RQT complex dissociates ribosomes collided on endogenous RQC substrate SDD1
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA542921 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR9054693.fastq.gz | Fastqsanger.gz | |||
| SRR9054694.fastq.gz | Fastqsanger.gz | |||
| SRR9054695.fastq.gz | Fastqsanger.gz | |||
| SRR9054696.fastq.gz | Fastqsanger.gz |
Items per page: 5 1 - 4 of 4 |
Similar Datasets
Project description:Ribosome-associated quality control (RQC) represents a rescue pathway in eukaryotic cells triggered upon translational stalling. Collided ribosomes are recognized for subsequent dissociation followed by degradation of nascent peptides. However, endogenous RQC-inducing sequences and the mechanism underlying the ubiquitin-dependent ribosome dissociation remain poorly understood. Here, we identified the SDD1 mRNA from S. cerevisiae as an endogenous RQC substrate and reveal its mRNA and nascent peptide dependent stalling mechanism by mutational and cryo-EM analyses. In vitro translation of SDD1 mRNA enabled the reconstitution of Hel2-dependent poly-ubiquitination of collided di- and preferentially tri-ribosomes. Distinct trisome architecture was visualized by cryo-EM and provides the structural basis for more efficient recognition by Hel2 over disomes. Subsequently, the Slh1 helicase subunit of the RQC trigger (RQT) complex preferentially dissociates the first stalled poly-ubiquitinated ribosome in an ATP-dependent manner. Together, these findings provide fundamental mechanistic insights into RQC and its physiological role in maintaining cellular protein homeostasis.
2020-01-27 | GSE131214 | GEO
Project description:The multiprotein bridging factor 1 (Mbf1) proteins are a family of conserved eukaryotic proteins thought to mediate the activity of stress-induced transcription factors. In yeast, Mbf1 has been proposed to function in the integrated stress response (ISR) by mediating an interaction between the basal transcription machinery and the process’s key effector Gcn4. Curiously, mounting recent evidence has strongly suggested that the factor and its human homologue to be recruited to collided ribosomes, the very signal newly recognized to activate the ISR. Here we provide data that connect these otherwise supposedly disparate functions of the factor. Our findings revealed that Mbf1 functions as a core factor in the ISR process, responding early to stress and mediating the activation of Gcn2. We further show that the factor serves no role as a transcriptional coactivator of Gcn4; instead, it is required for optimal stress-induced eIF2a phosphorylation and downstream de-repression of GCN4 translation. Detailed mutational and biochemical analysis, together with a cryo-EM structure of the factor bound to collided ribosomes, showed that Mbf1’s activity in the ISR is enabled through its interaction with ribosomes. Collectively, our data resolve an important question about how Mbf1 factors function in signaling by acting as sensors of stress-induced ribosomes collisions, and not as coactivators of the effector proteins as widely accepted in the field.
2024-12-18 | GSE255383 | GEO
Project description:Transcriptome-wide sites of collided ribosomes reveal sequence determinants of translational pausing in vivo
| PRJNA555528 | ENA
Project description:Primary outcome(s): To determine the correlation between the baseline endogenous DPD substrate plasma ratios of DHU/U and DHT/T with the pharmacokinetics of 5-FU in patients with pancreas or colorectal cancer treated with intravenous 5-FU-based chemotherapy.
Study Design: N/A: single arm study, Open (masking not used), N/A , unknown, Other
| 2442076 | ecrin-mdr-crc
Project description:Ribosome-associated quality control (RQC) represents a rescue pathway in eukaryotic cells triggered upon translational stalling. Collided ribosomes are recognized for subsequent dissociation followed by targeting of the faulty nascent peptides for degradation. However, endogenous RQC inducing sequences and the mechanism underlying the ubiquitin-dependent ribosome dissociation remain poorly understood. Here, we identified the SDD1 mRNA from S. cerevisiae as an endogenous RQC substrate and reveal its mRNA and nascent peptide dependent stalling mechanism by mutational and cryo-EM analyses. In vitro translation of SDD1 mRNA enabled the reconstitution of Hel2-dependent poly-ubiquitination of colliding di- and preferentially tri-ribosomes. Their distinct architecture is visualized by cryo-EM and provides the structural basis for more efficient recognition by Hel2 over disomes. Subsequently, the Slh1/Rqt2 helicase subunit of the RQC trigger (RQT) complex preferentially dissociates the first stalled poly-ubiquitinated ribosome in an ATP dependent manner. Together, these findings provide fundamental mechanistic insights into RQC and its physiological role in dealing with endogenous substrates to maintain cellular protein homeostasis.
