Transcription profiling of yeast recovery after hydrogen peroxide stress
Ontology highlight
ABSTRACT:
ORGANISM(S): Saccharomyces cerevisiae
SUBMITTER: Vitor Costa
PROVIDER: E-MEXP-326 | biostudies-arrayexpress |
REPOSITORIES: biostudies-arrayexpress
Publications
mRNA/microRNA gene expression profile in microsatellite unstable colorectal cancer.
Lanza Giovanni G Ferracin Manuela M Gafà Roberta R Veronese Angelo A Spizzo Riccardo R Pichiorri Flavia F Liu Chang-gong CG Calin George A GA Croce Carlo M CM Negrini Massimo M
Molecular cancer 20070823
<h4>Background</h4>Colorectal cancer develops through two main genetic instability pathways characterized by distinct pathologic features and clinical outcome.<h4>Results</h4>We investigated colon cancer samples (23 characterized by microsatellite stability, MSS, and 16 by high microsatellite instability, MSI-H) for genome-wide expression of microRNA (miRNA) and mRNA. Based on combined miRNA and mRNA gene expression, a molecular signature consisting of twenty seven differentially expressed genes ...[more]
Similar Datasets
Project description:The Ubiquitin-Proteasome System (UPS) regulates many cellular processes in eukaryotic cells. Ubiquitylation by the UPS mainly directs proteins to proteasomal degradation, but it can also have non-degradative functions, such as regulating protein activity or localization. The small protein ubiquitin is conjugated to its substrates via a cascade of E1-E2-E3 enzymes. Dysregulation of the UPS has been implicated in the genesis and progression of many diseases, such as neurodegenerative diseases and cancer; thus, the UPS components are attractive targets for developing pharmaceutical drugs. E2s, or ubiquitin conjugating enzymes, are central players of the UPS. E2s function in tandem with specific ubiquitin ligases (E3s) to transfer ubiquitin to substrates. Here, we present the first proteome stability analysis of two closely related ubiquitin conjugating enzymes, UBC4 and UBC5, in S. cerevisiae. These two E2s are nearly identical, having 92% sequence identity and differing by only 11 amino acid residues. This dataset is of broad interest because higher eukaryotes express ubiquitin conjugating enzymes that are analogous to the yeast UBC4/5.
2022-09-02 | PXD035897 | Pride
Project description:BY4741 (S288c haploid) cells have different gene expression in response to 0.4mM H2O2 when pretreated with 0.7M NaCl compared to cells that are not pretreated with NaCl (mock cells). BY4741 cells were grown in log phase for 3 doublings (t0) and then the genomic expression of mock cells to 0.4mM H2O2 was assessed every 10 mins for 40 mins. To study the effects of NaCl treatement on H2O2 response, BY4741 cells were grown in log phase for 3 doublings (t0) and then the genomic expression of cells was measured in response to 0.7M NaCl over the course of 60 min every 15 mins. The cells were then removed from stress and grown in stress free media for four hours (T240). Then these cells were exposed to 0.4mM H2O2 and the genomic expression was measured every 10 minutes during the H2O2 timecourse of 40 minutes. To see if the handling of cells had an affect on gene expression, BY4741 cells were grown for exponentially for 3 doublings (t0), received a mock YPD treatment for 60 mins, grown for 4 hours (T240) and then collected to asses genomic expression. Duplicates were done for at 30 and 45 minutes for the NaCl timecourse, triplicate were done for 0, 10 and 20 minutes in H2O2 timecourse and duplicates were done for 30 and 40 minutes in the H2O2 timecourse.
