Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

Transcription profiling of wild type and rpd3- yeast cells in response to osmotic stress

ABSTRACT: Comparison of wild type and rpd3- S. cerevisiae cells in response to osmotic stress. Wild type (MATalpha ura3 leu2 his3) and rpd3- (MATalpha ura3 leu2 his3 rpd3::KANMX) were grown to OD660=1 in YPD media and then subjected or not to a brief osmotic stress (5 or 20 min / 0.4 M NaCl). Cells were collected by centrifugation and total RNA was extracted as described.

ORGANISM(S): Saccharomyces cerevisiae

SUBMITTER: Glòria Mas

PROVIDER: E-MEXP-48 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Publications

The MAPK Hog1 recruits Rpd3 histone deacetylase to activate osmoresponsive genes.

De Nadal Eulàlia E Zapater Meritxell M Alepuz Paula M PM Sumoy Lauro L Mas Glòria G Posas Francesc F

Nature 20040101 6972

Regulation of gene expression by mitogen-activated protein kinases (MAPKs) is essential for proper cell adaptation to extracellular stimuli. Exposure of yeast cells to high osmolarity results in rapid activation of the MAPK Hog1, which coordinates the transcriptional programme required for cell survival on osmostress. The mechanisms by which Hog1 and MAPKs in general regulate gene expression are not completely understood, although Hog1 can modify some transcription factors. Here we propose that ...[more]

PMID: 14737171

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Project description:Despite various efforts to develop tools to detect and compare the activity and catabolic potential and activity for pollutant degradation of microorganisms in environmental samples, an open-source, curated and reliable method is still required. Here we report on a customize normalization system that can be applied to any microarray design, allowing the assessment of reliability of signals and enabling cross-experiment comparisons. Probes for the underlying catabolic gene array were designed based on manually curated databases for catabolic key genes. Signals were assigned to the respective catabolic protein subfamily that allows to inferring the functions and substrate specificity. The placement of probes for critical degradation nodes and subsequent metabolic steps allows the retrieval of information on the metabolic net. Information on gene localization from genome surveys was correlated to signals of putative hosts to generate phylogenetic community information. Hence, this novel array system was validated using genomic DNA of genome sequenced bacterial strains hosting biodegradation functions and applied to genomic DNA and RNA extracted from environmental samples under aromatic pollution pressure. Catabolic microarray was optimized for detection and expression of catabolic genes involved in the degradation of pollutant compounds using genome genomic DNA of type strains: Burkholderia xenovorans LB400, Cupriavidus necator JMP134, Pseudomonas putida F1 and Sphingomonas wittichii RW1. Afterwards, this microarray was applied for environmental samples. For microcosm experiments, 200 ml of each groundwater were incubated in closed 1 l Erlenmeyer flasks at 20 degree C and 50 rpm. Second sets of 200 ml microcosms were supplemented with naphthalene (100 mg), which had above been identified as a contaminant present in both groundwaters in similar amounts. Naphthalene was supplied via the vapor phase and incubated under identical conditions as the control microcosms. After 4 days of incubations, 50 ml of each of the 4 microcosms were subjected to genomic DNA extraction and another 50 ml to RNA extraction.

Dataset Information

Transcription profiling of wild type and rpd3- yeast cells in response to osmotic stress

Publications

The MAPK Hog1 recruits Rpd3 histone deacetylase to activate osmoresponsive genes.

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