An evolutionarily conserved ribosome-rescue pathway maintains epidermal homeostasis
Ontology highlight
ABSTRACT:
ORGANISM(S): Mus musculus
PROVIDER: GSE106246 | GEO | 2018/03/01
REPOSITORIES: GEO
Similar Datasets
Project description:mRNA quality control mechanisms ensure fidelity of protein translation. An evolutionarily conserved component of the quality control machinery, Dom34/Pelota (Pelo), rescues stalled ribosomes. Here we show that Pelo is required for mammalian epidermal homeostasis. Conditional deletion in murine epidermal stem cells expressing Lrig1 results in hyperproliferation and abnormal differentiation, whereas deletion in other stem cells does not. Loss of Pelo results in truncated ribosome footprints and global upregulation of translation. Translational inhibition by rapamycin-mediated down regulation of mTOR rescues the epidermal phenotype. Our study reveals a novel role for the ribosome-rescue machinery in mammalian tissue homeostasis and an unanticipated specificity in its impact on different stem cell populations.
2017-02-02 | GSE94385 | GEO
Project description:Ribosome stalling at problematic sequences in mRNAs leads to collisions that trigger a collection of quality control events including ribosome rescue, targeting the nascent polypeptide for decay (Ribosome-mediated Quality Control or RQC), and targeting of the mRNA for decay (No Go Decay or NGD). Using a reverse genetic screen in yeast, we identify Cue2 as the endonuclease that is recruited to stalled ribosomes to promote NGD. Following Cue2-mediated cleavage, ribosomes upstream of the cleavage site translate to the end of the truncated mRNA and are rescued by the Dom34:Hbs1 complex. We also show that the putative helicase Slh1 (part of the RQC Trigger or RQT complex) removes collided ribosomes behind the lead stalled ribosome and thereby reduces endonucleolytic cleavage by Cue2. The synergistic activities of Cue2 and Slh1 define two parallel pathways that allow cells to recognize and respond to ribosomes trapped on problematic mRNAs.
2019-06-25 | GSE129128 | GEO
Project description:Ribosomes that stall before completing peptide synthesis must be recycled and returned to the cytoplasmic pool. The protein Dom34 and cofactors Hbs1 and Rli1 can dissociate stalled ribosomes in vitro, but the identity of targets in the cell is unknown. Here we use ribosome profiling methodology to reveal a high- resolution molecular characterization of Dom34 function in vivo. We show that Dom34 removes stalled ribosomes from mRNAs that are truncated but, in contrast, does not generally dissociate ribosomes on coding sequences known to trigger stalling, such as polyproline. We also show that Dom34 targets arrested ribosomes near the ends of 3 ? UTRs. These ribosomes appear to gain access to the 3 ? UTR via a mechanism that does not require decoding of the mRNA. These results suggest that Dom34 carries out the important task of rescuing ribosomes found in noncoding regions. 25 samples are included in the study (2 mRNA-Seq samples and 23 ribosome footprint profiling samples). These include wild-type and dom34 or hbs1 knockout strains that were created in a variety of genetic backgrounds, treated with various agents in cell culture (e.g. diamide, 3-AT, or glucose starvation), treated differently during cell lysis (use of cycloheximide vs. other ribosome-stabilizing agents), or prepared in different ways after cell lysis (e.g. retention of short vs. long monosome-protected footprints or disome footprints).
2013-12-19 | E-GEOD-52968 | biostudies-arrayexpress
Project description:Ribosomes that stall before completing peptide synthesis must be recycled and returned to the cytoplasmic pool. The protein Dom34 and cofactors Hbs1 and Rli1 can dissociate stalled ribosomes in vitro, but the identity of targets in the cell is unknown. Here we use ribosome profiling methodology to reveal a high- resolution molecular characterization of Dom34 function in vivo. We show that Dom34 removes stalled ribosomes from mRNAs that are truncated but, in contrast, does not generally dissociate ribosomes on coding sequences known to trigger stalling, such as polyproline. We also show that Dom34 targets arrested ribosomes near the ends of 3 ́ UTRs. These ribosomes appear to gain access to the 3 ́ UTR via a mechanism that does not require decoding of the mRNA. These results suggest that Dom34 carries out the important task of rescuing ribosomes found in noncoding regions.
2013-12-19 | GSE52968 | GEO
Project description:Translation of poly(A) tails leads to mRNA cleavage but the mechanism and global pervasiveness of this “nonstop/no-go” decay process is not understood. Here we performed ribosome profiling of short 15-18 nt mRNA footprints to identify ribosomes stalled at 3’ ends of mRNA decay intermediates. We found mRNA cleavage extending hundreds of nucleotides upstream of ribosome stalling in poly(A) and predominantly in one reading frame. These observations suggest that cleavage is closely associated with the ribosome. Surprisingly, ribosomes appeared to stall when as few as 3 consecutive ORF-internal lysine codons were positioned in the A, P, and E sites though significant mRNA degradation was not observed. Endonucleolytic cleavage was widespread, however, at sites of premature polyadenylation and rescue of the ribosomes stalled at these sites was dependent on Dom34. These results suggest this process may be critical when changes in polyadenylation occur during development, tumorigenesis, or when translation termination/recycling is impaired.
