Saccharomyces cerevisiae
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA312727 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR3180780_1.fastq.gz | Fastqsanger.gz | |||
| SRR3180780_2.fastq.gz | Fastqsanger.gz | |||
| SRR3180790_1.fastq.gz | Fastqsanger.gz | |||
| SRR3180790_2.fastq.gz | Fastqsanger.gz | |||
| SRR3180781_1.fastq.gz | Fastqsanger.gz |
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Project description:Cells maintain proteostasis by selectively recognizing and targeting misfolded proteins for degradation. In Saccharomyces cerevisiae, the Hsp70 nucleotide exchange factor Fes1 is essential for the degradation of chaperone-associated misfolded proteins by the ubiquitin-proteasome system. Here we show that the FES1 transcript undergoes unique 3' alternative splicing that results in two equally active isoforms with alternative C-termini, Fes1L and Fes1S. Fes1L is actively targeted to the nucleus and represents the first identified nuclear Hsp70 nucleotide exchange factor. In contrast, Fes1S localizes to the cytosol and is essential to maintain proteostasis. In the absence of Fes1S, the heat-shock response is constitutively induced at normally non-stressful conditions. Moreover, cells display severe growth defects when elevated temperatures, amino acid analogues or the ectopic expression of misfolded proteins, induce protein misfolding. Importantly, misfolded proteins are not targeted for degradation by the ubiquitin-proteasome system. These observations support the notion that cytosolic Fes1S maintains proteostasis by supporting the removal of toxic misfolded proteins by proteasomal degradation. This study provides key findings for the understanding of the organization of protein quality control mechanisms in the cytosol and nucleus. 4 strains (WT, fes1Î, fes1ÎS, fes1ÎL) were sequenced in triplicates from independent RNA isolations.
2016-02-29 | E-GEOD-78136 | biostudies-arrayexpress
Project description:Cells maintain proteostasis by selectively recognizing and targeting misfolded proteins for degradation. In Saccharomyces cerevisiae, the Hsp70 nucleotide exchange factor Fes1 is essential for the degradation of chaperone-associated misfolded proteins by the ubiquitin-proteasome system. Here we show that the FES1 transcript undergoes unique 3' alternative splicing that results in two equally active isoforms with alternative C-termini, Fes1L and Fes1S. Fes1L is actively targeted to the nucleus and represents the first identified nuclear Hsp70 nucleotide exchange factor. In contrast, Fes1S localizes to the cytosol and is essential to maintain proteostasis. In the absence of Fes1S, the heat-shock response is constitutively induced at normally non-stressful conditions. Moreover, cells display severe growth defects when elevated temperatures, amino acid analogues or the ectopic expression of misfolded proteins, induce protein misfolding. Importantly, misfolded proteins are not targeted for degradation by the ubiquitin-proteasome system. These observations support the notion that cytosolic Fes1S maintains proteostasis by supporting the removal of toxic misfolded proteins by proteasomal degradation. This study provides key findings for the understanding of the organization of protein quality control mechanisms in the cytosol and nucleus.
2016-02-29 | GSE78136 | GEO
Project description:The ATP-dependent chaperones of the Hsp70 class (DnaK in E. coli) function in protein folding in cooperation with J proteins and nucleotide exchange factors (DnaJ and GrpE in E. coli, respectively). Hsp70 prevents protein aggregation, increasing the folding yield, but whether it also enhances the rate of folding is unclear. Equilibrium hydrogen/deuterium exchange – mass spectrometry showed that DnaK stabilizes a poorly structured state of firefly luciferase (FLuc). Pulsed-label experiments, together with orthogonal analyses by spFRET, identified compact inter-domain misfolded states of FLuc that convert slowly to the native state. DnaK binding expands the misfolded region and thereby resolves the kinetically-trapped intermediates, with folding occurring upon GrpE-mediated release. By resolving misfolding and accelerating folding the Hsp70 system can maintain proteins in their native states under otherwise denaturing stress conditions.
