNA damage: insights from yeast and p53. Nat. Cell Biol., 3: E277 - E286, 2001.
3. Jelinsky, S. A. and Samson, L. D. Global response of Saccharomyces cerevisiae to an alkylating agent. Proc. Natl. Acad. Sci. USA, 96: 1486-1491, 1999.
4. Jelinsky, S. A., Estep, P., Church, G. M., and Samson, L. D. Regulatory networks revealed by transcriptional profiling of damaged Saccharomyces cerevisiae cells: rpn4 links base excision repair with proteasomes [In Process Citation]. Mol. Cell. Biol., 20: 8157-8167, 2000.
5. Gasch, A. P., Huang, M., Metzner, S., Botstein, D., Elledge, S. J., and Brown, P. O. Genomic expression responses to DNA-damaging agents and the regulatory role of the yeast ATR homolog Meclp. Mol. Biol. Cell, 12: 2987-3003, 2001.
6. Causton, H. C., Ren, B., Koh, S. S., Harbison, C. T., Kanin, E., Jennings, E. G., Lee, T. L., True, H. L., Lander, E. S., and Young, R. A. Remodeling of yeast genome expression in response to environmental changes. Mol. Biol. Cell, 12: 323-337, 2001.
7. Uetz, P., Giot, L., Cagney, G., Mansfield, T. A., Judson, R. S., Knight, J. R., Lockshon, D., Narayan, V., Srinivasan, M., Pochart, P., Qureshi-Emili, A., Li, Y., Godwin, B., Conover, D., Kalbfleisch, T., Vijayadamodar, G., Yang, M., Johnston, M., Fields, S., and Rothberg, J. M. A comprehensive analysis of protein-protein interactions in Saccharomyces cerevisiae. Nature, 403: 623 -627, 2000.
8. Ito, T., Chiba, T., Ozawa, R., Yoshida, M., Hattori, M., and Sakaki, Y. A comprehensive two-hybrid analysis to explore the yeast protein interactome. Proc. Natl. Acad. Sci. USA, 98: 4569-4574, 2001.
9. Ho, Y., Gruhler, A., Heilbut, A., Bader, G. D., Moore, L., Adams, S. L., Millar, A., Taylor, P., Bennett, K., Boutilier, K., Yang, L., Wolfing, C., Donaldson, I., Schandorff, S., Shewnarane, J., Vo, M., Taggart, J., Goudreault, M., Muskat, B., Alfarano, C., Dewar, D., Lin, Z., Michalickova, K., Willems, A. R., Sassi, H., Nielsen, P. A., Rasmussen, K. J., Andersen, J. R., Johansen, L. E., Hansen, L. H., Jespersen, H., Podtelejnikov, A., Nielsen, E., Crawford, J., Poulsen, V., Sorensen, B. D., Matthiesen, J., Hendrickson, R. C., Gleeson, F., Pawson, T., Moran, M. F., Durocher, D., Mann, M., Hogue, C. W., Figeys, D., and Tyers, M. Systematic identification of protein complexes in Saccharomyces cerevisiae by mass spectrometry. Nature, 415: 180-183, 2002.
10. Ren, B., Robert, F., Wyrick, J. J., Aparicio, O., Jennings, E. G., Simon, I., Zeitlinger, J., Schreiber, J., Hannett, N., Kanin, E., Volkert, T. L., Wilson, C. J., Bell, S. P., and Young, R. A. Genome-wide location and function of DNA binding proteins. Science, 290: 2306-2309, 2000.
11. Bader, G. D., Donaldson, I., Wolting, C., Ouellette, B. F., Pawson, T., and Hogue, C. W. BIND - The Biomolecular Interaction Network Database. Nucleic Acids Res. 29: 242-245, 2001.
12. Gavin, A. C., Bosche, M., Krause, R., Grandi, P., Marzioch, M., Bauer, A., Schultz, J., Rick, J. M., Michon, A. M., Cruciat, C. M., Remor, M., Hofert, C., Schelder, M., Brajenovic, M., Ruffner, H., Merino, A., Klein, K., Hudak, M., Dickson, D., Rudi, T., Gnau, V., Bauch, A., Bastuck, S., Huhse, B., Leutwein, C., Heurtier, M. A., Copley, R. R., Edelmann, A., Querfurth, E., Rybin, V., Drewes, G., Raida, M., Bouwmeester, T., Bork, P., Seraphin, B., Kuster, B., Neubauer, G., and Superti-Furga, G. Functional organization of the yeast proteome by systematic analysis of protein complexes. Nature, 415: 141 -147, 2002.
13. Wingender, E., Chen, X., Fricke, E., Geffers, R., Hehl, R., Liebich, I., Krull, M., Matys, V., Michael, H., Ohnhauser, R., Pruss, M., Schacherer, F., Thiele, S., and Urbach, S. The TRANSFAC system on gene expression regulation. Nucleic Acids Res., 29: 281-283, 2001.
14. Chen, J., Derfler, B., Maskati, A., and Samson, L. Cloning a eukaryotic DNA glycosylase repair gene by the suppression of a DNA repair defect in Escherichia coli. Proc. Natl. Acad. Sci. USA, 86: 7961-7965, 1989.
15. Bankmann, M., Prakash, L., and Prakash, S. Yeast RAD14 and human xeroderma pigmentosum group A DNA-repair genes encode homologous proteins. Nature, 355: 555-558, 1992.