2020-02-24 | PXD017196 | Pride
Project description:Translating ribosomes that slow excessively incur collisions with trailing ribosomes. Persistent collisions are detected by ZNF598, a ubiquitin ligase that ubiquitinates sites on the ribosomal 40S subunit to initiate pathways of mRNA and protein quality control. The collided ribosome complex must be disassembled to initiate downstream quality control, but the mechanistic basis of disassembly is unclear. Here, we reconstitute the disassembly of a collided polysome in a mammalian cell-free system. The widely conserved ASC-1 complex (ASCC) containing the ASCC3 helicase disassembles the leading ribosome in an ATP-dependent reaction. Disassembly, but not ribosome association, requires 40S ubiquitination by ZNF598, but not GTP-dependent factors, including the Pelo-Hbs1L ribosome rescue complex. Trailing ribosomes can elongate once the roadblock has been removed and only become targets if they subsequently stall and incur collisions. These findings define the specific role of ASCC during ribosome-associated quality control and identify the molecular target of its activity.
| S-EPMC7447978 | biostudies-literature
Project description:Ribosome collisions activate the ribotoxic stress response (RSR) mediated by the MAP3K ZAKα (ZAK), which in turn regulates downstream phosphorylation of the MAPKs JNK and p38 and cell fate consequences. Despite this critical role during cellular stress, a structural and mechanistic understanding of the ZAK-ribosome interaction and activation have remained elusive. Here, we combine biochemistry with cryo-electron microscopy (cryo-EM) to dissect ZAK interactions with ribosomes in various states both in vivo and in vitro. We identified regions of ZAK necessary for binding to ribosomes under normal and under stress-induced conditions. Moreover, we discovered how interactions between ZAK and the ribosomal protein RACK1 mediate ZAK activation by recognizing the collision-interface. Further, we provide insight into how this process can be negatively regulated to prevent constitutive ZAK activation. Characterizing novel variants as well as a known pathogenic variant of ZAK’s SAM domain supports a key role of this conserved domain in regulating kinase activity on and off the ribosome. Collectively, we show that ZAK directly binds at the collided ribosome interface giving molecular insight into kinase activity regulation at the ribosome.
2025-10-02 | GSE299329 | GEO
Project description:Multiprotein bridging factor 1 is required for robust activation of the integrated stress response on collided ribosomes
| PRJNA1074781 | ENA
Project description:Translation is initiated by binding of the eIF4F complex to the 5' cap of the mRNA, which is followed by scanning of the initiation codon by scanning ribosomes. Here we demonstrate that the ASC-1 complex (ASCC), which was previously shown to promote the dissociation of colliding 80S ribosomes, associates with the scanning ribosomes to regulate translation initiation. Sel-TCP-seq analysis revealed that ASCC3, a subunit of ASCC with a helicase domain, localizes predominantly to the 5' untranslated region of mRNAs. Knockdown of ASCC3 resulted in reduced translation efficiency associated with reduced 43S preinitiation complex (PIC) loading and a reduced speed of scanning ribosomes. In addition, depletion of the ubiquitin ligase ZNF598, a sensor of collided 80S ribosomes, also reduces the PIC loading and speed of scanning ribosomes. Our results have thus revealed that ASCC is required not only for dissociation of colliding 80S ribosomes, but also for efficient translation initiation by scanning ribosomes.
2023-03-31 | GSE186502 | GEO
Project description:The cGAS-STING pathway, a central component of the innate immune system, senses cytosolic DNA and induces interferon-stimulated genes (ISGs) to mediate inflammation. Here we report the unexpected discovery that cGAS senses dysfunctional protein production. Purified ribosomes interact with and stimulate the catalytic activity of recombinant cGAS in vitro. Disruption of the ribosome-associated protein quality control pathway, which detects and resolves ribosome collisions, results in cGAS- and STING-dependent ISG expression, and causes the re-localization of cGAS from the nucleus to the cytosol. Indeed, cGAS preferentially binds collided ribosomes in vitro, and other orthogonal perturbations that lead to elevated levels of collided ribosomes cause re-localization of cGAS as well. Thus, the cGAS-STING pathway senses and responds to translation stress. These findings have implications for the inflammatory responses to viral infection and tumorigenesis, both of which substantially reprogram cellular protein synthesis.
2021-09-09 | PXD019359 | Pride