2011-09-17 | E-GEOD-32196 | biostudies-arrayexpress
Project description:Adaptation to altered osmotic conditions is a fundamental property of living cells and has been studied in particular detail in the yeast Saccharomyces cerevisiae. Yeast cells accumulate glycerol as compatible solute, controlled at different levels by the High Osmolarity Glycerol (HOG) response pathway. Up to now, essentially all osmostress studies in yeast have been performed with glucose as carbon and energy source, which is metabolised by glycolysis with glycerol is as a normal by-product. Here we investigated the response of yeast to osmotic stress when yeast is respiring ethanol as carbon and energy source. Remarkably, yeast cells do not accumulate glycerol under these conditions and it appears that trehalose may partly take over the role as compatible solute. The HOG pathway is activated in very much the same way as in during growth on glucose medium and is also required for osmotic adaptation. Slower volume recovery was observed in ethanol-grown cells as compared to glucose-grown cells. Dependence on key regulators as well as the global gene expression profile were similar in many ways to those previously observed in glucose-grown cells. However, there are indications that cells re-arrange redox-metabolism when respiration is hampered under osmostress, a feature that could not be observed in glucose-grown cells.
2017-02-27 | E-MTAB-5313 | biostudies-arrayexpress
Project description:Cell division is a highly regulated process that secures the generation of healthy progeny in all organisms, from yeast to human. Dysregulation of this process can lead to uncontrolled cell proliferation and genomic instability, both which are hallmarks of cancer. Cell cycle progression is dictated by a complex network of kinases and phosphatases. These enzymes act on their substrates in a highly specific temporal manner ensuring that the process of cell division is unidirectional and irreversible. Key events of the cell cycle, such as duplication of genetic material and its redistribution to daughter cells, occur in S-phase and mitosis, respectively. Deciphering the dynamics of phosphorylation/dephosphorylation events during these cell cycle phases is important. Here we showcase a quantitative proteomic and phosphoproteomic mass spectrometry dataset that profiles both early and late phosphorylation events and associated proteome alterations that occur during S-phase and mitotic arrest in the model organism S. cerevisiae. This dataset is of broad interest as the molecular mechanisms governing cell cycle progression are conserved throughout evolution.
2022-09-02 | PXD035896 | Pride
Project description:Ubiquitination is a post-translational modification that signals multiple processes, including protein degradation, trafficking and DNA repair. Polyubiquitin accumulates globally during the oxidative stress response, and this has been mainly attributed to increased ubiquitin conjugation and perturbations in protein degradation. Here we show that the unconventional Lys 63 (K63)-linked polyubiquitin accumulates in the yeast Saccharomyces cerevisiae in a highly sensitive and regulated manner as a result of exposure to peroxides. We demonstrate that hydrogen peroxide inhibits the deubiquitinating enzyme Ubp2, leading to accumulation of K63 conjugates assembled by the Rad6 ubiquitin conjugase and the Bre1 ubiquitin ligase. Using linkage-specific isolation methods and stable isotope labeling by amino acids in cell culture (SILAC)–based quantitative proteomics, we identified >100 new K63-polyubiquitinated targets, which were substantially enriched in ribosomal proteins. Finally, we demonstrate that impairment of K63 ubiquitination during oxidative stress affects polysome stability and protein expression, rendering cells more sensitive to stress, and thereby reveal a new redox-regulatory role for this modification.
2015-01-26 | PXD000979 | Pride
Project description:The initial translational response of the yeast Saccharomyces cerevisiae in response to acetic acid-induced apoptosis was investigated by microarray profiling of mRNAs contained in polysomal fractions obtained upon 0 (used as control), 15 and 30 minutes of acetic acid treatment. The mRNA fraction thus investigated corresponds to the mRNAs capable of overcoming the inhibition of cap-mediated translation initiation.
