The E3 ubiquitin ligase LTN1 downregulates RNF10 level and uS3 ubiquitination
Ontology highlight
ABSTRACT:
ORGANISM(S): Mus musculus
PROVIDER: GSE303675 | GEO | 2025/10/25
REPOSITORIES: GEO
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Project description:18S nonfunctional rRNA decay (NRD) detects and eliminates translationally nonfunctional 18S rRNA. The underlying mechanisms associated with the detection and turnover of nonfunctional 18S rRNA remain elusive. While NRD has been identified and exclusively studied in Saccharomyces cerevisiae, it is unclear whether this quality control pathway exists in mammals. Here we demonstrate the conservation of 18S NRD in mammalian cells. Using genome-wide CRISPR genetic interaction screens, we identify two molecular events triggered by nonfunctional 18S rRNA— activation of the integrated stress response (ISR) and ubiquitination of ribosomal proteins elicited by GCN2 and RNF10, respectively. Selective ribosome profiling reveals nonfunctional 18S rRNA induces translation arrest at start sites. Biochemical analyses show that activation of the ISR limits translation initiation, attenuating collisions between scanning 43S preinitiation complexes and nonfunctional 80S ribosomes arrested at start sites. Thus, the ISR facilitates the turnover of nonfunctional 18S rRNA and 40S ribosomal proteins by RNF10-mediated ubiquitination. Altogether, these results establish a dynamic feedback mechanism by which cells finetune translation initiation to enable ribosome functionality surveillance through the GCN2-RNF10 axis.
2025-02-26 | GSE255783 | GEO
Project description:18S nonfunctional rRNA decay (NRD) detects and eliminates translationally nonfunctional 18S rRNA. The underlying mechanisms associated with the detection and turnover of nonfunctional 18S rRNA remain elusive. While NRD has been identified and exclusively studied in Saccharomyces cerevisiae, it is unclear whether this quality control pathway exists in mammals. Here we demonstrate the conservation of 18S NRD in mammalian cells. Using genome-wide CRISPR genetic interaction screens, we identify two molecular events triggered by nonfunctional 18S rRNA— activation of the integrated stress response (ISR) and ubiquitination of ribosomal proteins elicited by GCN2 and RNF10, respectively. Selective ribosome profiling reveals nonfunctional 18S rRNA induces translation arrest at start sites. Biochemical analyses show that activation of the ISR limits translation initiation, attenuating collisions between scanning 43S preinitiation complexes and nonfunctional 80S ribosomes arrested at start sites. Thus, the ISR facilitates the turnover of nonfunctional 18S rRNA and 40S ribosomal proteins by RNF10-mediated ubiquitination. Altogether, these results establish a dynamic feedback mechanism by which cells finetune translation initiation to enable ribosome functionality surveillance through the GCN2-RNF10 axis.
2025-02-26 | GSE255781 | GEO
Project description:18S nonfunctional rRNA decay (NRD) detects and eliminates translationally nonfunctional 18S rRNA. The underlying mechanisms associated with the detection and turnover of nonfunctional 18S rRNA remain elusive. While NRD has been identified and exclusively studied in Saccharomyces cerevisiae, it is unclear whether this quality control pathway exists in mammals. Here we demonstrate the conservation of 18S NRD in mammalian cells. Using genome-wide CRISPR genetic interaction screens, we identify two molecular events triggered by nonfunctional 18S rRNA— activation of the integrated stress response (ISR) and ubiquitination of ribosomal proteins elicited by GCN2 and RNF10, respectively. Selective ribosome profiling reveals nonfunctional 18S rRNA induces translation arrest at start sites. Biochemical analyses show that activation of the ISR limits translation initiation, attenuating collisions between scanning 43S preinitiation complexes and nonfunctional 80S ribosomes arrested at start sites. Thus, the ISR facilitates the turnover of nonfunctional 18S rRNA and 40S ribosomal proteins by RNF10-mediated ubiquitination. Altogether, these results establish a dynamic feedback mechanism by which cells finetune translation initiation to enable ribosome functionality surveillance through the GCN2-RNF10 axis.
2025-02-26 | GSE255780 | GEO
Project description:18S nonfunctional rRNA decay (NRD) detects and eliminates translationally nonfunctional 18S rRNA. The underlying mechanisms associated with the detection and turnover of nonfunctional 18S rRNA remain elusive. While NRD has been identified and exclusively studied in Saccharomyces cerevisiae, it is unclear whether this quality control pathway exists in mammals. Here we demonstrate the conservation of 18S NRD in mammalian cells. Using genome-wide CRISPR genetic interaction screens, we identify two molecular events triggered by nonfunctional 18S rRNA— activation of the integrated stress response (ISR) and ubiquitination of ribosomal proteins elicited by GCN2 and RNF10, respectively. Selective ribosome profiling reveals nonfunctional 18S rRNA induces translation arrest at start sites. Biochemical analyses show that activation of the ISR limits translation initiation, attenuating collisions between scanning 43S preinitiation complexes and nonfunctional 80S ribosomes arrested at start sites. Thus, the ISR facilitates the turnover of nonfunctional 18S rRNA and 40S ribosomal proteins by RNF10-mediated ubiquitination. Altogether, these results establish a dynamic feedback mechanism by which cells finetune translation initiation to enable ribosome functionality surveillance through the GCN2-RNF10 axis.
