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ABSTRACT:
PROVIDER: PRJEB27297 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Cytoplasmic degradation of eukaryotic mRNAs in 3’ to 5’ direction is catalyzed by the exosome complex together with the Ski complex and, in the yeast Saccharomyces cerevisiae, the Ski7 protein. This exosome-Ski-system also degrades ribosome-associated aberrant mRNAs lacking a stop codon, a pathway called non-stop-mRNA decay (NSD). However, the interplay between the Ski components and the ribosome is unknown. Here, we report that the Ski complex can associate with ribosomes in vitro and in vivo independently of Ski7. Ribosome profiling suggests that this association is important for NSD but also for general mRNA turnover. A cryo-electron microscopy structure reveals that the Ski complex binds near the mRNA entry site of the 40S subunit, facilitating the threading of the mRNA into the Ski2 helicase. Collectively, these results demonstrate an unanticipated role for the Ski complex in mRNA decay of ribosome-associated mRNAs, mediated by a direct interaction with the translation machinery.
2017-02-10 | GSE70259 | GEO
Project description:A multi-subunit exosome complex is a major eukaryotic exoribonuclease that in the cytoplasm requires the SKI complex for activity. In yeast, SKI forms a heterotetramer and delivers RNA substrates directly into the exosome channel. Such cooperation requires Ski7 protein, which links the exosome and SKI complexes. However, since the human genome does not encode an orthologue of the yeast Ski7, the factor mediating SKI and exosome linkage in human cells is unknown. Proteomic analysis revealed that the human cytoplasmic exosome interacts with HBS1LV3, a protein encoded by a newly discovered short splicing isoform of HBS1L. HBS1LV3 recruits the SKI complex to the exosome. In contrast, the canonical HBS1L variant, HBS1LV1, acting as a ribosome dissociation factor, does not associate with the exosome and instead interacts with the mRNA surveillance factor PELOTA. HBS1LV3 contains a new domain of unknown structure with the short linear motif RxxxFxxxL, which is responsible for exosome binding, and may interact with the exosome core subunit RRP43 in way that resembles the association between Rrp6 RNase and Rrp43 in yeast. Depletion of HBS1LV3 and the SKI complex helicase SKI2W similarly affected the transcriptome by strongly upregulating a large number of genes. Moreover, following HBS1LV3 or SKI2W depletion the half-lives of representative upregulated mRNAs were increased, thus supporting the involvement of HBS1LV3 and SKI2W in the same mRNA degradation pathway. In contrast, HBS1LV1 depletion had little effect on transcriptome homeostasis. Our data indicate that human HBS1LV3 is the long-sought factor that links the exosome and SKI complexes to regulate cytoplasmic mRNA decay.
2017-02-15 | GSE77926 | GEO
Project description:Super killer (SKI) complex is a well-known cytoplasmic 3′ to 5′ mRNA decay complex that functions with the exosome to degrade excessive and aberrant mRNAs. Recently, SKIV2L, the 3′ to 5′ RNA helicase of the human SKI (hSKI) complex has been implicated with the extraction of mRNA at stalled ribosomes, tackling aberrant translation. Here, we show that SKIV2L and TTC37 of the hSKI complex are present within the nucleus, localise on chromatin and at some telomeres during the G2 cell cycle phase. In cells, SKIV2L prevents telomere replication stress shown as fragile telomeres and increases the stability of telomere DNA-RNA hybrids in G2 of the cell cycle whereas its absence decreases the amount of those structures. We further demonstrate that purified hSKI complex binds telomeric DNA and RNA substrates in vitro. Moreover, SKIV2L association with telomeres is dependent on DNA-RNA hybrids but its helicase activity is dispensable for its telomeric function. Taken together, our results provide a nuclear function for SKIV2L of the hSKI complex in overcoming replication stress at telomeres mediated by its recruitment to DNA-RNA hybrid structures in G2 and thus maintaining telomere stability.
