The transcription factor bZIP60 links the Unfolded Protein Response (UPR) to the Heat Stress Response (HSR) in maize
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ABSTRACT:
PROVIDER: PRJNA646054 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR12214335.fastq.gz | Fastqsanger.gz | |||
| SRR12214336.fastq.gz | Fastqsanger.gz | |||
| SRR12214337.fastq.gz | Fastqsanger.gz | |||
| SRR12214338.fastq.gz | Fastqsanger.gz | |||
| SRR12214339.fastq.gz | Fastqsanger.gz |
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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:Unfolded protein response (UPR) and endoplasmic reticulum (ER) stress in acromegaly
| PRJNA643979 | ENA
Project description:This was a comparative transcriptome analysis by using high throughput sequencing. To assess the effects of heat stress on maize we used a controlled environment facility called the Enviratron to simulate field conditions. For our experiments, maize plants were subjected to conditions simulating normal diurnal rhythms of light and temperature, with increasing maximal daily temperature (MDT). Maize plants were grown continuously under four different temperature regimes with simulated morning temperatures ramped up over 6 hr to the MDT of 31°C, 33°C, 35°C or 37°C and simulated evening/night time temperatures ramped down over 8 hr to 10°C below the MDT. We tracked the gene expression events of maize W22 seedlings grow under different temperatures (MDT of 31°C, 33°C, 35°C or 37°C) to evaluate how different MDTs affect the program of gene expression in maize. At the same time, we analyzed the effects of temperature on gene expression in bzip60-2 and W22 V4 plants (20 DAG) and V5 plants (27 DAG) in the Enviratron as the temperature reached its MDT to investigate whether and how bZIP60 confers heat stress tolerance in maize. RNA was extracted from small strips of leaf lamina excised from the first fully expanded leaf of V4 and V5 W22 plants (at 20 and 27 DAG, respectively). Plants were sampled in triplicates.
2020-08-31 | GSE154373 | GEO
Project description:To dissect the requirements of membrane protein degradation from the ER, we expressed the mouse major histocompatibility complex class I heavy chain H-2K(b) in yeast. Like other proteins degraded from the ER, unassembled H-2K(b) heavy chains are not transported to the Golgi but are degraded in a proteasome-dependent manner. The overexpression of H-2K(b) heavy chains induces the unfolded protein response (UPR). In yeast mutants unable to mount the UPR, H-2K(b) heavy chains are greatly stabilized. This defect in degradation is suppressed by the expression of the active form of Hac1p, the transcription factor that upregulates UPR-induced genes. These results indicate that induction of the UPR is required for the degradation of protein substrates from the ER. Set of arrays organized by shared biological context, such as organism, tumors types, processes, etc. Computed
2005-08-16 | E-GEOD-3130 | biostudies-arrayexpress
Project description:Protein homeostasis is maintained by a combination of tightly controlled processes which include synthesis, folding, trafficking and degradation. Transient accumulation of unfolded / misfolded proteins in the endoplasmic reticulum (ER) due to cell intrinsic and / or extrinsic signals results in the activation of unfolded protein response (UPR), an adaptation mechanism. Failure to resolve the transient accumulation results in UPR mediated programmed cell death. Loss of tumor suppressor gene or oncogene addiction in cancer cells result in a sustained higher basal UPR levels. This higher basal UPR levels in cancer cells when compared to normal cells provides a therapeutic window that can be exploited by UPR activators. Here we explored covalent modification of surface exposed cysteine (SEC) residues to simulate unfolded / misfolded proteins and induce UPR activation. A proteome-wide click-pulldown-MS study using an alkyne tagged isatin-derived spirocyclic -methylene--butyrolactone analog identified > 330 protein targets that were covalently modified. Evaluation for UPR activation with a set of analogs that can covalently modify SECs identified a spirocyclic -methylene--butyrolactone dimer (SpiD7) as a UPR activator. SpiD7 induced XBP1 splicing protected normal cells from caspase-mediated apoptosis, no such induction was observed in cancer cells, which resulted in caspase-mediated apoptosis in cancer cells. SpiD7 inhibits growth of high-grade serous carcinoma (HGSC) cell lines ~3-15 fold more potently than immortalized fallopian tube epithelial (normal) cells and reduced clonogenic growth of HGSC cell lines. Our results suggest that induction of UPR by covalent modification of SEC residues is a cancer cell vulnerability and can be exploited to discover novel therapeutics.
2022-05-20 | PXD029783 | Pride
Project description:Erguler2013 - Unfolded protein stress response
The model investigates the mechanism by which UPR (unfolded protein response) outcome switches between survival and death.
This model is described in the article:
A mathematical model of the unfolded protein stress response reveals the decision mechanism for recovery, adaptation and apoptosis.
Erguler K, Pieri M, Deltas C.
BMC Syst Biol. 2013 Feb 21;7(1):16.
Abstract:
BACKGROUND: The unfolded protein response (UPR) is a major signalling cascade acting in the quality control ofprotein folding in the endoplasmic reticulum (ER). The cascade is known to play an accessory rolein a range of genetic and environmental disorders including neurodegenerative and cardiovasculardiseases, diabetes and kidney diseases. The three major receptors of the ER stress involved withthe UPR, i.e. IRE1a, PERK and ATF6, signal through a complex web of pathways to convey anappropriate response. The emerging behaviour ranges from adaptive to maladaptive depending on theseverity of unfolded protein accumulation in the ER; however, the decision mechanism for the switchand its timing have so far been poorly understood.
