The Ski complex binds 80S ribosomes for 3’ to 5’ decay of mRNA
Ontology highlight
ABSTRACT:
ORGANISM(S): Saccharomyces cerevisiae BY4741
PROVIDER: GSE70259 | GEO | 2017/02/10
SECONDARY ACCESSION(S): PRJNA288089
REPOSITORIES: GEO
Similar Datasets
Project description:Translation-dependent mRNA quality control systems protect the protein homeostasis of eukaryotic cells by eliminating aberrant transcripts and stimulating the decay of their protein products. Although these systems are intensively studied in animals, little is known about the translation-dependent quality control systems in plants. Here we characterize the mechanism of nonstop decay (NSD) system in Nicotiana benthamiana model plant. We show that plant NSD efficiently degrades nonstop mRNAs, which can be generated by premature polyadenylation, and stop codon-less transcripts, which can be produced by endonucleolytic cleavage. We demonstrate that in plants, like in animals, Pelota, Hbs1 and SKI2 proteins are required for NSD, supporting that NSD is an ancient and conserved eukaryotic quality control system. Relevantly, we found that NSD and RNA silencing systems cooperate in plants. Plant silencing predominantly represses target mRNAs through endonucleolytic cleavage in the coding region. The cleavage products are degraded by general decay systems or subjected to silencing amplification. The balance between decay and silencing amplification might be finely regulated by unknown mechanisms. Here we show that NSD is required for the elimination of 5’cleavage product when mi- or siRNA-guided silencing complex cleaves in the coding region. Thus NSD might regulate the frequency of silencing amplification.
2018-07-01 | GSE99805 | 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:Post-transcriptional gene silence (PTGS) is employed in plants to shut down transgenes, invading viral genes and a certain group of endogenous genes. Meanwhile, it is not clear how the risk of expansive PTGS from endogenous genes featured by transitive siRNA production is minimized. Here we demonstrate two essential components of the SKI complex in cytoplasmic 3 -5 mRNA decay pathway, SKI2 and SKI3, function as negative regulators of transgene PTGS in Arabidopsis. The ski2 mutants manifested severe synthetic phenotypes with a 5 -3 exoribonuclease mutant, ein5, which were substantially suppressed by the PTGS mutants, rdr6 and ago1. RDR6 is essential for the altered gene expression in ein5 ski2 on a transcriptome-wide scale. mRNA-seq approach was used to investigate the physiological relevance veiled by the myriad developmental phenotypes in Col-0 (C), ein5-1 (e), ski2-3 (s), ein5-1 ski2-3 (es), rdr6-11 (r) and rdr6-11 ein5-1 ski2-3 (res). A number of endogenous genes, including many miRNA target genes, manifest transitive 21-22 nt siRNA production and compromised gene expression in ein5 ski2 in an RDR6-dependent manner. Taken together, our study brings to light a dual-safeguard system in preventing the expansive siRNA production by the 5 -3 and 3 -5 cytoplasmic mRNA decay pathways. In this experiment, we did three replicates in sequencing that help increase the power in identify the differentially represented genes.The sequencing depth was also increased. Therefore we identified more siRNA-generating loci than that in previous study (GSE52408) (441 vs. 200 loci). Examination of small RNA profiles in 4 genotypes with 3 biological replicates each.
2015-04-13 | E-GEOD-57936 | biostudies-arrayexpress
Project description:Post-transcriptional gene silence (PTGS) is employed in plants to shut down transgenes, invading viral genes and a certain group of endogenous genes. Meanwhile, it is not clear how the risk of expansive PTGS from endogenous genes featured by transitive siRNA production is minimized. Here we demonstrate two essential components of the SKI complex in cytoplasmic 3’-5’ mRNA decay pathway, SKI2 and SKI3, function as negative regulators of transgene PTGS in Arabidopsis. The ski2 mutants manifested severe synthetic phenotypes with a 5’-3’ exoribonuclease mutant, ein5, which were substantially suppressed by the PTGS mutants, rdr6 and ago1. RDR6 is essential for the altered gene expression in ein5 ski2 on a transcriptome-wide scale. mRNA-seq approach was used to investigate the physiological relevance veiled by the myriad developmental phenotypes in Col-0 (C), ein5-1 (e), ski2-3 (s), ein5-1 ski2-3 (es), rdr6-11 (r) and rdr6-11 ein5-1 ski2-3 (res). A number of endogenous genes, including many miRNA target genes, manifest transitive 21-22 nt siRNA production and compromised gene expression in ein5 ski2 in an RDR6-dependent manner. Taken together, our study brings to light a dual-safeguard system in preventing the expansive siRNA production by the 5’-3’ and 3’-5’ cytoplasmic mRNA decay pathways.
