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Originally published In Press as doi:10.1074/jbc.M211604200 on March 18, 2003
J. Biol. Chem., Vol. 278, Issue 22, 20345-20357, May 30, 2003
Genome-wide Analysis of the Response to Cell Wall Mutations in the Yeast Saccharomyces cerevisiae*
Arnaud Lagorce ,
Nicole C. Hauser ¶,
Delphine Labourdette ||,
Cristina Rodriguez **,
Helene Martin-Yken ,
Javier Arroyo **,
Jörg D. Hoheisel ¶ and
Jean François || 
From the
Centre de Bioingenierie Gilbert Durand, UMR-CNRS 5504 and INRA 792, France, ||Transcriptome-Biochips plateform, Genopole de Toulouse, 135 Avenue de Rangeuil, 31077 Toulouse, France, the ¶Division of Functional Genome Analysis, Deutsches Krebsforschungszentrum, Im Neuenheimer Feld 506, 69120 Heidelberg, Germany, and the **Departamento de Microbiología II, Facultad de Farmacia, Universidad Complutense de Madrid, 28040 Madrid, Spain
Perturbations of the yeast cell wall trigger a repair mechanism that reconfigures its molecular structure to preserve cell integrity. To investigate this mechanism, we compared the global gene expression in five mutant strains, each bearing a mutation (i.e. fks1, kre6, mnn9, gas1, and knr4 mutants) that affects in a different manner the cell wall construction. Altogether, 300 responsive genes were kept based on high stringency criteria during data processing. Functional classification of these differentially expressed genes showed a substantial subset of induced genes involved in cell wall construction and an enrichment of metabolic, energy generation, and cell defense categories, whereas families of genes belonging to transcription, protein synthesis, and cellular growth were underrepresented. Clustering methods isolated a single group of 80 up-regulated genes that could be considered as the stereotypical transcriptional response of the cell wall compensatory mechanism. The in silico analysis of the DNA upstream region of these co-regulated genes revealed pairwise combinations of DNA-binding sites for transcriptional factors implicated in stress and heat shock responses (Msn2/4p and Hsf1p) with Rlm1p and Swi4p, two PKC1-regulated transcription factors involved in the activation genes related to cell wall biogenesis and G1/S transition. Moreover, this computational analysis also uncovered the 6-bp 5'-AGCCTC-3' CDRE (calcineurin-dependent response element) motif in 40% of the co-regulated genes. This motif was recently shown to be the DNA binding site for Crz1p, the major effector of calcineurin-regulated gene expression in yeast. Taken altogether, the data presented here lead to the conclusion that the cell wall compensatory mechanism, as triggered by cell wall mutations, integrates three major regulatory systems: namely the PKC1-SLT2 mitogen-activated protein kinase-signaling module, the "global stress" response mediated by Msn2/4p, and the Ca2+/calcineurin-dependent pathway. The relative importance of these regulatory systems in the cell wall compensatory mechanism is discussed.
Received for publication, November 14, 2002
, and in revised form, January 30, 2003.
* This work was supported in part by European Union Grant QLK3-2000-01537 (to J. F., J. A., and J. H.) and by Fonds de Recherche Hoechst Marion Roussel Grant FRHMR 2/9922 (to J. F.). The costs of publication of this article were defrayed in part by the payment of page charges. This article must therefore be hereby marked "advertisement" in accordance with 18 U.S.C. Section 1734 solely to indicate this fact.
Recipient of a predoctoral fellowship from the French Ministry of Research and Technology Education.
 To whom correspondence should be addressed. Tel.: 33-5-61-55-9492; Fax: 33-5-61-55-9400; E-mail: fran_jm{at}insa-tlse.fr.

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M. Parveen, Md. K. Hasan, J. Takahashi, Y. Murata, E. Kitagawa, O. Kodama, and H. Iwahashi
Response of Saccharomyces cerevisiae to a monoterpene: evaluation of antifungal potential by DNA microarray analysis
J. Antimicrob. Chemother.,
July 1, 2004;
54(1):
46 - 55.
[Abstract]
[Full Text]
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G. Lesage, A.-M. Sdicu, P. Menard, J. Shapiro, S. Hussein, and H. Bussey
Analysis of {beta}-1,3-Glucan Assembly in Saccharomyces cerevisiae Using a Synthetic Interaction Network and Altered Sensitivity to Caspofungin
Genetics,
May 1, 2004;
167(1):
35 - 49.
[Abstract]
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R. Garcia, C. Bermejo, C. Grau, R. Perez, J. M. Rodriguez-Pena, J. Francois, C. Nombela, and J. Arroyo
The Global Transcriptional Response to Transient Cell Wall Damage in Saccharomyces cerevisiae and Its Regulation by the Cell Integrity Signaling Pathway
J. Biol. Chem.,
April 9, 2004;
279(15):
15183 - 15195.
[Abstract]
[Full Text]
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G. Belli, M. M. Molina, J. Garcia-Martinez, J. E. Perez-Ortin, and E. Herrero
Saccharomyces cerevisiae Glutaredoxin 5-deficient Cells Subjected to Continuous Oxidizing Conditions Are Affected in the Expression of Specific Sets of Genes
J. Biol. Chem.,
March 26, 2004;
279(13):
12386 - 12395.
[Abstract]
[Full Text]
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M. Lommel, M. Bagnat, and S. Strahl
Aberrant Processing of the WSC Family and Mid2p Cell Surface Sensors Results in Cell Death of Saccharomyces cerevisiae O-Mannosylation Mutants
Mol. Cell. Biol.,
January 1, 2004;
24(1):
46 - 57.
[Abstract]
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C. Reinoso-Martin, C. Schuller, M. Schuetzer-Muehlbauer, and K. Kuchler
The Yeast Protein Kinase C Cell Integrity Pathway Mediates Tolerance to the Antifungal Drug Caspofungin through Activation of Slt2p Mitogen-Activated Protein Kinase Signaling
Eukaryot. Cell,
December 1, 2003;
2(6):
1200 - 1210.
[Abstract]
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Copyright © 2003 by the American Society for Biochemistry and Molecular Biology.
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