2024-10-03 | PXD046955 | Pride
Project description:The RNA exosome is a key 3’-5’ exoribonuclease with evolutionary conserved structure and roles. Its cytosolic functions require the co-factors SKI7 and the Ski complex. Here we demonstrate by co-purification experiments that the ARM repeat protein RESURRECTION1 (RST1) and RST1 INTERACTING PROTEIN (RIPR) connect the cytosolic Arabidopsis RNA exosome to the Ski complex. rst1 and ripr mutants accumulate small RNAs many of which are quality control siRNAs (rqc-siRNAs) produced by the postranscriptional gene silencing (PTGS) machinery when mRNA degradation is compromised. Indeed, quasi identical small RNA populations are observed in mutants lacking the RRP45B/CER7 subunit of the core exosome. This biochemical and genetic evidence supports a physical and functional link between RST1, RIPR and the RNA exosome. Our data reveal the existence of additional cytosolic exosome co-factors besides the known SKI subunits. Interestingly, RST1 is not restricted to plants, as homologues with a similar domain architecture exist in animals, including humans.
2019-07-17 | PXD013435 | Pride
Project description:NAC (nascent polypeptide-associated complex) post-meiotic heterodimeric αβ-complex promoting chaperone-like cotranslational protein folding on the ribosome and its early role in the birth of nascent proteins is suggested. Here, we demonstrate the presence of specific NAC complex (NACtes) associated with ribosomes in spermatocytes. The RNAseq analysis of mRNAs associated with testis-specific and immunoprecipitated NACtes-carrying ribosomes revealed a preferential association of the latter with mRNAs encoding meiotic and post meiotic proteins. The NACtes ribosomes are also shown to be enriched in mRNAs encoding proteins of central metabolism pathways that have been reported as overexpressed in testes. The specificity of association of NACtes ribosomes with particular mRNA sets was also demonstrated by the observation of significant underrepresentation of abundant mRNAs encoding ubiquitously expressed ribosomal proteins in NACtes-associated ribosomes. At the same time, NACtes ribosomes are enriched in mRNA encoding a testis specific ribosomal protein. These results bring new arguments in favor of “specialized ribosomes hypothesis” proposing a special composition of ribosomes necessary for the control of selected gene expression.
2017-10-12 | GSE101060 | GEO
Project description:GMUCT 2.0 data were analyzed to globally identify 5’ ends differentially accumulated in SKI3 RNAi roots as compared with GUS RNAi, as well as those that change in abundance in response to rhizobia SUPERKILLER3 (*SKI3),* a member of SKI complex that guides RNAs to the 3 to 5' exoribonuclease of the exosome complex. In the absence of a functional SKI complex to thread transcripts to the exosome, the bulk of the mRNAs that accumulate in the cytoplasm are diverted to the 5 -to-3 XRN4 pathway for degradation. We explored the function of *SKI3* during root nodule symbiosis using RNA interference to knockdown *SKI3* in *M. truncatula* hairy roots. To evaluate whether silencing of *SKI3* in *M. truncatula* roots altered RNA decay in response to rhizobia, we performed genome-wide mapping of uncapped and cleaved transcripts (GMUCT 2.0) on *GUS* RNA and *SKI3*RNAi roots. This method identifies products of miRNA or siRNA guided-endonucleolytic cleavage as well as decapped mRNAs by selecting for molecules with a free 5 monophosphate (5 P) (Willmann et al., 2014). GMUCT 2.0 data were analyzed to globally identify 5' ends differentially accumulated in *SKI3* RNAi roots as compared with *GUS* RNAi, as well as those that change in abundance in response to rhizobia.
2022-10-01 | GSE135920 | GEO
Project description:The Ski complex binds 80S ribosomes for 3’ to 5’ decay of mRNA
| PRJNA288089 | ENA
Project description:A short splicing isoform of HBS1L links the cytoplasmic exosome and SKI complexes in humans
| PRJNA312116 | ENA
Project description:Formaldehyde (FA) is a commercially important chemical with numerous and diverse uses. In this study, a functional toxicogenomics approach was utilized in the model eukaryotic yeast Saccharomyces cerevisiae to identify genes and cellular processes modulating the cellular toxicity of FA. Our results demonstrate mutant strains deficient in multiple DNA repair pathways were sensitive to FA. The SKI complex and its associated factors, which regulate mRNA degradation by the exosome, were also required for FA tolerance..
2016-11-09 | GSE83398 | GEO