scholarly journals Reconstitution of the Human Nuclear RNA Exosome

2019 ◽  
pp. 467-489
Author(s):  
Kurt Januszyk ◽  
Eva-Maria Weick ◽  
Christopher D. Lima
Keyword(s):  
Nuclear Rna ◽  
Rna Exosome

scholarly journals Nuclear RNA Exosome and Pervasive Transcription: Dual Sculptors of Genome Function

2021 ◽  
Vol 22 (24) ◽  
pp. 13401
Author(s):  
Koichi Ogami ◽  
Hiroshi I. Suzuki
Keyword(s):  
Mammalian Cells ◽  
Rna Surveillance ◽  
Cellular Processes ◽  
Small Nuclear Rnas ◽  
Nuclear Rna ◽  
Rna Exosome ◽  
Nucleolar Rnas ◽  
Exosome Complex ◽  
Pervasive Transcription ◽  
Layer Control

The genome is pervasively transcribed across various species, yielding numerous non-coding RNAs. As a counterbalance for pervasive transcription, various organisms have a nuclear RNA exosome complex, whose structure is well conserved between yeast and mammalian cells. The RNA exosome not only regulates the processing of stable RNA species, such as rRNAs, tRNAs, small nucleolar RNAs, and small nuclear RNAs, but also plays a central role in RNA surveillance by degrading many unstable RNAs and misprocessed pre-mRNAs. In addition, associated cofactors of RNA exosome direct the exosome to distinct classes of RNA substrates, suggesting divergent and/or multi-layer control of RNA quality in the cell. While the RNA exosome is essential for cell viability and influences various cellular processes, mutations and alterations in the RNA exosome components are linked to the collection of rare diseases and various diseases including cancer, respectively. The present review summarizes the relationships between pervasive transcription and RNA exosome, including evolutionary crosstalk, mechanisms of RNA exosome-mediated RNA surveillance, and physiopathological effects of perturbation of RNA exosome.

scholarly journals Substrate Specificity of the TRAMP Nuclear Surveillance Complexes

2020 ◽  
Author(s):  
Clémentine Delan-Forino ◽  
Christos Spanos ◽  
Juri Rappsilber ◽  
David Tollervey
Keyword(s):  
Gene Expression ◽  
Mass Spectrometry ◽  
Binding Sites ◽  
Rna Binding ◽  
Rna Binding Proteins ◽  
Rna Binding Protein ◽  
Rna Helicase ◽  
Nuclear Rna ◽  
Rna Exosome

ABSTRACTDuring nuclear surveillance in yeast, the RNA exosome functions together with the TRAMP complexes. These include the DEAH-box RNA helicase Mtr4 together with an RNA-binding protein (Air1 or Air2) and a poly(A) polymerase (Trf4 or Trf5). To better determine how RNA substrates are targeted, we analyzed protein and RNA interactions for TRAMP components. Mass spectrometry identified three distinct TRAMP complexes formed in vivo. These complexes preferentially assemble on different classes of transcripts. Unexpectedly, on many substrates, including pre-rRNAs and pre-mRNAs, binding specificity was apparently conferred by Trf4 and Trf5. Clustering of mRNAs by TRAMP association showed co-enrichment for mRNAs with functionally related products, supporting the significance of surveillance in regulating gene expression. We compared binding sites of TRAMP components with multiple nuclear RNA binding proteins, revealing preferential colocalization of subsets of factors. TRF5 deletion reduced Mtr4 recruitment and increased RNA abundance for mRNAs specifically showing high Trf5 binding.

scholarly journals Substrate discrimination and quality control require each catalytic activity of TRAMP and the nuclear RNA exosome

2021 ◽  
Vol 118 (14) ◽  
pp. e2024846118
Author(s):  
Mom Das ◽  
Dimitrios Zattas ◽  
John C. Zinder ◽  
Elizabeth V. Wasmuth ◽  
Julien Henri ◽  
...  
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Quality Control ◽  
Catalytic Activity ◽  
Rna Quality ◽  
Data Support ◽  
Nuclear Rna ◽  
Rna Quality Control ◽  
Tramp Complex ◽  
Rna Exosome ◽  
Substrate Discrimination