16. Lawrence, C. W. and Christensen, R. UV mutagenesis in radiation-sensitive strains of yeast. Genetics, 82: 207-232, 1976.
17. Ross-Macdonald, P., Coelho, P. S., Roemer, T., Agarwal, S., Kumar, A., Jansen, R., Cheung, K. H., Sheehan, A., Symoniatis, D., Umansky, L., Heidtman, M., Nelson, F. K., Iwasaki, H., Hager, K., Gerstein, M., Miller, P., Roeder, G. S., and Snyder, M. Large-scale analysis of the yeast genome by transposon tagging and gene disruption. Nature, 402: 413-418, 1999.
18. Bennett, C. B., Lewis, L. K., Karthikeyan, G., Lobachev, K. S., Jin, Y. H., Sterling, J. F., Snipe, J. R., and Resnick, M. A. Genes required for ionizing radiation resistance in yeast. Nat. Genet., 29: 426 -434, 2001.
19. Birrell, G. W., Brown, J. A., Wu, H. I., Giaever, G., Chu, A. M., Davis, R. W., and Brown, J. M. Transcriptional response of Saccharomyces cerevisiae to DNA-damaging agents does not identify the genes that protect against these agents. Proc. Natl. Acad. Sci. USA, 99: 8778-8783, 2002.
20. Eisen, M. B., Spellman, P. T., Brown, P. O., and Botstein, D. Cluster analysis and display of genome-wide expression patterns. Proc. Natl. Acad. Sci. USA, 95: 14863-14868, 1998.
21. Kaufman, R. J. Stress signaling from the lumen of the endoplasmic reticulum: coordination of gene transcriptional and translational controls. Genes Dev., 13: 1211-1233, 1999.
22. Bernstein, B. E., Tong, J. K., and Schreiber, S. L. Genomewide studies of historic deacetylase function in yeast. Proc. Natl. Acad. Sci. USA, 97: 13708-13713, 2000.
23. Robyr, D., Suka, Y., Xenarios, I., Kurdistani, S. K., Wang, A., Suka, N., and Grunstein, M. Microarray deacetylation maps determine genome-wide functions for yeast histone deacetylases. Cell, 109: 437-446, 2002.
24. Lee, D. Y., Hayes, J. J., Pruss, D., and Wolffe, A. P. A positive role for histone acetylation in transcription factor access to nucleosomal DNA. Cell, 72: 73-84, 1993.
25. Belotserkovskaya, R., Sterner, D. E., Deng, M., Sayre, M. H., Lieberman, P. M., and Berger, S. L. Inhibition of TATA-binding protein function by SAGA subunits Spt3 and Spt8 at Gcn4-activated promoters. Mol. Cell. Biol., 20: 634-647, 2000.
26. Devary, Y., Gottlieb, R. A., Smeal, T., and Karin, M. The mammalian ultraviolet response is triggered by activation of Src tyrosine kinases. Cell, 71: 1081-1091, 1992.
27. Devary, Y., Rosette, C., DiDonato, J. A., and Karin, M. NF-kappa B activation by ultraviolet light not dependent on a nuclear signal. Science, 261: 1442-1445, 1993.
28. Sachsenmaier, C., Radler-Pohl, A., Zinck, R., Nordheim, A., Herrlich, P., and Rahmsdorf, H. J. Involvement of growth factor receptors in the mammalian UVC response. Cell, 78: 963-972, 1994.
29. Rosette, C. and Karin, M. Ultraviolet light and osmotic stress: activation of the JNK cascade through multiple growth factor and cytokine receptors. Science, 274: 1194-1197, 1996.
30. Sitcheran, R., Emter, R., Kralli, A., and Yamamoto, K. R. A genetic analysis of glucocorticoid receptor signaling. Identification and characterization of ligand-effect modulators in Saccharomyces cerevisiae. Genetics, 156: 963-972, 2000.
31. Ideker, T., Ozier, O., Schwikowski, B., Siegel, A. Discovering regulatory and signaling circuits in molecular interaction networks. Bioinformatics, 18: 233-240, 2002.
32. Kuge, S. and Jones, N. YAP I dependent activation of TRX2 is essential for the response of Saccharomyces cerevisiae to oxidative stress by hydroperoxides. EMBO J., 13: 655-664, 1994.
33. Sui, G., Soohoo, C., Affar el, B., Gay, F., Shi, Y., and Forrester, W. C. A DNA vector-based RNAi technology to suppress gene expression in mammalian cells. Proc. Natl. Acad. Sci. USA, 99: 5515-5520, 2002.
34. Brummelkamp, T. R., Bemards, R., and Agami, R. A system for stable expression of short interfering RNAs in mammalian cells. Science, 296: 550-553, 2002.
35. Costanzo, M. C., Crawford, M. E., Hirschman, J. E., Kranz, J. E., Olsen, P., Robertson, L. S., Skrzypek, M. S., Braun, B. R., Hopkins, K. L., Kondu, P., Lengieza, C., Lew-Smith, J. E., Tillberg, M., and Garrels, J. I. YPD, PombePD and WormPD: model organism volumes of the BioKnowledge library, an integrated resource for protein information. Nucleic Acids Res., 29: 75-79, 2001.
36. Cherry, J. M., SGD. "Saccharomyces Genome Database" (http://genome-www.stanford.edu/Saccharomyces/).