2017-01-22 | GSE85944 | GEO
Project description:Translation initiation at alternative start sites can dynamically control the synthesis of two or more functionally distinct protein isoforms from a single mRNA. Alternate isoforms of the hematopoietic transcription factor C/EBPα produced from different start sites exert opposing effects during myeloid cell development. This alternative initiation depends on sequence features of the CEBPA transcript, including a regulatory upstream open reading frame (uORF), but the molecular basis is not fully understood. Here we identify trans-acting factors that affect C/EBPα isoform choice using a sensitive and quantitative two-color fluorescence reporter coupled with CRISPRi screening. Our screen uncovered a role for the ribosome rescue factor PELOTA (PELO) in promoting expression of the longer C/EBPα isoform, by directly removing inhibitory unrecycled ribosomes and through indirect effects mediated by the mechanistic target of rapamycin (mTOR) kinase. Our work provides further mechanistic insights into coupling between ribosome recycling and translation reinitiation in regulation of a key transcription factor, with implications for normal hematopoiesis and leukemiagenesis.
2023-03-08 | GSE226436 | GEO
Project description:Translation initiation at alternative start sites can dynamically control the synthesis of two or more functionally distinct protein isoforms from a single mRNA. Alternate isoforms of the hematopoietic transcription factor C/EBPα produced from different start sites exert opposing effects during myeloid cell development. This alternative initiation depends on sequence features of the CEBPA transcript, including a regulatory upstream open reading frame (uORF), but the molecular basis is not fully understood. Here we identify trans-acting factors that affect C/EBPα isoform choice using a sensitive and quantitative two-color fluorescence reporter coupled with CRISPRi screening. Our screen uncovered a role for the ribosome rescue factor PELOTA (PELO) in promoting expression of the longer C/EBPα isoform, by directly removing inhibitory unrecycled ribosomes and through indirect effects mediated by the mechanistic target of rapamycin (mTOR) kinase. Our work provides further mechanistic insights into coupling between ribosome recycling and translation reinitiation in regulation of a key transcription factor, with implications for normal hematopoiesis and leukemiagenesis.
2023-03-08 | GSE226435 | GEO
Project description:Translation-dependent quality control pathways govern protein synthesis and proteostasis by degrading potentially toxic peptide products derived from aberrant mRNAs. However, little is known about the in vivo defects that arise in the absence of these pathways and how translation is altered in the absence of these pathways. Here, we demonstrate that the ribosome rescue factors Pelo/Hbs1l are both critical for embryonic and neuronal development but dispensable for neuronal survival in the adult brain. Loss of Pelo/Hbs1l in cerebellar progenitors impaired differentiation of these cells. Our analysis of Pelo/Hbs1l deficient fibroblasts revealed translational reprogramming of multiple pathways including mTORC1 signaling likely to restore cellular homeostasis. Interestingly, similar affects on the translatome, signaling pathways and neurogenesis were observed when we conditionally deleted Upf2 to inhibit NMD. These data reveal that translation-dependent quality control pathways, which set out to mitigate errors in translation and to clear defective peptide products and aberrant mRNAs can trigger similar cellular responses and neurodevelopmental abnormalities.
2021-03-15 | GSE162556 | GEO
Project description:Hbs1 has been established as a central component of the cell’s translational quality control pathways in both yeast and prokaryotic models; however, the functional characteristics of its human ortholog (Hbs1L) have not been well-defined. We recently reported a novel human phenotype resulting from a mutation in the critical coding region of the HBS1L gene characterized by facial dysmorphism, severe growth restriction, axial hypotonia, global developmental delay and retinal pigmentary deposits. Here we further characterize downstream effects of the human HBS1L mutation. HBS1L has three transcripts in humans, and RT-PCR demonstrated reduced mRNA levels corresponding with transcripts V1 and V2 whereas V3 expression was unchanged. Western blot analyses revealed HBS1L protein was absent in proband samples. Additionally, polysome profiling revealed an abnormal aggregation of 80S monosomes in patient cells under baseline conditions. RNASeq data corresponded to the patient phenotype, with biological process analysis showing skeletal system development and sensory development genes being most altered between patient and controls. Ribosomal sequencing demonstrated an increased translation efficiency of ribosomal RNA in Hbs1L-deficient fibroblasts, suggesting that there may be a compensatory increase in ribosome translation to accommodate the increased 80S monosome peak. Furthermore, lack of Hbs1L caused depletion of Pelota protein in both patient cells and mouse tissues, while PELO mRNA levels were unaffected. Inhibition of proteasomal function partially restored Pelota expression in human Hbs1L-deficient cells. We also describe a mouse model harboring a knockdown mutation in the murine Hbs1l gene that shared several of the phenotypic elements observed in the Hbs1L-deficient human including facial dysmorphism, growth restriction and retinal deposits. The Hbs1lKO mice similarly demonstrate diminished Pelota levels that were rescued by proteasome inhibition.
2019-01-15 | GSE123564 | GEO
Project description:An evolutionarily conserved ribosome-rescue pathway maintains epidermal homeostasis
| PRJNA415988 | ENA