Increased level of glutathione contributes to stress tolerances and global translational changes in Arabidopsis
Ontology highlight
ABSTRACT:
ORGANISM(S): Arabidopsis thaliana
SUBMITTER: Tsan-Piao Lin
PROVIDER: E-GEOD-67356 | biostudies-arrayexpress |
REPOSITORIES: biostudies-arrayexpress
Similar Datasets
Project description:The I/11 and R10 erythroid progenitor cell line was cultivated in serum free medium (StemPro34) supplemented with Epo (0,5U/ml), SCF (100ng/ml) and dexamethasone (10-6M). To identify genes specifically regulated by Epo/SCF-induced polysome recruitment, cells were factor deprived for 4h and subsequently treated for 2h with 5U/ml Epo and 200ng/ml SCF or left untreated. Subsequently we isolated both total and polysome bound mRNA from each condition, which was hybridised to oligonucleotide arrays (Affymetrix). Analysis of data with Rosetta Resolver allowed to identify and compare Epo/SCF induced gene expression in total and polysome bound RNA. To assess gene expression during erythroid differentiation, cells were induced to differentiate in presence of 5U/ml Epo and 0.5mg/ml Fe-loaded transferrin. Polysome bound mRNA was isolated from cells proliferating in presence of Epo, SCF and dexamethasone (renewal conditions), and from cells induced to differentiate for 48h or 60h.
2008-07-11 | E-MEXP-1689 | biostudies-arrayexpress
Project description:To understand the contribution of the k subunit of eukaryotic transcription factor 3 (eif3k) to the translation of specific mRNAs, we compared the polysome loading states and overall transcript levels of wild type Arabidopsis and the eif3k T-DNA insertion mutant by Affymetrix arrays. We analyzed the transcript levels of wild type Arabidopsis and the eif3k mutant using the Arabidopsis Affymetrix ATH1 array. Data from 3 biological replicates were collected.
2011-03-29 | E-GEOD-28222 | biostudies-arrayexpress
Project description:To understand the contribution of the k subunit of eukaryotic transcription factor 3 (eif3k) to the translation of specific mRNAs, we compared the polysome loading states and overall transcript levels of wild type Arabidopsis and the eif3k T-DNA insertion mutant by Affymetrix arrays. We analyzed the polysome loading states of wild type Arabidopsis and the eif3k mutant using the Arabidopsis Affymetrix ATH1 array. Data from 3 biological replicates were collected.
2011-03-29 | E-GEOD-28223 | biostudies-arrayexpress
Project description:This SuperSeries is composed of the following subset Series: GSE28222: eif3k/WT transcript levels GSE28223: eif3k/WT polysome loading Refer to individual Series
2011-03-29 | E-GEOD-28224 | biostudies-arrayexpress
Project description:Malaria is caused by Plasmodium parasites, which are transmitted via the bites of infected Anopheline mosquitoes. Midgut invasion is a major bottleneck for Plasmodium development inside the mosquito vectors as a rapidly responding immune system recognizes ookinetes and recruits killing factors from the midgut and surrounding tissues, dramatically reducing the population of invading ookinetes before they can successfully traverse the midgut epithelium. Understanding molecular details of the parasite-vector interactions requires precise measurement of nascent protein synthesis in the mosquito during Plasmodium infection. Current expression profiling primarily monitors alterations in steady-state levels of mRNA, but does not address the equally critical issue of whether the proteins encoded by the mRNAs are actually synthesized. In this study, we used sucrose density gradient centrifugation to isolate actively translating Anopheles gambiae mRNAs based upon their association with polyribosomes (polysomes). The proportion of individual gene transcripts associated with polysomes, which is determined by RNA deep sequencing, reflects mRNA translational status. This approach led to identification of 1017 mosquito transcripts that were primarily regulated at the translational level after ingestion of Plasmodium falciparum-infected blood. Caspar, a negative regulator of the NF-kappaB transcription factor Rel2, appears to be substantially activated at the translational levels during Plasmodium infection. In addition, transcripts of Dcr1, Dcr2 and Drosha, which are involved in small RNA biosynthesis, exhibited enhanced associations with polysomes after P. falciparum challenge. This observation suggests that mosquito microRNAs may play an important role in reactions against Plasmodium invasion. We analyzed both total cellular mRNAs and mRNAs that are associated with polysomes to simultaneously monitor transcriptomes and nascent protein synthesis in the mosquito. This approach provides more accurate information regarding the rate of protein synthesis, and identifies some mosquito factors that might have gone unrecognized because expression of these proteins is regulated mainly at the translational level rather than at the transcriptional level after mosquitoes ingest a Plasmodium-infected blood meal. Midguts from female Anopheles gambiae mosquitoes were dissected at around 24 h after ingestion of P. falciparum-infected blood. Mosquitoes fed on uninfected blood were used as control. A portion of the midguts were used for isolation of total cellular RNA. Extracts of the remaining midguts were fractionated over sucrose density gradients, and fifteen fractions were collected from the top of each gradient. Non-polysomal fractions, as well as polysomal fractions were combined, respectively, to obtain two RNA pools per gradient for three independent experiments. The first, last and the sample between non-polysomal and polysomal, were all discarded to ensure pure pools from each set. A fourth experiment was conducted where the polysomal and non-polysomal samples were not pooled, to be used later for qRT-PCR. The mRNA levels of individual mosquito genes in polysome (PS) fractions, nonpolysome (NP) fractions and unfractionated steady-state (total) RNA were determined using high throughput RNA deep sequencing. Each RNA pool generated 2.1-9.8 million raw read . Signal intensities of transcripts from each PS pool were compared to those of transcripts from a matching NP pool. To quantify the translational status of individual mRNA species, we define the relative PS loading [PL=P/(P+NP)] as the extent of mRNA association with polysomes. PL values were compared between the mosquitoes fed on P. falciparum-infected or -uninfected blood.