2013-02-24 | E-MEXP-3570 | biostudies-arrayexpress
Project description:A universal feature of the response to stress and nutrient limitation is transcriptional upregulation of genes encoding proteins important for survival. Interestingly, under many of these conditions overall protein synthesis levels are reduced, thereby dampening the stress response at the level of protein expression. For example, during glucose starvation in yeast, translation is rapidly and reversibly repressed, yet transcription of many stress- and glucose-repressed genes is increased. Using ribosome profiling and microscopy, we found that this transcriptionally upregulated gene set consists of two classes: (1) one producing mRNAs that are preferentially translated during glucose limitation and are diffusely localized in the cytoplasm – this class includes many heat shock protein mRNAs; and (2) another producing mRNAs that are poorly translated during glucose limitation, have high rates of translation initiation, and are concentrated in foci that co-localize with P bodies and stress granules – this class is enriched for glucose metabolism mRNAs. Remarkably, the information specifying differential localization and translation of these two classes of mRNAs is encoded in the promoter sequence – promoter responsiveness to heat shock factor (Hsf1) specifies diffuse cytoplasmic localization and preferential translation upon glucose starvation, whereas different promoter elements upstream of genes encoding poorly translated glucose metabolism mRNAs direct these mRNAs to RNA granules under glucose starvation. Thus, promoter sequences and transcription factor binding can influence not only mRNA levels, but also subcellular localization of mRNAs and the efficiency with which they are translated, enabling cells to tailor protein production to environmental conditions. Examination of mRNA translation in S. cerevisiae upon glucose starvation.
2014-07-28 | E-GEOD-56622 | biostudies-arrayexpress
Project description:We examined whether the budding yeast Saccharomyces cerevisiae can sense chemical signals from prokaryotes, specifically a variety of quorum sensing molecules from different bacteria species and from Candida albicans. We found that only N-acyl-3-oxo-dodecanoyl homoserine lactone (C12) from the opportunistic human pathogen Pseudomonas aeruginosa induces a stress response in yeast. Microarray experiments were performed in order to continue investigating the stress response. We treated S. cerevesiae (WT strain W303) with N-(3-oxo-dodecanoyl) homoserine lactone (C12), a quorum sensing molecule of Pseudomonas aeruginosa, which we found causes a stress response using a GFP reporter for HSP-12. Treatment conditions: 100 uM C12, 100 uM C12-lactam (control: synthetic analogue of C12 that is inactive in P. aeruginosa), DMSO (control: solvent), and 0.3 mM H2O2 (for comparison to oxidative stress).
2020-03-02 | E-MTAB-4802 | biostudies-arrayexpress
Project description:Changes in the transcriptome of Isc1p deficient mutants. The inositolphosphosphingolipid phospholipase C (Isc1p) of Saccharomyces cerevisiae belongs to the family of neutral sphingomyelinases that generates the bioactive sphingolipid ceramide. In this work the role of Isc1p in oxidative stress resistance and chronological lifespan was investigated. Loss of Isc1p resulted in a higher sensitivity to hydrogen peroxide that was associated with an increase in oxidative stress markers, namely intracellular oxidation, protein carbonylation and lipid peroxidation. Microarray analysis showed that Isc1p deficiency upregulated the iron regulon leading to increased levels of iron, which is known to catalyze the production of the highly reactive hydroxyl radicals via the Fenton reaction. In agreement, iron chelation suppressed hydrogen peroxide sensitivity of isc1D mutants. Cells lacking Isc1p also displayed a shortened chronological lifespan associated with oxidative stress markers and ageing of parental cells was correlated with a decrease in Isc1p activity. The analysis of DNA fragmentation and caspase activity showed that Isc1p deficiency increased apoptotic programmed cell death associated with oxidative stress and ageing. Furthermore, deletion of Yca1p metacaspase suppressed the oxidative stress sensitivity and premature ageing phenotypes of isc1D mutants. These results indicate that Isc1p plays an important role in the regulation of cellular redox homeostasis, through modulation of iron levels, and of apoptosis.
2008-02-05 | E-MEXP-1136 | biostudies-arrayexpress
Project description:Microarray measurements are susceptible to error caused by cross-hybridization and bulk hybridization. To characterize the effect of these off-target interactions, we analyzed samples made from baseline (S. cerevisiae) alone or mixed with a high-concentration 1kb spike. The spike is a 1 kb sequence amplified from the Schizosaccharomyces pombe gene SPAC27D7.10c, with an added oligo(dT)-T7 promoter. The baseline and spike samples were mixed at the double-stranded cDNA stage. Three arrays: 100% baseline, 99% baseline + 1% spike, 90% baseline + 10% spike. There are no replicates.
2010-03-21 | E-GEOD-16980 | biostudies-arrayexpress