RESULTS:
Here, we propose a mechanism by which the UPR outcome switches between survival and death.We compose a mathematical model integrating the three signalling branches, and perform a comprehensivebifurcation analysis to investigate possible responses to stimuli. The analysis reveals threedistinct states of behaviour, low, high and intermediate activity, associated with stress adaptation, tolerance,and the initiation of apoptosis. The decision to adapt or destruct can, therefore, be understoodas a dynamic process where the balance between the stress and the folding capacity of the ER playsa pivotal role in managing the delivery of the most appropriate response. The model demonstratesfor the first time that the UPR is capable of generating oscillations in translation attenuation and theapoptotic signals, and this is supplemented with a Bayesian sensitivity analysis identifying a set ofparameters controlling this behaviour.
CONCLUSIONS:
This work contributes largely to the understanding of one of the most ubiquitous signalling pathwaysinvolved in protein folding quality control in the metazoan ER. The insights gained have direct consequenceson the management of many UPR-related diseases, revealing, in addition, an extended listof candidate disease modifiers. Demonstration of stress adaptation sheds light to how preconditioningmight be beneficial in manifesting the UPR outcome to prevent untimely apoptosis, and paves the wayto novel approaches for the treatment of many UPR-related conditions.
In the paper, PERKA refers to the amount of phosphorylated PERK monomer. However, it refers to the active complex in the model. The complex with the model parameterization is formed of 4 monomers (n=4). So, the value of PERKA should be multiplied by 4, in order to generate the figures in the paper (eg. Figure 12).
An additional parameter (tmr=10)) is used in the model. This parameter is not mentioned in the paper. The model values of kf(=10) and kr(=1) are not consistent with that of the paper (kf=100, kr=10, in the paper). However, this is corrected by the introduction of "tmr" in the model, which is multiplied with kf and kr to get the resulting values.
The term "tmr" was missing in the kinetic laws of the reactions reu7 and reu8, in the original model. This has been corrected as per the author's request.
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2024-09-02 | BIOMD0000000446 | BioModels
Project description:The hepatic unfolded protein response (UPR) is an adaptive cellular response to endoplasmic reticulum stress that is important in the pathogenesis of many liver diseases. In this study, we utilized liver biopsies from patients after liver transplantation as a disease model to determine the transcriptional profile and hepatic UPR gene expression that is associated with liver injury and cholestasis.
2022-08-17 | GSE203453 | GEO
Project description:The accumulation of misfolded proteins in the endoplasmic reticulum (ER) defines a condition called ER stress that induces the unfolded protein response (UPR). The UPR in mammalian cells attenuates protein synthesis initiation, which prevents the piling up of misfolded proteins in the ER. Mammalian cells rely on Protein Kinase RNA-Like Endoplasmic Reticulum Kinase (PERK) phosphorylation of eIF2alpha to arrest protein synthesis, however, plants do not have a PERK homolog, so the question is whether plants control translation in response to ER stress. We compared changes in RNA levels in the transcriptome to the RNA levels protected by ribosomes and found a decline in translation efficiency, including many UPR genes, in response to ER stress. The decline in translation efficiency is due to the fact that many mRNAs are not loaded onto polyribosomes (polysomes) in proportion to their increase in total RNA, instead some of the transcripts accumulate in stress granules (SGs). The RNAs that populate SGs are not derived from the disassembly of polysomes because protein synthesis remains steady during stress. Thus, the surge in transcription of UPR genes in response to ER stress is accompanied by the formation of SGs, and the sequestration of mRNAs in SGs may serve to temporarily relieve the translation load during ER stress.
2020-07-08 | GSE153969 | GEO
Project description:To dissect the requirements of membrane protein degradation from the ER, we expressed the mouse major histocompatibility complex class I heavy chain H-2K(b) in yeast. Like other proteins degraded from the ER, unassembled H-2K(b) heavy chains are not transported to the Golgi but are degraded in a proteasome-dependent manner. The overexpression of H-2K(b) heavy chains induces the unfolded protein response (UPR). In yeast mutants unable to mount the UPR, H-2K(b) heavy chains are greatly stabilized. This defect in degradation is suppressed by the expression of the active form of Hac1p, the transcription factor that upregulates UPR-induced genes. These results indicate that induction of the UPR is required for the degradation of protein substrates from the ER. Set of arrays organized by shared biological context, such as organism, tumors types, processes, etc. Keywords: Logical Set
2005-08-16 | GSE3130 | GEO
Project description:We measured steady-state mRNA levels by microarray hybridization, comparing WT, (delta)ire1, (delta)gcn4, and (delta)gcn2 cells treated with 2 mM DTT for 30 min (by which time the UPR is qualitatively complete) to untreated samples of the same genotype. WT cells were taken as a positive control for UPR induction, and (delta)ire1 cells as a negative control. Fold change in expression of a given gene was computed as the ratio of mRNA level in the treated sample to the level in an untreated sample of the same genotype. Values reported here are the log2 fold change. Keywords = unfolded protein response Keywords = UPR Keywords = ire1 Keywords = gcn4 Keywords = gcn2
2010-06-06 | E-GEOD-1688 | biostudies-arrayexpress