MRNA-seq of Arabidopsis mutants of UPR modulators responding to UPR inducers
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ABSTRACT:
ORGANISM(S): Arabidopsis thaliana
PROVIDER: GSE100371 | GEO | 2018/03/07
REPOSITORIES: GEO
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Project description:Transcriptome responsiveness was further tested by attempts to invoke the unfolded protein repsonse (UPR), a classic ER-based pathway stimulated by the presence of increased levels of unfolded polypeptides. The UPR is mediated via transcriptional responses in both yeast and metazoan cells, and can be reliably activated by addition of dithiothreitol (DTT). Using DTT at concentrations that invoke a UPR in mammalian cells, Arabidopsis, yeast and other systems, we found that, in T. brucei, DTT exposure led to rapid cell death. We analysed the transcriptome at 1 mM DTT, under conditions where cells remained viable, as assessed by motility. <br><br>part 1: 3 biological replicates of SMB cells grown under normal conditions, and 3 replicates of SMB cells treated with 1mM DTT for 1hr, as well as dye swaps were used. <br><br>part 2: 3 biological replicates of SMB cells <br>grown under normal conditions, and 3 replicates of SMB cells treated <br>with 1mM DTT for 4hr, as well as dye swaps were used.<br><br>The UPR can also be activated by addition of tunicamycin. Using tunicamycin at concentrations that invoke a UPR in mammalian cells, Arabidopsis, yeast and other systems, we found that, in T. brucei, tunicamycin exposure efficiently inhibits trypanosome N-glycosylation and that it resulted in growth arrest over a period of up to 24 hours. We analysed the transcriptome at 5 ?g/ml tunicamycin under conditions where cells remained viable, as assessed by motility.<br><br>part 3: 3 biological replicates of SMB cells grown under normal conditions, and 3 replicates of SMB cells treated with 5 ?g/ml tunicamycin for 4hr, as well as dye swaps were used.<br><br>part 4: 3 biological replicates of SMB cells grown under normal conditions, and 3 replicates of SMB cells treated with 5 ?g/ml tunicamycin for 24hr, as well as dye swaps were used.
2008-06-26 | E-MEXP-1533 | biostudies-arrayexpress
Project description:We are currently studying how these information-carrying oligosaccharides are involved in cellular stress responses, particularly in human genetic diseases called Congenital Disorders Of Glycosylation in which oligosaccharide assembly is defective. We are interested in endoplasmic stress responses/unfolded protein responses. ER glycans and ER lectins are intimately involved in the folding of ER proteins. Therefore, ER lectins and ER glycosyltransferases may be controlled by these stress responses, to produce and/or recognize key glycans in the stress response. Our model system is the human dermal fibroblast. We have successfully calibrated the ER stress responses in these cells by determining the magnitudes of various stress effects (such as chaperone transcription) with different forms of ER stress. We are also completing a study in which activation the signaling molecules Ire1 and ATF6 are also calibrated. We prepared multiple identical aliquots of RNA from cells stressed under several of these calibrated conditions. Endoplasmic reticulum (ER) stress and the unfolded protein response (UPR): Study of the role of ER stress in the expression of genes for ER transferases and lectins that participate in ER folding and quality control using human skin fibroblasts. The UPR response in these cells has been calibrated using various readouts in response to different stresses: 1) 40 nM L-azetidine-2-carboxylate (AZC) 1 hour, 2) 0.2 mg/ml castanospermine, 24 hours, 3) 2 mM Dithiothreitol (DTT), 20 minutes, 4) 100nm Thapsigargin (TG), 30 minutes, 5) 5 ug/ml tunicamycin, 5 hours, 6) untreated control cells
2011-02-17 | E-GEOD-27349 | biostudies-arrayexpress
Project description:The unfolded protein response (UPR) is a cellular defense mechanism against glucose deprivation, a cell condition that occurs in solid tumors. A key feature of the UPR is the activation of the transcription program that allows the cell to cope with endoplasmic reticulum (ER) stress. We used micoarrays to show that the UPR transcription program is disrupted by the antitumor macrocyclic compound versipelostatin (VST) and antidiabetic biguanides metformin, buformin and phenformin, depending on cellular glucose availability. Keywords: stress response, drug response
2009-05-20 | GSE13548 | GEO
Project description:Understanding the functional roles of bZIP28 and bZIP60 in Arabidopdis
2015-06-16 | E-MTAB-2657 | biostudies-arrayexpress
Project description:The unfolded protein response (UPR) is a cellular defense mechanism against glucose deprivation, a cell condition that occurs in solid tumors. A key feature of the UPR is the activation of the transcription program that allows the cell to cope with endoplasmic reticulum (ER) stress. We used micoarrays to show that the UPR transcription program is disrupted by the antitumor macrocyclic compound versipelostatin (VST) and antidiabetic biguanides metformin, buformin and phenformin, depending on cellular glucose availability. Experiment Overall Design: Total 42 samples were prepared for RNA extraction and hybridization on Affymetrix microarrays. Experiment Overall Design: To induce the UPR, we treated cells (HeLa, HT-29, HT1080, MKN74) for 15 or 18 hours under ER stress conditions by replacing the medium with glucose-free medium or by adding either 2-Deoxy-D-glucose (2DG) or Tunicamycin (TM) to glucose-containing medium. UPR modulators (VST, biguanides or pyrvinium pamoate) were added at various final concentrations immediately after cells were placed in glucose-free medium or just before the chemical stressors were added to glucose-containing culture medium.