2025-02-26 | GSE255779 | GEO
Project description:Abstract - 18S nonfunctional rRNA decay (NRD) detects and eliminates translationally nonfunctional 18S rRNA. While this process is critical for ribosome quality control, the mechanisms underlying nonfunctional 18S rRNA turnover remain elusive, particularly in mammals. Here, we show that mammalian 18S NRD initiates through the integrated stress response (ISR) via GCN2. Nonfunctional 18S rRNA induces translational arrest at start sites. Biochemical analyses demonstrate that ISR activation limits translation initiation and attenuates collisions between scanning 43S preinitiation complexes and stalled nonfunctional ribosomes. The ISR promotes 18S NRD and 40S ribosomal protein turnover by RNF10-mediated ubiquitination. Ultimately, RIOK3 binds the resulting ubiquitinated 40S subunits and facilitates 18S rRNA decay. Overall, mammalian 18S NRD acts through GCN2, followed by ubiquitin-dependent 18S rRNA degradation involving the ubiquitin E3 ligase RNF10 and the atypical protein kinase RIOK3. These findings establish a dynamic feedback mechanism by which the GCN2-RNF10-RIOK3 axis surveils ribosome functionality at the translation initiation step.
2024-12-09 | MSV000096620 | MassIVE
Project description:Translation elongation stalling has the potential to produce toxic truncated protein fragments. Translation of either non-stop mRNA or transcripts coding for poly-basic sequences induces ribosome stalling, and the arrest product is degraded by the ribosome-mediated quality control (RQC) system. During this process, the stalled ribosome is dissociated into subunits, and the polypeptide is ubiquitinated by the E3 ubiquitin ligase Listerin on the 60S large ribosomal subunit, leading to subsequent proteasomal degradation. However, it is largely unknown how the specific stalled ribosomes are recognized as aberrant to engage the RQC system. Here, we report that ubiquitination of the ribosomal protein uS10 of the 40S small ribosomal subunit, by the E3 ubiquitin ligase Hel2 (or RQC-trigger (Rqt) 1) initiates RQC. We identified a novel RQC-trigger (RQT) complex composed of the RNA helicase-family protein Slh1/Rqt2, the ubiquitin binding protein Cue3/Rqt3, and yKR023W/Rqt4 that is required for RQC. The defects in RQC of the RQT mutants correlated with sensitivity to anisomycin, which stalls ribosome at the rotated form, suggesting that RQT factors rescue ribosomes stalled by this drug. Our un-biased survey by ribosome profiling revealed that ribosomes stalled at the rotated state with specific pairs of codons at P-A sites serve as RQC substrates. Rqt1 specifically ubiquitinates these arrested ribosomes to target them to the RQT complex, allowing subsequent RQC reactions including dissociation of the stalled ribosome into subunits. Our results provide mechanistic insight into the surveillance system for aberrant proteins induced by ribosome stalling and mediated by ribosome ubiquitination.
2017-07-31 | GSE90919 | GEO
Project description:Ribosome-associated quality control (RQC) pathways target ribosomes whose progression becomes impaired during various phases of the translation cycle. Ribosome ubiquitylation is a key RQC licensing step. Previous studies identified an initiation specific RQC branch (iRQC) that is activated when translation initiation complexes fail to transition to elongation competent 80S ribosomes. Upon iRQC activation, RNF10 ubiquitylates the 40S proteins uS3 and uS5 which leads to 40S decay. How iRQC is activated in the absence of pharmacological translation inhibitors and what mechanisms govern iRQC capacity and activity remain unanswered questions. Here, we demonstrate that altering ribosome subunit stoichiometry by broadly disrupting 60S biogenesis triggers RNF10-dependent uS3 and uS5 ubiquitylation and 40S decay. Reducing the levels of the critical scanning helicase, eIF4A1, impairs ribosomal protein ubiquitylation and subsequent degradation, indicating that actively scanning translation initiation complexes are required for 40S decay. We show that RNF10 protein abundance increases upon iRQC pathway stimulation through a translational activation mechanism using conserved upstream open reading frames. Amino acid starvation conditions also stimulate 40S decay leading to ribosomal subunit imbalance. We identify RIOK3 as a new and critical iRQC factor that interacts with ubiquitylated 40S subunits to mediate 40S decay. We demonstrate that RIOK3 loss of function blocks 40S degradation triggered by either 60S biogenesis disruption or amino acid starvation despite elevated uS3 and uS5 ubiquitylation. These findings suggest that RIOK3 abundance, and not ribosome ubiquitylation, limits 40S decay capacity. Collectively, these results establish a feed-forward mechanism that regulates iRQC capacity and subsequent 40S decay.
