The 'yeast cell wall chip' - a tool to analyse the regulation of cell wall biogenesis in Saccharomyces cerevisiae

• Published in: Microbiology (Society for General Microbiology) Vol. 151; no. 7; pp. 2241 - 2249
• Main Authors: Rodriguez-Pena, Jose M, Perez-Diaz, Rosa M, Alvarez, Sara, Bermejo, Clara, Garcia, Raul, Santiago, Catalina, Nombela, Cesar, Arroyo, Javier
• Format: Journal Article
• Language: English
• Published: Reading Soc General Microbiol 01.07.2005; Society for General Microbiology
• Subjects: Biological and medical sciences; Cell Wall - genetics; Cell Wall - metabolism; Fundamental and applied biological sciences. Psychology; Gene Expression Profiling; Gene Expression Regulation, Fungal; Genome, Fungal; Growth, nutrition, metabolism, transports, enzymes. Molecular biology; MAP Kinase Signaling System; Microbiology; Mitogen-Activated Protein Kinases - genetics; Mitogen-Activated Protein Kinases - metabolism; Mycology; Oligonucleotide Array Sequence Analysis - methods; Saccharomyces cerevisiae; Saccharomyces cerevisiae - genetics; Saccharomyces cerevisiae - growth & development; Saccharomyces cerevisiae - metabolism; Fungi; Regulation(control); Statistical analysis; Yeast; DNA chip; Ascomycetes; Biosynthesis; Gene expression; Saccharomyces cerevisiae; Cell wall; Thallophyta
• ISSN: 1350-0872; 1465-2080
• DOI: 10.1099/mic.0.27989-0

1 Departamento de Microbiología II, Facultad de Farmacia, Universidad Complutense de Madrid, 28040 Madrid, Spain 2 Unidad de Genómica, Parque Científico de Madrid/UCM, Campus de Moncloa, Facultad de Ciencias Biológicas, Universidad Complutense de Madrid, 28040 Madrid, Spain Correspondence Jose M. Rodríguez-Peña josemanu{at}farm.ucm.es Within the field of Saccharomyces cerevisiae 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 hog1 mutant and a wild-type strain in the presence of Congo red. Two genes, YFL014W ( HSP12 ) and YLR414C , 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. Abbreviations: CR, Congo red; MAPK, MAP kinase; Q-RT-PCR, quantitative RT-PCR; SD , standard deviation Present address: Departamento de Toxicología y Legislación Sanitaria, Facultad de Medicina, Universidad Complutense de Madrid, 28040 Madrid, Spain.