Genome-wide analysis of the response to cell wall mutations in the yeast Saccharomyces cerevisiae

Arnaud Lagorce (1) , Nicole C. Hauser (2) , Delphine Labourdette (1, 3) , Cristina Rodríguez (4) , Hélène Martin-Yken (1) , Javier Arroyo (4) , Jörge D. Hobeisel (2) , Jean François (1, 3)

1 Unité mixte de recherche biotechnologies bioprocédés
2 DKFZ - German Cancer Research Center - Deutsches Krebsforschungszentrum [Heidelberg]
3 Géno Toul - Génopole de Toulouse Midi-Pyrénées
4 UCM - Universidad Complutense de Madrid = Complutense University of Madrid [Madrid]

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.

Mots clés: STRUCTURE

Domaines: Biochimie [q-bio.BM]

Arnaud Lagorce, Nicole C. Hauser, Delphine Labourdette, Cristina Rodríguez, Hélène Martin-Yken, et al.. Genome-wide analysis of the response to cell wall mutations in the yeast Saccharomyces cerevisiae. Journal of Biological Chemistry, 2003, 278 (22), pp.20345-20357. ⟨10.1074/jbc.M211604200⟩. ⟨hal-02681963⟩