Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Transcriptional profiling of yeast cells lacking either the protein phosphatase Ptc6 or Ptc1 and Ptc6, members of the 2C family of protein phosphatases in Saccharomyces cerevisiae.

ABSTRACT: Type 2C protein phosphatases are encoded in Saccharomyces cerevisiae by several related genes (PTC1-7). To gain insight into the functions attributable to a specific member of this gene family, we have investigated the transcriptional profile of ptc6 mutants under standard growth conditions. We have found that lack of Ptc6 did not alter the transcriptional profile when cells were in log phase in YPD medium. Only one gene, involved in iron transport (FIT3), in addition to PTC6 itself, was considered down-regulated. We also identified the transcriptional changes induced by the simultaneous lack of Ptc1 and Ptc6 proteins.

ORGANISM(S): Saccharomyces cerevisiae

PROVIDER: GSE38244 | GEO | 2013/04/19

SECONDARY ACCESSION(S): PRJNA167587

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Similar Datasets

Transcriptional profiling of yeast cells lacking either the protein phosphatase Ptc6 or Ptc1 and Ptc6, members of the 2C family of protein phosphatases in Saccharomyces cerevisiae.

Project description:Type 2C protein phosphatases are encoded in Saccharomyces cerevisiae by several related genes (PTC1-7). To gain insight into the functions attributable to a specific member of this gene family, we have investigated the transcriptional profile of ptc6 mutants under standard growth conditions. We have found that lack of Ptc6 did not alter the transcriptional profile when cells were in log phase in YPD medium. Only one gene, involved in iron transport (FIT3), in addition to PTC6 itself, was considered down-regulated. We also identified the transcriptional changes induced by the simultaneous lack of Ptc1 and Ptc6 proteins. * In a first set of experiments we compared the expression profile of ptc6 mutant cells with that of wt cells. We performed 2 biological replicates, and for each experiment we performed two chips (dye swap). Overall we analyzed 4 chips: Biological replicate 1: GSM937247, GSM937248 Biological replicate 2: GSM937251, GSM937252 * In the second set of data we compared the expression profile of ptc1ptc6 double mutant cells with that of wt cells. We performed 2 biological replicates, and for each experiment we performed two chips (dye swap). Overall we analyzed 4 chips: Biological replicate 1: GSM937312, GSM937316 Biological replicate 2: GSM937319, GSM937320

2013-04-19 | E-GEOD-38244 | biostudies-arrayexpress

Transcriptional profiling of the protein phosphatase 2C family in yeast

Project description:Type 2C protein phosphatases are encoded in Saccharomyces cerevisiae by several related genes (PTC1-5 and PTC7). To gain insight into the functions attributable to specific members of this gene family, we have investigated the transcriptional profiles of ptc1-5 mutants. Two main patterns were obtained as follows: the one generated by the ptc1 mutation and the one resulting from the lack of Ptc2-5. ptc4 and ptc5 profiles were quite similar, whereas that of ptc2 was less related to this group. Mutation of PTC1 resulted in increased expression of numerous genes that are also induced by cell wall damage, such as YKL161c, SED1, or CRH1, as well as in higher amounts of active Slt2 mitogen-activated protein kinase, indicating that lack of the phosphatase activates the cell wall integrity pathway. ptc1 cells were even more sensitive than slt2 mutants to a number of cell wall-damaging agents, and both mutations had additive effects. The sensitivity of ptc1 cells was not dependent on Hog1. Besides these phenotypes, we observed that calcineurin was hyperactivated in ptc1 cells, which were also highly sensitive to calcium ions, heavy metals, and alkaline pH, and exhibited a random haploid budding pattern. Remarkably, many of these traits are found in certain mutants with impaired vacuolar function. As ptc1 cells also display fragmented vacuoles, we hypothesized that lack of Ptc1 would primarily cause vacuolar malfunction, from which other phenotypes would derive. In agreement with this scenario, overexpression of VPS73, a gene of unknown function involved in vacuolar protein sorting, largely rescues not only vacuolar fragmentation but also sensitivity to cell wall damage, high calcium, alkaline pH, as well as other ptc1-specific phenotypes. Keywords: yeast, type 2C protein phosphatases, mutant strains, transcriptional profiles

2007-01-24 | GSE6801 | GEO

Transcriptional profiling of Rapamycin treatment in yeast cells lacking the Ptc1 protein phosphatase.