2016-11-15 | GSE52408 | GEO
Project description:Post-transcriptional gene silence (PTGS) is employed in plants to shut down transgenes, invading viral genes and a certain group of endogenous genes. Meanwhile, it is not clear how the risk of expansive PTGS from endogenous genes featured by transitive siRNA production is minimized. Here we demonstrate two essential components of the SKI complex in cytoplasmic 3’-5’ mRNA decay pathway, SKI2 and SKI3, function as negative regulators of transgene PTGS in Arabidopsis. The ski2 mutants manifested severe synthetic phenotypes with a 5’-3’ exoribonuclease mutant, ein5, which were substantially suppressed by the PTGS mutants, rdr6 and ago1. RDR6 is essential for the altered gene expression in ein5 ski2 on a transcriptome-wide scale. mRNA-seq approach was used to investigate the physiological relevance veiled by the myriad developmental phenotypes in Col-0 (C), ein5-1 (e), ski2-3 (s), ein5-1 ski2-3 (es), rdr6-11 (r) and rdr6-11 ein5-1 ski2-3 (res). Compared with Col-0, 4394 genes exhibited differential expression in ein5-1 ski2-3, much more than those in the ein5-1 (1138 genes) or ski2-3 (1040 genes) single mutant (2-fold cutoff, p < 0.01, FDR < 0.05), suggesting a largely disturbed transcriptome in the absence of both EIN5 and SKI2. While a small overlap was found between the differentially expressed genes in e/C and s/C comparisons, the gene lists from es/C, es/e and es/s comparisons (2-fold cutoff, p < 0.01, FDR < 0.05) largely overlapped with each other, indicating a collaborative function of EIN5 and SKI2 on a transcriptome-wide scale. The 1670 genes overlapped in the es/C, es/e and es/s comparisons included 1306 upregulated genes and 360 downregulated genes with only 4 genes as exception. 994 of the 1306 upregulated genes (76.1%) and 273 of the 360 downregulated genes (75.8%) were differentially expressed in the es/res comparison like that in es/C, es/e and es/s, indicating a substantial supression of the redundant function of EIN5 and SKI2 by RDR6. Taken together, our study brings to light a dual-safeguard system in preventing the expansive siRNA production by the 5’-3’ and 3’-5’ cytoplasmic mRNA decay pathways. Examination of transcriptomes in 6 genotypes.
2015-04-13 | E-GEOD-52407 | biostudies-arrayexpress
Project description:Post-transcriptional gene silence (PTGS) is employed in plants to shut down transgenes, invading viral genes and a certain group of endogenous genes. Meanwhile, it is not clear how the risk of expansive PTGS from endogenous genes featured by transitive siRNA production is minimized. Here we demonstrate two essential components of the SKI complex in cytoplasmic 3 -5 mRNA decay pathway, SKI2 and SKI3, function as negative regulators of transgene PTGS in Arabidopsis. The ski2 mutants manifested severe synthetic phenotypes with a 5 -3 exoribonuclease mutant, ein5, which were substantially suppressed by the PTGS mutants, rdr6 and ago1. RDR6 is essential for the altered gene expression in ein5 ski2 on a transcriptome-wide scale. mRNA-seq approach was used to investigate the physiological relevance veiled by the myriad developmental phenotypes in Col-0 (C), ein5-1 (e), ski2-3 (s), ein5-1 ski2-3 (es), rdr6-11 (r) and rdr6-11 ein5-1 ski2-3 (res). A number of endogenous genes, including many miRNA target genes, manifest transitive 21-22 nt siRNA production and compromised gene expression in ein5 ski2 in an RDR6-dependent manner. Taken together, our study brings to light a dual-safeguard system in preventing the expansive siRNA production by the 5 -3 and 3 -5 cytoplasmic mRNA decay pathways. In this experiment, we did three replicates in sequencing that help increase the power in identify the differentially represented genes.The sequencing depth was also increased. Therefore we identified more siRNA-generating loci than that in previous study (GSE52408) (441 vs. 200 loci).