2020-01-15 | PXD016509 | Pride
Project description:Elimination of misfolded proteins is crucial for proteostasis and to prevent proteinopathies. Nedd4/Rsp5 emerged as a major E3 ligase involved in multiple quality control pathways that target misfolded plasma membrane proteins, aggregated polypeptides, and cytosolic heat-induced misfolded proteins for degradation. It remained unclear how in one case cytosolic heat-induced Rsp5 substrates are destined for proteasomal degradation, whereas other Rsp5 quality control substrates are otherwise directed to lysosomal degradation. Here we find that Ubp2 and Ubp3 deubiquitinases are required for the proteasomal degradation of cytosolic misfolded proteins targeted by Rsp5 after heat-shock. The two deubiquitinases associate more with Rsp5 upon heat stress to prevent the assembly of K63-linked ubiquitin on Rsp5 heat-induced substrates. This activity was required to promote the K48-mediated proteasomal degradation of Rsp5 heat-shock induced substrates. Our results indicate that ubiquitin chain editing is key to the cytosolic protein quality control under stress conditions.
2022-03-01 | PXD004747 | Pride
Project description:HSC70 is the cytosolic isoform of plant HSP70. We have found that HSC70 family proteins bind to the heat shock transcription factor A1s (HsfA1s), which are the master regulators of the heat shock response in plants, and supress their activity. To investigate the role of HSC70s in the regulation of HsfA1s and heat shock responses, we evaluated the effect of triple knock out of HSC70s on the transcriptome under the normal growth condition.
2021-12-01 | E-MTAB-8721 | biostudies-arrayexpress
Project description:Protein quality controls (PQC) systems rely on three main activities to prevent the accumulation of misfolded proteins upon stress conditions and aging: refolding, degradation and sequestration. In Saccharomyces cerevisiae the Hsp70 chaperone system plays a central role in protein refolding, while degradation is predominantly executed by the ubiquitin proteasome system (UPS). The sequestrases Hsp42 and Btn2 deposit misfolded proteins in cytosolic and nuclear inclusions. This activity prevents exhaustion of limited Hsp70 resources by restricting the accessibility of misfolded proteins upon sequestration. Sequestrase mutants therefore show negative genetic interactions with yeast Hsp70 co-chaperone mutants (fes1D hsp104D, DD) that suffer from low Hsp70 capacity. Growth of DDbtn2D mutants is highly temperature-sensitive and results in proteostasis breakdown at non-permissive temperatures. Here, we probed for the role of the UPS system in maintaining protein homeostasis in DDbtn2D cells, affected in two major PQC branches. We show that DDD cells induce expression of diverse stress-related pathways including the UPS to counteract the proteostasis defects. UPS dependent degradation of the stringent Hsp70 substrate Luciferase in the mutant cells mirrors such compensatory activities of the PQC system. However, the enhanced UPS activity does not improve but aggravates the phenotypes of DDbtn2D cells. Reducing UPS activity in the mutant by lowering the levels of functional 26S proteasomes improved growth, increased refolding yield of the Luciferase reporter and attenuated global stress responses. This indicates that an imbalance between Hsp70-dependent refolding and UPS-mediated degradation activities strongly affects protein homeostasis of yeast Hsp70 capacity mutants and contributes to their severe growth phenotypes.
2023-03-10 | PXD037835 | Pride
Project description:Misfolded membrane proteins are retained in the endoplasmic reticulum (ER) and are subject to the ER associated degradation pathway, which clears the secretory pathway of potentially toxic species. While the transcriptional response to environmental stressors has been extensively studied, limited data exist describing the cellular response to misfolded membrane proteins. To this end, we expressed and then compared the transcriptional profiles elicited by the synthesis of three ER retained, misfolded ion channels: The α subunit of the epithelial sodium channel, ENaC, the cystic fibrosis transmembrane conductance regulator, CFTR, and an inwardly rectifying potassium channel, Kir2.1, which vary in their mass, membrane topologies, and quaternary structures. To examine transcriptional profiles in a null background, the proteins were expressed in yeast, which was previously used to examine the degradation requirements for each substrate. Surprisingly, the proteins failed to induce a canonical unfolded protein response or heat shock response, although messages encoding several cytosolic and ER lumenal protein folding factors rose when αENaC or CFTR were expressed. In contrast, the levels of these genes were unaltered by Kir2.1 expression; instead, the yeast iron regulon was activated. Nevertheless, a significant number of genes that respond to various environmental stressors were upregulated by all three substrates, and when compared to previous microarray data we deduced the existence of a group of genes that reflect a novel misfolded membrane protein response. These data indicate that aberrant proteins in the ER elicit profound yet unique cellular responses. Yeast heterologously expressing αENaC, CFTR, Kir2.1 or harboring a vector control were grown under identical conditions (at least 3 biological replicates) and subject to gene expression analysis.