2012-09-21 | E-GEOD-38707 | biostudies-arrayexpress
Project description:Gene expression in the total RNA and heavy polysome fractions of Eif4g3 siRNA treated lymph node stromal cells (LNSCs) compared to control-sIRNA treated samples The objective of this study was to identify genes whose translation are reduced after silencing Eif4g3 (the gene which encodes the translation initiation factor eIF4GII). Genes with reduced translation are expected to have lower expression in RNA samples isolated from heavy polysomes but not in RNA samples isolated from whole cell lysates. LNSCs were grown in 10 cm plates, allowed to reach M-bM-^IM-% 80% confluency and then transfected with 400 pmol of control or Eif4g3 siRNA using Lipofectamine 2000. 7 plates were transfected with control or Eif4g3 siRNA. Total RNA was extracted from cells 48h after transfection. To isolate RNA from the heavy polysome fractions, cells were pooled, lysed and fractionated on a 10% to 60% continuous sucrose gradient. Fractions containing the heavy polysome fractions were pooled. RNA was extracted from these samples and used for microarrays on the Agilent Whole Mouse Genome Microarray Kit, 4M-CM-^W44K 2-color arrays.
2012-07-19 | E-GEOD-39408 | biostudies-arrayexpress
Project description:Studies of human fetal lung in explant culture and in isolated epithelial cells have demonstrated that both glucocorticoids and cyclic AMP promote differentiated alveolar type II cell phenotype as assessed by ultrastructural morphology and surfactant production. This project profiles changes in gene expression associated with hormone induced differentiation. Undifferentiated human fetal lung (13-20 wk) epithelial cells were cultured in serum-free medium (control) or with dexamethasone/8-Bromo cyclic AMP/isobutylmethylxanthine (DCI) to promote type II cell differentiation. RNA from five sets of experiments (10 samples) was evaluated using the U133A Affymetrix GeneChip set. Experiment Overall Design: Cells were isolated from 13 individual lungs and the cells from each were cultured in the absence (control) and presence of DCI dexamethasone (10 nM)/8-Br-cyclic AMP (0.1 mM)/isobutylxanthine for 72 h. RNA was isolated from the control and treated cells of each prep. For the 5 sets of microarray experiments (10 total chips, 2 for each control and treated pair), RNA from 2 of the cell preps was analysed as individual microarray comparisons. RNA from 11 cell preps was pooled for the other 3 experiments (4, 4, and 3 cell preps) to provide control and DCI-treated RNA pools.
2007-11-22 | E-GEOD-3306 | biostudies-arrayexpress
Project description:The toxicity of NBP and its four major metabolites were compared in both PHHs and PRHs, and 3-OH-NBP was found to be the most toxic metabolite. 3-OH-NBP induced remarkable cell death and oxidative stresses in hepatocytes, which correlated well with the levels of glutathione and N-acetylcysteine adducts (3-GSH-NBP and 3-NAC-NBP) in cell supernatants. Additionally, 3-OH-NBP covalently conjugated with intracellular Cys, Lys and Ser, with preferable binding to Cys sites at Myh9 Cys1380, Prdx4 Cys53, Vdac2 Cys48 and Vdac3 Cys36. Furthermore, we found that CYP3A4 induction by rifampicin augmented NBP-induced cell toxicity and supplementing with GSH or NAC alleviated the oxidative stresses and reactive metabolites caused by 3-OH-NBP.
2022-10-22 | PXD029480 | Pride
Project description:Murine or human cancer cells have high glutathione levels. Depletion of the elevated GSH inhibits proliferation of cancer cells. Molecular basis for this observation is little understood. In an attempt to find out the underlying mechanism, we reproduced these effects in transformed C3H10T1/2 and BALB/c 3T3 cells using diethyl maleate and studied cytogenomic changes in the whole mouse genome using spotted 8 M-CM-^W 60K arrays. Transformed cells revealed an increase in GSH levels. GSH depletion by DEM inhibited the growth of transformed cells. The non-cytotoxic dose of DEM (0.25 mM) resulted in GSH depletion, ROS generation, cell cycle arrest, apoptosis, decrease in anchorage independent growth, gene expression changes and activation of all three members of the MAPK family. Increase in intracellular GSH levels by GSHe countered the effect of DEM. These results support the physiological importance of GSH in regulation of gene expression for transformed cell growth restraint. This study is of interest in not only understanding the molecular biology of the transformed cells, but also in identifying new targets for development of gene therapy together with the chemotherapy. Agilent one-color experiment; Organism: Mus musculus; Agilent Custom Mouse Whole Genome Mouse 8x60k gene expression designed by Genotypic Technology Private Limited; Labeling kit: Agilent Quick-Amp labeling Kit (p/n5190-0442).
2014-06-02 | E-GEOD-44650 | biostudies-arrayexpress
Project description:Ribosomes expanded during evolution on the protein and rRNA level. The expanded regions do not change the active sites of ribosomes and thus do not alter the peptide bond formation reaction catalysed by the ribosome. To what purpose these expansions were selected is not fully understood. Here, we deleted one rRNA expansion segment (ES7La) and addressed physiological consequences. We found a mild ribosome biogenesis defect accompanied by slightly reduced translation. On a molecular level, ribosomes displayed reduced association to three aminoacyl-tRNA synthetases. Loss of ribosome binding however did not alter synthetase activity suggesting, that tRNAs are not channelled for enhanced local translation in the case of these synthetases.
2022-02-16 | PXD029751 | Pride