2009-06-01 | E-GEOD-13548 | biostudies-arrayexpress
Project description:The Unfolded Protein Response (UPR) is activated in plants in response to ER stress and plays an important role in mitigating stress damage. We have analyzed an ire1a ire1b bzip17 triple mutant in Arabidopsis with defects in stress signaling and found that the mutant is also impaired in vegetative plant growth under conditions without externally applied stress. This raises the question as to whether the UPR functions in plant development in same manner as it does in responding to stress. bZIP17 is an ER-associated membrane transcription factor that is mobilized to the nucleus in response to stress. Through the analysis of a mobilization defective bZIP17 mutant, we found that bZIP17 must be capable of mobilization to support normal plant development. Likewise, through the analysis of ire1 mutants, we found that protein kinase and ribonuclease activities of IRE1 must be functional to support normal development. These findings demonstrate that the UPR is active, albeit at low levels, during unstressed conditions, and that these activities are required for normal development.
2019-04-17 | GSE120672 | GEO
Project description:ER stress and the unfolded protein response (UPR) involve extensive proteome remodeling in many cell compartments. However, a comprehensive analysis has been lagging due to technological limitations. Here we employ SILAC-based proteomics to quantify over 6,200 proteins at increasing concentrations of tunicamycin in HeLa cells. We further compare the effects of tunicamycin to those of thapsigargin and DTT, both activating the UPR through different mechanisms. The systematic description of the proteome-wide expression changes following proteostatic stress is a resource for the scientific community, which enables to discover novel players involved the pathophysiology of disorders linked to proteostasis. Here, we identified 38 proteins, not previously linked to the UPR, whose expression increases, of which 15 would likely remediate ER stress, and the remainder may contribute to pathological outcomes. Unexpectedly, we see few strongly downregulated proteins, despite expression of the pro-apoptotic transcription factor CHOP, suggesting that IRE1-dependent mRNA decay (RIDD) has a limited contribution to ER-stress mediated cell death in our system.
2019-11-01 | PXD013496 | Pride
Project description:Transcriptional profiling of ER stress condition comparing control (untreated), dithiothreitol (DTT) treated, or tunicamycin (TM) treated conditions on P. angusta DL1 strain.
2015-07-22 | GSE68528 | GEO
Project description:Sse1, yeast cytosolic Hsp110 chaperone, is a wellknown Nucleotide Exchange Factor (NEF), a protein-disaggregase and a Chaperone linked to Protein Synthesis (CLIPS). Here we demonstrate SSE1’s genetic interaction with IRE1 and HAC1, the Endoplasmic Reticulum-Unfolded Protein Response (ER-UPR) sensors. sse1Δ strain exhibits an ER-UPR signalling-dependent resistance to tunicamycin-induced ER stress. Importantly, ER-stress-responsive reorganization of translating ribosomes from polysomes to monosomes is inefficient in SSE1 deleted strain leading to uninterrupted protein translation and starkly different ER-UPR kinetics. sse1Δ exhibits faster ER-UPR induction and quicker reversal to basal state compared to wildtype (WT) cells. Interestingly, ER-stress mediated yeast cell division arrest is escaped in sse1Δ strain during long term tunicamycin stress indicating important role of this chaperone in controlling cell division during ER stress. Furthermore, sse1Δ strain shows significantly higher cell viability in comparison to WT yeast, following short-term as well as long-term tunicamycin stress. In summary, we show that cytosolic chaperone Sse1 genetically interacts with ER-UPR pathway, controls the kinetics of ER-UPR, stress-induced cell division arrest and cell viability during global ER stress by tunicamycin.
2024-04-19 | PXD045382 | Pride
Project description:Quantitative proteomic experiments were performed on tryptic digests of proteins purified from the leaves of Arabidopsis thaliana. Wild type plants were compared to bzip28 bzip60 mutant plants. WT and bzip28 bzip60 mutant plants were infected with Drecslera gigantea and compared to non¬-infected control plants
2021-09-09 | PXD018099 | Pride