Quality control requires discrimination between functional and aberrant species to selectively target aberrant substrates for destruction. Nuclear RNA quality control in Saccharomyces cerevisiae includes the TRAMP complex that marks RNA for decay via polyadenylation followed by helicase-dependent 3′ to 5′ degradation by the RNA exosome. Using reconstitution biochemistry, we show that polyadenylation and helicase activities of TRAMP cooperate with processive and distributive exoribonuclease activities of the nuclear RNA exosome to protect stable RNA from degradation while selectively targeting and degrading less stable RNA. Substrate discrimination is lost when the distributive exoribonuclease activity of Rrp6 is inactivated, leading to degradation of stable and unstable RNA species. These data support a proofreading mechanism in which deadenylation by Rrp6 competes with Mtr4-dependent degradation to protect stable RNA while selectively targeting and degrading unstable RNA.

scholarly journals The splicing factor SRSF3 is functionally connected to the nuclear RNA exosome for intronless mRNA decay

2018 ◽  
Vol 8 (1) ◽  
Author(s):  
Fabrice Mure ◽  
Antoine Corbin ◽  
Nour El Houda Benbahouche ◽  
Edouard Bertrand ◽  
Evelyne Manet ◽  
...  
Keyword(s):  
Mrna Decay ◽  
Splicing Factor ◽  
Nuclear Rna ◽  
Rna Exosome

scholarly journals Arabidopsis SMN2/HEN2, Encoding DEAD-Box RNA Helicase, Governs Proper Expression of the Resistance Gene SMN1/RPS6 and Is Involved in Dwarf, Autoimmune Phenotypes of mekk1 and mpk4 Mutants

2020 ◽  
Vol 61 (8) ◽  
pp. 1507-1516
Author(s):  
Momoko Takagi ◽  
Naoki Iwamoto ◽  
Yuta Kubo ◽  
Takayuki Morimoto ◽  
Hiroki Takagi ◽  
...  
Keyword(s):  
Pseudomonas Syringae ◽  
Rna Helicase ◽  
Mitogen Activated Protein Kinase ◽  
Proper Function ◽  
Positive Contribution ◽  
Defense Genes ◽  
Basal Resistance ◽  
Dead Box ◽  
Nuclear Rna ◽  
Rna Exosome

Abstract In Arabidopsis thaliana, a mitogen-activated protein kinase pathway, MEKK1–MKK1/MKK2–MPK4, is important for basal resistance and disruption of this pathway results in dwarf, autoimmune phenotypes. To elucidate the complex mechanisms activated by the disruption of this pathway, we have previously developed a mutant screening system based on a dwarf autoimmune line that overexpressed the N-terminal regulatory domain of MEKK1. Here, we report that the second group of mutants, smn2, had defects in the SMN2 gene, encoding a DEAD-box RNA helicase. SMN2 is identical to HEN2, whose function is vital for the nuclear RNA exosome because it provides non-ribosomal RNA specificity for RNA turnover, RNA quality control and RNA processing. Aberrant SMN1/RPS6 transcripts were detected in smn2 and hen2 mutants. Disease resistance against Pseudomonas syringae pv. tomato DC3000 (hopA1), which is conferred by SMN1/RPS6, was decreased in smn2 mutants, suggesting a functional connection between SMN1/RPS6 and SMN2/HEN2. We produced double mutants mekk1smn2 and mpk4smn2 to determine whether the smn2 mutations suppress the dwarf, autoimmune phenotypes of the mekk1 and mpk4 mutants, as the smn1 mutations do. As expected, the mekk1 and mpk4 phenotypes were suppressed by the smn2 mutations. These results suggested that SMN2 is involved in the proper function of SMN1/RPS6. The Gene Ontology enrichment analysis using RNA-seq data showed that defense genes were downregulated in smn2, suggesting a positive contribution of SMN2 to the genome-wide expression of defense genes. In conclusion, this study provides novel insight into plant immunity via SMN2/HEN2, an essential component of the nuclear RNA exosome.

scholarly journals Altered rRNA processing disrupts nuclear RNA homeostasis via competition for the poly(A)-binding protein Nab2