2014-09-10 | E-GEOD-61244 | biostudies-arrayexpress
Project description:Misfolded membrane proteins are retained in the endoplasmic reticulum (ER) and are subject to the ER associated degradation pathway, which clears the secretory pathway of potentially toxic species. While the transcriptional response to environmental stressors has been extensively studied, limited data exist describing the cellular response to misfolded membrane proteins. To this end, we expressed and then compared the transcriptional profiles elicited by the synthesis of three ER retained, misfolded ion channels: The α subunit of the epithelial sodium channel, ENaC, the cystic fibrosis transmembrane conductance regulator, CFTR, and an inwardly rectifying potassium channel, Kir2.1, which vary in their mass, membrane topologies, and quaternary structures. To examine transcriptional profiles in a null background, the proteins were expressed in yeast, which was previously used to examine the degradation requirements for each substrate. Surprisingly, the proteins failed to induce a canonical unfolded protein response or heat shock response, although messages encoding several cytosolic and ER lumenal protein folding factors rose when αENaC or CFTR were expressed. In contrast, the levels of these genes were unaltered by Kir2.1 expression; instead, the yeast iron regulon was activated. Nevertheless, a significant number of genes that respond to various environmental stressors were upregulated by all three substrates, and when compared to previous microarray data we deduced the existence of a group of genes that reflect a novel misfolded membrane protein response. These data indicate that aberrant proteins in the ER elicit profound yet unique cellular responses. Yeast heterologously expressing αENaC, CFTR, Kir2.1 or harboring a vector control were grown under identical conditions (at least 3 biological replicates) and subject to gene expression analysis.
2014-09-10 | E-GEOD-61243 | biostudies-arrayexpress
Project description:Misfolded membrane proteins are retained in the endoplasmic reticulum (ER) and are subject to the ER associated degradation pathway, which clears the secretory pathway of potentially toxic species. While the transcriptional response to environmental stressors has been extensively studied, limited data exist describing the cellular response to misfolded membrane proteins. To this end, we expressed and then compared the transcriptional profiles elicited by the synthesis of three ER retained, misfolded ion channels: The α subunit of the epithelial sodium channel, ENaC, the cystic fibrosis transmembrane conductance regulator, CFTR, and an inwardly rectifying potassium channel, Kir2.1, which vary in their mass, membrane topologies, and quaternary structures. To examine transcriptional profiles in a null background, the proteins were expressed in yeast, which was previously used to examine the degradation requirements for each substrate. Surprisingly, the proteins failed to induce a canonical unfolded protein response or heat shock response, although messages encoding several cytosolic and ER lumenal protein folding factors rose when αENaC or CFTR were expressed. In contrast, the levels of these genes were unaltered by Kir2.1 expression; instead, the yeast iron regulon was activated. Nevertheless, a significant number of genes that respond to various environmental stressors were upregulated by all three substrates, and when compared to previous microarray data we deduced the existence of a group of genes that reflect a novel misfolded membrane protein response. These data indicate that aberrant proteins in the ER elicit profound yet unique cellular responses. Yeast heterologously expressing αENaC, CFTR, Kir2.1 or harboring a vector control were grown under identical conditions (at least 3 biological replicates) and subject to gene expression analysis.
2014-09-10 | E-GEOD-61245 | biostudies-arrayexpress
Project description:HSC70 is the cytosolic isoform of plant HSP70. We have found that HSC70 family proteins bind to the heat shock transcription factor A1s (HsfA1s), which are the master regulators of the heat shock response in plants, and suppress their activity. We additionally found that the triple knock out of HSC70s alters responses of Arabidopsis plants to salt stress. To investigate the role of the HSC70s in salt stress responses, we evaluated the effects of the triple knock out on the transcriptome under salt stress.
2021-12-01 | E-MTAB-8723 | biostudies-arrayexpress