Project description:We are interested in the study of the already reported sensitivity of yeast cells lacking the type 1 protein phosphatase Ptc1 to the drug rapamycin. In order to carry out our studies, we analyzed the changes in the transcription profile that a short-term incubation with rapamycin (200 ng/mL) has in both, wild type and ptc1 cells. It has been shown that inhibition of the TOR pathway by treatment with rapamycin has profound effects on the global transcriptional profile. We confirmed the previously described transcription changes induced by the drug in wild type cells. Under our working conditions rapamycin increased, in wild type cells, at least 2-fold the expression of 667 genes, whereas it decreased the mRNA level of 721 genes (13.8% and 14.9% of genes with measurable expression level, respectively). Gene ontology analysis shows that, as previously documented, many induced genes falls into the NCR, Msn2/Msn4 regulated stress response or Retrograde response categories, whereas genes encoding cytoplasmic, but not mitochondrial, ribosomal proteins and the so called RIBI regulon where largely repressed. Deletion of PTC1 decreases the number of genes induced or repressed at least 2-fold by rapamycin treatment. Remarkably, lack of Ptc1 seems to lead to a general attenuation of changes triggered by rapamycin.

2008-12-31 | GSE11530 | GEO

Transcriptional profiling of Rapamycin treatment in yeast cells lacking the Ptc1 protein phosphatase.

2008-12-31 | E-GEOD-11530 | biostudies-arrayexpress

PTC1 mutant Yeast Genomic Expression Patterns in Response to deoxynivalenol

Project description:The evaluation of the toxicity of deoxynivalenol using yeast gene expressions. Yeast PTC1 mutant strain was used for this study. SDS was used to raise the penetration of the yeast cell membrane. Keywords: stress response Two conditions were compared by the gene expression profiles. Both samples were grown in 0.01% SDS contained YPD media, and one of them was also supplied with 50 ppm of deoxynivalenol.

2011-07-21 | E-GEOD-20378 | biostudies-arrayexpress

Yeast Genomic Expression Patterns of Wild-type and PTC1 null mutant in Response to Aflatoxin B1 (AFB1)

Project description:The evaluation of the toxicity of Aflatoxin B1 using yeast gene expressions. Two yeast strains; parental BY4743 and PTC1 mutant, were used for this study. SDS was used to raise the penetration of the yeast cell membrane. Two conditions are compared with three replicates each. Both strains were grown in 0.01% SDS containing YPD media or 0.01% SDS, 25 ppm ABF1 containing YPD media. Publication can be found at http://www.cbi.or.jp/cbi/CBIj/vol9/9_94-E.pdf.

2010-04-12 | E-GEOD-17367 | biostudies-arrayexpress

miRNA profile induced by RET/PTC1 oncogene in human thyrocytes

Project description:To obtain a PTC cell model, primary human thyrocytes have been infected with a retrovirus expressing RET/PTC1 oncogene, using parental thyrocytes as control. The obtained RET/PTC-dependent differential miRNA expression profile, representing the effects of RET/PTC1 oncogene present in about one third of papillary thyroid carcinoma (PTC), models the early event of thyrocytes transformation ending to PTC.

2014-06-30 | GSE49400 | GEO

Arabidopsis PP6 phosphatases dephosphorylate PIF proteins to repress photomorphogenesis.

Project description:Light-induced phosphorylation is necessary and essential for the degradation of phytochrome-interacting factors (PIFs), the central repressors of photomorphogenesis. Although the kinases responsible for PIF phosphorylation have been extensively studied, the phosphatases underlying PIF dephosphorylation are largely unknown. Here, we real that mutation of FyPP1 and FyPP3, two catalytic subunits of PP6 phosphatases, promoted photomorphogenesis of seedlings in the dark. PP6 and PIFs functioned synergistically to repress photomorphogenesis. FyPP1 and FyPP3 directly interacted with and dephosphorylated PIF3 and PIF4. The light-induced degradation of PIF4 and the PIF transcriptional activities were dependent on PP6 activity. These data demonstrate that PP6 phosphatases repress photomorphogenesis through regulation of PIF phosphorylation, protein stability and transcriptional activity.

2019-09-04 | GSE128498 | GEO

miRNA profile induced by RET/PTC1 oncogene in human thyrocytes

2014-06-30 | E-GEOD-49400 | biostudies-arrayexpress