2025-02-07 | PXD060208 | Pride
Project description:Ribosome-associated quality control (RQC) pathways target ribosomes whose progression becomes impaired during various phases of the translation cycle. Ribosome ubiquitylation is a key RQC licensing step. Previous studies identified an initiation specific RQC branch (iRQC) that is activated when translation initiation complexes fail to transition to elongation competent 80S ribosomes. Upon iRQC activation, RNF10 ubiquitylates the 40S proteins uS3 and uS5 which leads to 40S decay. How iRQC is activated in the absence of pharmacological translation inhibitors and what mechanisms govern iRQC capacity and activity remain unanswered questions. Here, we demonstrate that altering ribosome subunit stoichiometry by broadly disrupting 60S biogenesis triggers RNF10-dependent uS3 and uS5 ubiquitylation and 40S decay. Reducing the levels of the critical scanning helicase, eIF4A1, impairs ribosomal protein ubiquitylation and subsequent degradation, indicating that actively scanning translation initiation complexes are required for 40S decay. We show that RNF10 protein abundance increases upon iRQC pathway stimulation through a translational activation mechanism using conserved upstream open reading frames. Amino acid starvation conditions also stimulate 40S decay leading to ribosomal subunit imbalance. We identify RIOK3 as a new and critical iRQC factor that interacts with ubiquitylated 40S subunits to mediate 40S decay. We demonstrate that RIOK3 loss of function blocks 40S degradation triggered by either 60S biogenesis disruption or amino acid starvation despite elevated uS3 and uS5 ubiquitylation. These findings suggest that RIOK3 abundance, and not ribosome ubiquitylation, limits 40S decay capacity. Collectively, these results establish a feed-forward mechanism that regulates iRQC capacity and subsequent 40S decay.
2025-02-07 | PXD060349 | Pride
Project description:Ribosome-associated quality control (RQC) pathways target ribosomes whose progression becomes impaired during various phases of the translation cycle. Ribosome ubiquitylation is a key RQC licensing step. Previous studies identified an initiation specific RQC branch (iRQC) that is activated when translation initiation complexes fail to transition to elongation competent 80S ribosomes. Upon iRQC activation, RNF10 ubiquitylates the 40S proteins uS3 and uS5 which leads to 40S decay. How iRQC is activated in the absence of pharmacological translation inhibitors and what mechanisms govern iRQC capacity and activity remain unanswered questions. Here, we demonstrate that altering ribosome subunit stoichiometry by broadly disrupting 60S biogenesis triggers RNF10-dependent uS3 and uS5 ubiquitylation and 40S decay. Reducing the levels of the critical scanning helicase, eIF4A1, impairs ribosomal protein ubiquitylation and subsequent degradation, indicating that actively scanning translation initiation complexes are required for 40S decay. We show that RNF10 protein abundance increases upon iRQC pathway stimulation through a translational activation mechanism using conserved upstream open reading frames. Amino acid starvation conditions also stimulate 40S decay leading to ribosomal subunit imbalance. We identify RIOK3 as a new and critical iRQC factor that interacts with ubiquitylated 40S subunits to mediate 40S decay. We demonstrate that RIOK3 loss of function blocks 40S degradation triggered by either 60S biogenesis disruption or amino acid starvation despite elevated uS3 and uS5 ubiquitylation. These findings suggest that RIOK3 abundance, and not ribosome ubiquitylation, limits 40S decay capacity. Collectively, these results establish a feed-forward mechanism that regulates iRQC capacity and subsequent 40S decay.
2025-02-07 | PXD060296 | Pride
Project description:Ribosome-associated quality control (RQC) pathways target ribosomes whose progression becomes impaired during various phases of the translation cycle. Ribosome ubiquitylation is a key RQC licensing step. Previous studies identified an initiation specific RQC branch (iRQC) that is activated when translation initiation complexes fail to transition to elongation competent 80S ribosomes. Upon iRQC activation, RNF10 ubiquitylates the 40S proteins uS3 and uS5 which leads to 40S decay. How iRQC is activated in the absence of pharmacological translation inhibitors and what mechanisms govern iRQC capacity and activity remain unanswered questions. Here, we demonstrate that altering ribosome subunit stoichiometry by broadly disrupting 60S biogenesis triggers RNF10-dependent uS3 and uS5 ubiquitylation and 40S decay. Reducing the levels of the critical scanning helicase, eIF4A1, impairs ribosomal protein ubiquitylation and subsequent degradation, indicating that actively scanning translation initiation complexes are required for 40S decay. We show that RNF10 protein abundance increases upon iRQC pathway stimulation through a translational activation mechanism using conserved upstream open reading frames. Amino acid starvation conditions also stimulate 40S decay leading to ribosomal subunit imbalance. We identify RIOK3 as a new and critical iRQC factor that interacts with ubiquitylated 40S subunits to mediate 40S decay. We demonstrate that RIOK3 loss of function blocks 40S degradation triggered by either 60S biogenesis disruption or amino acid starvation despite elevated uS3 and uS5 ubiquitylation. These findings suggest that RIOK3 abundance, and not ribosome ubiquitylation, limits 40S decay capacity. Collectively, these results establish a feed-forward mechanism that regulates iRQC capacity and subsequent 40S decay.
2025-02-07 | PXD060301 | Pride