Saccharomyces cerevisiae
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA122333 | ENA |
REPOSITORIES: ENA
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Project description:The eukaryotic cytoplasmic chaperonin-containing TCP-1 (CCT) is a complex formed by two back-to-back stacked hetero-octameric rings that assists the folding of actins, tubulins and other proteins in an ATP-dependent manner. Here, we decided to test the significance of the hetero-oligomeric nature of CCT for its function by introducing, in each of the eight subunits in turn, an identical mutation at a position involved in ATP binding and conserved in all the subunits, in order to establish the extent of ‘individuality’ of the various subunits. Our results show that these identical mutations lead to dramatically different phenotypes. For example, cells with the mutation in CCT2 have an excess of actin patches and are the only pseudo-diploid strain. By contrast, cells with the mutation in CCT7 are the only ones to accumulate juxta-nuclear protein aggregates that may reflect the absence of stress response in this strain. System-level analysis of the strains using RNA microarrays reveals connections between CCT and several cellular networks including ribosome biogenesis and TOR2 that help to explain the phenotypic variability observed We used microarrays to reveal the differences in mRNA expression caused by the different mutations. All yeast strains were grown at 30 °C to OD(600)=0.5. Their total RNA was extracted and reverse transcribed to cDNA and transcribed back to RNA in the presence of biotinylated nucleotide analog. The biotinylated RNA was fragmented and hybridized to GenCHip Yeast Genome 2.0 array.
2010-06-30 | E-GEOD-19511 | biostudies-arrayexpress
Project description:The eukaryotic cytoplasmic chaperonin-containing TCP-1 (CCT) is a complex formed by two back-to-back stacked hetero-octameric rings that assists the folding of actins, tubulins and other proteins in an ATP-dependent manner. Here, we decided to test the significance of the hetero-oligomeric nature of CCT for its function by introducing, in each of the eight subunits in turn, an identical mutation at a position involved in ATP binding and conserved in all the subunits, in order to establish the extent of ‘individuality’ of the various subunits. Our results show that these identical mutations lead to dramatically different phenotypes. For example, cells with the mutation in CCT2 have an excess of actin patches and are the only pseudo-diploid strain. By contrast, cells with the mutation in CCT7 are the only ones to accumulate juxta-nuclear protein aggregates that may reflect the absence of stress response in this strain. System-level analysis of the strains using RNA microarrays reveals connections between CCT and several cellular networks including ribosome biogenesis and TOR2 that help to explain the phenotypic variability observed We used microarrays to reveal the differences in mRNA expression caused by the different mutations.
2010-07-01 | GSE19511 | GEO
Project description:The molecular chaperonin TRiC/CCT is a large hetero-oligomeric structure that serves an essential role in eukaryotic cells by minimally supporting protein homeostasis including the folding of nascent polypeptides and the assembly/disassembly of protein complexes. TRiC/CCT is typically considered a strict cytosolic machine. Here, we investigated the influence of TRiC/CCT on nuclear features including epigenetic marks, chromatin accessibility, and transcription. Despite being linked to several chromatin modifiers, our work indicates TRiC/CCT does not have a sustained role with these factors. TRiC/CCT did actively contribute to transcription. Inactivation of TRiC/CCT resulted in a significant increase in the production of RNA leading to an accumulation of noncoding transcripts. Our data support a direct role for TRiC/CCT with RNA polymerase II as the chaperonin modulated nascent RNA production both in vivo and in vitro. Overall, our studies reveal a new avenue by which TRiC/CCT contributes to cell homeostasis by regulating the activity of nuclear RNA polymerase II.
2025-09-01 | GSE274455 | GEO
Project description:The molecular chaperonin TRiC/CCT is a large hetero-oligomeric structure that serves an essential role in eukaryotic cells by minimally supporting protein homeostasis including the folding of nascent polypeptides and the assembly/disassembly of protein complexes. TRiC/CCT is typically considered a strict cytosolic machine. Here, we investigated the influence of TRiC/CCT on nuclear features including epigenetic marks, chromatin accessibility, and transcription. Despite being linked to several chromatin modifiers, our work indicates TRiC/CCT does not have a sustained role with these factors. TRiC/CCT did actively contribute to transcription. Inactivation of TRiC/CCT resulted in a significant increase in the production of RNA leading to an accumulation of noncoding transcripts. Our data support a direct role for TRiC/CCT with RNA polymerase II as the chaperonin modulated nascent RNA production both in vivo and in vitro. Overall, our studies reveal a new avenue by which TRiC/CCT contributes to cell homeostasis by regulating the activity of nuclear RNA polymerase II.
