Saccharomyces cerevisiae
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ABSTRACT:
PROVIDER: PRJNA125097 | ENA |
REPOSITORIES: ENA
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Project description:Expression analysis of Saccharomyces cerevisiae TAF5 and taf5 temperature conditional mutants grown at permissive and non-permissive temperature. Investigation of whole genome gene expression level changes in Saccharomyces cerevisae taf5-17, taf5-45, taf5-408 and taf5-10.4 mutants, compared to the wild-type strain. The mutations engineered into the strains confer temperature conditional growth. The mutants analyzed in this study are further described in Layer et. al., 2010. Direct Transactivator-Transcription Factor IID (TFIID) Contacts Drive Yeast Ribosomal Protein Gene Transcription. Journal of Biological Chemistry.
2010-03-06 | GSE20444 | GEO
Project description:Expression analysis of Saccharomyces cerevisiae TAF5 and taf5 temperature conditional mutants grown at permissive and non-permissive temperature. Investigation of whole genome gene expression level changes in Saccharomyces cerevisae taf5-17, taf5-45, taf5-408 and taf5-10.4 mutants, compared to the wild-type strain. The mutations engineered into the strains confer temperature conditional growth. The mutants analyzed in this study are further described in Layer et. al., 2010. Direct Transactivator-Transcription Factor IID (TFIID) Contacts Drive Yeast Ribosomal Protein Gene Transcription. Journal of Biological Chemistry. A twenty chip study using total RNA recovered from four separate wild-type cultures of Saccharomyces cerevisiae and four separate cultures for each of four taf5 temperature conditional mutants (16 mutant cultures). Each chip measures the expression level of 5,777 genes from Saccharomyces S288C with eight 60-mer probe pairs (PM/MM) per gene, with three-fold technical redundancy.
2010-05-06 | E-GEOD-20444 | biostudies-arrayexpress
Project description:The formation of heterochromatin at HML, HMR, and telomeres in Saccharomyces cerevisiae involves two main steps: Recruitment of Sir proteins to silencers and their spread throughout the silenced domain. For the following datasets, we created a fusion protein between the heterochromatin protein Sir3 and the non-site-specific bacterial adenine methyltransferase M.EcoGII. We mapped sites of Sir3-chromatin interactions genome-wide using long-read Nanopore sequencing to detect adenines methylated by the fusion protein. We also used a temperature-sensitive allele of SIR3 (sir3-8) fused to M.ECOGII to induce m6A methylation over time. Time courses involved a switch from restrictive temperature (37°C) to permissive temperature (25°C).
2022-01-17 | GSE190136 | GEO
Project description:The target of rapamycin (TOR) plays a central role in eukaryotic cell growth control. With prevalent hyper-activation of the mTOR pathway in human cancers, novel strategies to enhance TOR pathway inhibition are highly desirable. We used a yeast-based high-throughput chemical genetic screen to identify small-molecule enhancers of rapamycin (SMERs) and used whole genome expression analysis to identify their mechanisms of action. We incubated Met30 temperature-sensitive yeast strain at either the permissive (room temperature) or non-permissive (35°C) temperature for 1 hour prior to RNA extraction and hybridization on Affymetrix microarrays. Comparison of expression profiles enabled identification of gene-signature characteristic of Met30 inhibition.
2011-06-30 | E-GEOD-22270 | biostudies-arrayexpress
Project description:Gentamicin is a highly efficacious antibiotic against gram-negative bacteria. However, its usefulness in treating infection is compromised by its poorly understood renal toxicity. This toxic effect is seen in a variety of organisms. While the yeast Saccharomyces cerevisiae is relatively insensitive to gentamicin, mutations in any one of 20 or so genes causes a dramatic increase in sensitivity. Many of these genes encode proteins important for translation termination or specific protein trafficking complexes. Here, we demonstrate by microarray analysis that gentamicin treatment leads to dramatic decreases in genes under the control of the MADS box protein Mcm1, including genes encoding products involved in mating, nitrogen utilization, and ribosome biogenesis. Furthermore, microarray analysis also demonstrates an increase in a Rlm1-dependent set of genes involved in maintaining the structure of the cell wall that are also induced by the antifungal agents caspofungin and calcofluor white. Subsequent inspection of the physical and genetic interactions of the remaining gentamicin sensitive mutants revealed a network centered around chitin synthase and the Arf Pathway. Furthermore, conditional arf1 mutants are hypersensitive to gentamicin even under permissive conditions. These results suggest that gentamicin may act as a cell wall stress, possibly by disrupting Arf-dependent trafficking of proteins involved in forming the cell wall. Keywords: disease state analysis, comparative genomic analysis +/- gentamicin treatment
2007-10-14 | GSE7188 | GEO
Project description:In the present study transcriptome and proteome of recombinant, xylose-utilising S. cerevisiae grown in aerobic batch cultures on xylose were compared with glucose-grown cells both in glucose repressed and derepressed states. The aim was to study at genome-wide level how signalling and carbon catabolite repression differed in cells grown on either glucose or xylose. The more detailed knowledge about is xylose sensed as a fermentable carbon source, capable of catabolite repression like glucose, or is it rather recognised as a non-fermentable carbon source is important in achieving understanding for further engineering this yeast for more efficient anaerobic fermentation of xylose.
2008-09-24 | GSE12890 | GEO
Project description:Investigation of Saccharomyces cerevisiae phosphate metabolism. Cells starved for phosphate, cells grown with intermediate and high phosphate concentrations, and PHO4 mutant cells examined. Keywords: other
2003-08-29 | GSE603 | GEO
Project description:CRAC of yeast RNA polymerase II in various thermosensitive strains at permissive and non-permissive temperature and anchor-away strains with the addition of rapamycin.
| PRJNA383311 | ENA
Project description:Cordycepin (3â deoxyadenosine) is a biologically active compound that, when incorporated during RNA synthesis in vitro, provokes chain termination due to the absence of a 3â hydroxyl moiety. We were interested in the effects mediated by this drug in vivo and analysed its impact on RNA metabolism of yeast. Our results support the view that cordycepin-triphosphate (CoTP) is the toxic component that is limiting cell growth through inhibition of RNA synthesis. Unexpectedly, cordycepin treatment modulated 3â end heterogeneity of ACT1 and ASC1 mRNAs and rapidly induced extended transcripts derived from CYH2 and NEL025c loci. Moreover, cordycepin ameliorated the growth defects of poly(A) polymerase mutants and the pap1-1 mutation neutralized the effects of the drug on gene expression. Our observations are consistent with an epistatic relationship between poly(A) polymerase function and cordycepin action and suggest that a major mode of cordycepin activity reduces 3â end formation efficiency independently of its potential to terminate RNA chain elongation. Finally, chemical-genetic profiling revealed genome-wide pathways linked to cordycepin activity and identified novel genes involved in poly(A) homeostasis. Keywords: response to drug treatment Each experiment was performed as triplicate. We analyzed RNA obtained from wild-type cells, from wild-type cells treated with 40 microgram/ml cordycepin for 1 hour, from pap1-1 mutant cells grown at permissive temperature (25°C) and from pap1-1 mutant cells grown at permissive temperature (25°C) treated with 40 microgram/ml cordycepin for 1 hour.
2010-05-06 | E-GEOD-14619 | biostudies-arrayexpress
Project description:To understand the gene expression in Saccharomyces cerevisiae under fermentative and respiraotry conditions, we perfomred the genome-wide gene expression profiling for the log-phase cells of S. cerevisiae wild type, sef1 deletion, and hyperactive SEF1-VP16 mutants under the YPD and YPGly conditions.
2024-03-25 | GSE262043 | GEO