2015-04-13 | GSE57936 | GEO
Project description:Post-transcriptional gene silence (PTGS) is employed in plants to shut down transgenes, invading viral genes and a certain group of endogenous genes. Meanwhile, it is not clear how the risk of expansive PTGS from endogenous genes featured by transitive siRNA production is minimized. Here we demonstrate two essential components of the SKI complex in cytoplasmic 3’-5’ mRNA decay pathway, SKI2 and SKI3, function as negative regulators of transgene PTGS in Arabidopsis. The ski2 mutants manifested severe synthetic phenotypes with a 5’-3’ exoribonuclease mutant, ein5, which were substantially suppressed by the PTGS mutants, rdr6 and ago1. RDR6 is essential for the altered gene expression in ein5 ski2 on a transcriptome-wide scale. mRNA-seq approach was used to investigate the physiological relevance veiled by the myriad developmental phenotypes in Col-0 (C), ein5-1 (e), ski2-3 (s), ein5-1 ski2-3 (es), rdr6-11 (r) and rdr6-11 ein5-1 ski2-3 (res). Compared with Col-0, 4394 genes exhibited differential expression in ein5-1 ski2-3, much more than those in the ein5-1 (1138 genes) or ski2-3 (1040 genes) single mutant (2-fold cutoff, p < 0.01, FDR < 0.05), suggesting a largely disturbed transcriptome in the absence of both EIN5 and SKI2. While a small overlap was found between the differentially expressed genes in e/C and s/C comparisons, the gene lists from es/C, es/e and es/s comparisons (2-fold cutoff, p < 0.01, FDR < 0.05) largely overlapped with each other, indicating a collaborative function of EIN5 and SKI2 on a transcriptome-wide scale. The 1670 genes overlapped in the es/C, es/e and es/s comparisons included 1306 upregulated genes and 360 downregulated genes with only 4 genes as exception. 994 of the 1306 upregulated genes (76.1%) and 273 of the 360 downregulated genes (75.8%) were differentially expressed in the es/res comparison like that in es/C, es/e and es/s, indicating a substantial supression of the redundant function of EIN5 and SKI2 by RDR6. Taken together, our study brings to light a dual-safeguard system in preventing the expansive siRNA production by the 5’-3’ and 3’-5’ cytoplasmic mRNA decay pathways.
2015-04-13 | GSE52407 | 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 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:Microtubules play crucial roles in cellular architecture, intracellular transport, and mitosis. The availability of free tubulin subunits impacts polymerization dynamics and microtubule function. When cells sense excess free tubulin, they trigger degradation of the encoding mRNAs, which requires recognition of the nascent polypeptide by the tubulin-specific ribosome-binding factor TTC5. How TTC5 initiates decay of tubulin mRNAs is unknown. Here, our biochemical and structural analysis reveals that TTC5 recruits the poorly studied protein SCAPER to the ribosome. SCAPER in turn engages the CCR4-NOT deadenylase complex through its CNOT11 subunit to trigger tubulin mRNA decay. SCAPER mutants that cause intellectual disability and retinitis pigmentosa in humans are impaired in CCR4-NOT recruitment, tubulin mRNA degradation, and microtubule-dependent chromosome segregation. Our findings demonstrate how recognition of a nascent polypeptide on the ribosome is physically linked to mRNA decay factors via a relay of protein-protein interactions, providing a paradigm for specificity in cytoplasmic gene regulation.
2023-07-03 | PXD041096 | Pride