2025-09-01 | GSE274454 | GEO
Project description:The molecular chaperonin TRiC/CCT is a large hetero-oligomeric structure that serves an essential role in eukaryotic cells by minimally supporting protein homeostasis including the folding of nascent polypeptides and the assembly/disassembly of protein complexes. TRiC/CCT is typically considered a strict cytosolic machine. Here, we investigated the influence of TRiC/CCT on nuclear features including epigenetic marks, chromatin accessibility, and transcription. Despite being linked to several chromatin modifiers, our work indicates TRiC/CCT does not have a sustained role with these factors. TRiC/CCT did actively contribute to transcription. Inactivation of TRiC/CCT resulted in a significant increase in the production of RNA leading to an accumulation of noncoding transcripts. Our data support a direct role for TRiC/CCT with RNA polymerase II as the chaperonin modulated nascent RNA production both in vivo and in vitro. Overall, our studies reveal a new avenue by which TRiC/CCT contributes to cell homeostasis by regulating the activity of nuclear RNA polymerase II.
2025-09-01 | GSE274453 | GEO
Project description:Cells contain numerous abundant molecular machines assembled from multiple subunits. Imbalances in subunit production and failed assembly generate orphan subunits that are eliminated by poorly defined pathways. Here, we determined how orphan subunits of the cytosolic chaperonin CCT are recognized. Several unassembled CCT subunits recruited the E3 ubiquitin ligase HERC2 using ZNRD2 as an adaptor. Both factors were necessary for orphan CCT subunit degradation in cells, sufficient for CCT subunit ubiquitination with purified factors, and necessary for optimal cell fitness. Domain mapping and structure prediction defined the molecular features of a minimal HERC2-ZNRD2-CCT module. The structural model, whose key elements were validated in cells using point mutants, shows why ZNRD2 selectively recognizes multiple orphaned CCT subunits without engaging assembled CCT. Our findings reveal how failures during CCT assembly are monitored and provide a paradigm for the molecular recognition of orphan subunits, the largest source of quality control substrates in cells.
2023-07-26 | PXD042773 | Pride
Project description:The COP9 signalosome (CSN) is a highly conserved complex consisting of eight subunits, which influences key developmental pathways through its regulation of protein stability and transcription. Mutations in each of the CSN subunits exhibits diverse pleiotropic phenotypes We used microarrays to compare gene expression of two CSN mutants with their corresponding wild types: a non-lethal csn5a-1 mutant, vs. columbia ecotype, and a lethal, csn8 mutant, vs. Wassilewskija ecotype
2020-07-28 | GSE108376 | GEO
Project description:The APOBEC3 cytosine deaminases are implicated as the cause of a prevalent somatic mutation pattern found in cancer genomes. The APOBEC3 enzymes act as viral restriction factors by mutating viral genomes. Mutation of the cellular genome is presumed to be an off-target activity of the enzymes, although the regulatory measures for APOBEC3 expression and activity remain undefined. It is therefore difficult to predict the circumstances that enable APOBEC3 interaction with cellular DNA that leads to mutagenesis. The APOBEC3A (A3A) enzyme is the most potent deaminase of the family. Using proteomics, we evaluated protein interactors of A3A to identify potential regulators. We found that A3A interacts with the Chaperonin Containing TCP-1 (CCT) complex, a cellular machine that assists in protein folding and function. Importantly, depletion of CCT resulted in increased A3A-induced cytotoxicity. Evaluation of cancer genomes demonstrated an enrichment of A3A mutational signatures in cancers with silencing mutations in CCT subunit genes. Together, these data suggest that the CCT complex interacts with A3A, and that disruption of CCT function results in increased A3A mutational activity.
2021-07-02 | PXD024191 | Pride
Project description:Chemical cross-linking coupled to mass spectrometry was used to study the folding of the client protein, beta-tubulin, by the chaperonin TRiC/CCT. Different complexes containing TRiC/CCT and/or the chaperone prefoldin were cross-linked in absence or presence of nucleotides with the homobifunctional, noncleavable reagent, disuccinimidyl suberate (DSS).
2022-12-08 | PXD030590 | Pride
Project description:Chemical cross-linking coupled to mass spectrometry was used to study assembly intermediates of the chaperonin TRiC/CCT. Complex were cross-linked with the homobifunctional, noncleavable reagent, disuccinimidyl suberate (DSS).
2023-08-24 | PXD043532 | Pride