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Vol. 11, Issue 12, 4241-4257, December 2000
¶
and
*Departments of Biochemistry and
We explored genomic expression patterns in the yeast
Saccharomyces cerevisiae responding to diverse
environmental transitions. DNA microarrays were used to measure changes
in transcript levels over time for almost every yeast gene, as cells
responded to temperature shocks, hydrogen peroxide, the
superoxide-generating drug menadione, the sulfhydryl-oxidizing agent
diamide, the disulfide-reducing agent dithiothreitol, hyper- and
hypo-osmotic shock, amino acid starvation, nitrogen source depletion,
and progression into stationary phase. A large set of genes (~ 900)
showed a similar drastic response to almost all of these environmental
changes. Additional features of the genomic responses were specialized
for specific conditions. Promoter analysis and subsequent
characterization of the responses of mutant strains implicated the
transcription factors Yap1p, as well as Msn2p and Msn4p, in mediating
specific features of the transcriptional response, while the
identification of novel sequence elements provided clues to novel
regulators. Physiological themes in the genomic responses to specific
environmental stresses provided insights into the effects of those
stresses on the cell.
Genetics, Stanford University School of Medicine,
Stanford, CA 94305-5428; Cell Biology and Metabolism
Branch, National Institute of Child Health and Human Development,
National Institutes of Health, Bethesda, MD 20892-5430;
§Lawrence Berkeley National Labs and Department of
Molecular and Cellular Biology, University of California Berkeley,
Berkeley, CA 94720; and Howard Hughes Medical Institute,
Stanford, CA
Online version of this article contains data set
material, and is available at www.molbiolcell.org.
¶
Current address: Lawrence Berkeley National
Labs, Berkeley, CA 94720. current address: Department
of Chemical Engineering, Stanford University, Stanford, CA 94305-5428.
Corresponding author. E-mail address:
pbrown{at}cmgm.stanford.edu.
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K. Singh, P. J. Kang, and H.-O. Park The Rho5 GTPase is necessary for oxidant-induced cell death in budding yeast PNAS, February 5, 2008; 105(5): 1522 - 1527. [Abstract] [Full Text] [PDF]
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R. Kafri, O. Dahan, J. Levy, and Y. Pilpel Preferential protection of protein interaction network hubs in yeast: Evolved functionality of genetic redundancy PNAS, January 29, 2008; 105(4): 1243 - 1248. [Abstract] [Full Text] [PDF]
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S. G. Hershman, Q. Chen, J. Y. Lee, M. L. Kozak, P. Yue, L.-S. Wang, and F. B. Johnson Genomic distribution and functional analyses of potential G-quadruplex-forming sequences in Saccharomyces cerevisiae Nucleic Acids Res., January 17, 2008; 36(1): 144 - 156. [Abstract] [Full Text] [PDF]
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A. Joshi, Y. Van de Peer, and T. Michoel Analysis of a Gibbs sampler method for model-based clustering of gene expression data Bioinformatics, January 15, 2008; 24(2): 176 - 183. [Abstract] [Full Text] [PDF]
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I. Takigawa and H. Mamitsuka Probabilistic path ranking based on adjacent pairwise coexpression for metabolic transcripts analysis Bioinformatics, January 15, 2008; 24(2): 250 - 257. [Abstract] [Full Text] [PDF]
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 G. Yiu, A. McCord, A. Wise, R. Jindal, J. Hardee, A. Kuo, M. Y. Shimogawa, L. Cahoon, M. Wu, J. Kloke, et al. Pathways Change in Expression During Replicative Aging in Saccharomyces cerevisiae J. Gerontol. A Biol. Sci. Med. Sci., January 1, 2008; 63(1): 21 - 34. [Abstract] [Full Text] [PDF]
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M. J. Brauer, C. Huttenhower, E. M. Airoldi, R. Rosenstein, J. C. Matese, D. Gresham, V. M. Boer, O. G. Troyanskaya, and D. Botstein Coordination of Growth Rate, Cell Cycle, Stress Response, and Metabolic Activity in Yeast Mol. Biol. Cell, January 1, 2008; 19(1): 352 - 367. [Abstract] [Full Text] [PDF]
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D. Chen, C. R.M. Wilkinson, S. Watt, C. J. Penkett, W. M. Toone, N. Jones, and J. Bahler Multiple Pathways Differentially Regulate Global Oxidative Stress Responses in Fission Yeast Mol. Biol. Cell, January 1, 2008; 19(1): 308 - 317. [Abstract] [Full Text] [PDF]
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Y.-Q. Zhang and R. Rao Global Disruption of Cell Cycle Progression and Nutrient Response by the Antifungal Agent Amiodarone J. Biol. Chem., December 28, 2007; 282(52): 37844 - 37853. [Abstract] [Full Text] [PDF]
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C. Bausch, S. Noone, J. M. Henry, K. Gaudenz, B. Sanderson, C. Seidel, and J. L. Gerton Transcription Alters Chromosomal Locations of Cohesin in Saccharomyces cerevisiae Mol. Cell. Biol., December 15, 2007; 27(24): 8522 - 8532. [Abstract] [Full Text] [PDF]
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O. Odat, S. Matta, H. Khalil, S. C. Kampranis, R. Pfau, P. N. Tsichlis, and A. M. Makris Old Yellow Enzymes, Highly Homologous FMN Oxidoreductases with Modulating Roles in Oxidative Stress and Programmed Cell Death in Yeast J. Biol. Chem., December 7, 2007; 282(49): 36010 - 36023. [Abstract] [Full Text] [PDF]
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W. C. Burhans and M. Weinberger DNA replication stress, genome instability and aging Nucleic Acids Res., December 3, 2007; 35(22): 7545 - 7556. [Abstract] [Full Text] [PDF]
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R. De Nicola, L. A. Hazelwood, E. A. F. De Hulster, M. C. Walsh, T. A. Knijnenburg, M. J. T. Reinders, G. M. Walker, J. T. Pronk, J.-M. Daran, and P. Daran-Lapujade Physiological and Transcriptional Responses of Saccharomyces cerevisiae to Zinc Limitation in Chemostat Cultures Appl. Envir. Microbiol., December 1, 2007; 73(23): 7680 - 7692. [Abstract] [Full Text] [PDF]
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F. Lessing, O. Kniemeyer, I. Wozniok, J. Loeffler, O. Kurzai, A. Haertl, and A. A. Brakhage The Aspergillus fumigatus Transcriptional Regulator AfYap1 Represents the Major Regulator for Defense against Reactive Oxygen Intermediates but Is Dispensable for Pathogenicity in an Intranasal Mouse Infection Model Eukaryot. Cell, December 1, 2007; 6(12): 2290 - 2302. [Abstract] [Full Text] [PDF]
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