2020 ◽  
Vol 48 (20) ◽  
pp. 11675-11694
Author(s):  
Lisbeth-Carolina Aguilar ◽  
Biplab Paul ◽  
Taylor Reiter ◽  
Louis Gendron ◽  
Arvind Arul Nambi Rajan ◽  
...  
Keyword(s):  
Rna Binding ◽  
Rna Binding Proteins ◽  
Binding Protein ◽  
Rna Metabolism ◽  
Rdna Transcription ◽  
Cellular Processes ◽  
Genome Wide ◽  
Nuclear Rna ◽  
Rna Exosome ◽  
Nucleolar Rna

Abstract RNA-binding proteins (RBPs) are key mediators of RNA metabolism. Whereas some RBPs exhibit narrow transcript specificity, others function broadly across both coding and non-coding RNAs. Here, in Saccharomyces cerevisiae, we demonstrate that changes in RBP availability caused by disruptions to distinct cellular processes promote a common global breakdown in RNA metabolism and nuclear RNA homeostasis. Our data shows that stabilization of aberrant ribosomal RNA (rRNA) precursors in an enp1-1 mutant causes phenotypes similar to RNA exosome mutants due to nucleolar sequestration of the poly(A)-binding protein (PABP) Nab2. Decreased nuclear PABP availability is accompanied by genome-wide changes in RNA metabolism, including increased pervasive transcripts levels and snoRNA processing defects. These phenotypes are mitigated by overexpression of PABPs, inhibition of rDNA transcription, or alterations in TRAMP activity. Our results highlight the need for cells to maintain poly(A)-RNA levels in balance with PABPs and other RBPs with mutable substrate specificity across nucleoplasmic and nucleolar RNA processes.

scholarly journals The regulation and functions of the nuclear RNA exosome complex

2016 ◽  
Vol 17 (4) ◽  
pp. 227-239 ◽  
Author(s):  
Cornelia Kilchert ◽  
Sina Wittmann ◽  
Lidia Vasiljeva
Keyword(s):  
Nuclear Rna ◽  
Rna Exosome ◽  
Exosome Complex

scholarly journals Comparative poly(A)+ RNA interactome capture of fission yeast RNA exosome mutants reveals insights into RNA biogenesis

2020 ◽  
Author(s):  
Adrien Birot ◽  
Cornelia Kilchert ◽  
Krzysztof Kus ◽  
Emily Priest ◽  
Ahmad Al Alwash ◽  
...  
Keyword(s):  
Quality Control ◽  
Rna Polymerase Ii ◽  
Rna Binding ◽  
Zinc Finger Protein ◽  
Rna Binding Proteins ◽  
Protein Coding ◽  
Multiple Protein ◽  
Nuclear Rna ◽  
Control Step ◽  
Rna Exosome

ABSTRACTThe nuclear RNA exosome plays a key role in quality control and processing of multiple protein-coding and non-coding transcripts made by RNA polymerase II. A mechanistic understanding of exosome function remains a challenge given it has multiple roles in RNA regulation. Here we have analysed changes in the poly(A)+ RNA transcriptome and interactome provoked by mutations in three distinct subunits of the nuclear RNA exosome. We have identified multiple proteins whose occupancy on RNA is altered in the exosome mutants. We demonstrate that the Zinc-finger protein Mub1 regulates exosome dependent transcripts that encode stress-responsive proteins. Furthermore, we assess impact of the exosome inactivation upon RNA binding of the components of the mRNA processing machineries such as spliceosome and mRNA cleavage polyadenylation complex. We show that mutations in the exosome lead to accumulation of the components of U1 and U2 snRNPs on poly(A)+ RNA and depletion of the components of the activated spliceosome from RNA suggesting that the early stages of spliceosome assembly might provide a critical quality control step. Collectively, our data provide a global view of how RNA metabolism is affected in the exosome-deficient cells and reveal RNA-binding proteins that may act as novel exosome cofactors.

scholarly journals Targeting the nuclear RNA exosome: Poly(A) binding proteins enter the stage

RNA Biology ◽  
2017 ◽  
Vol 14 (7) ◽  
pp. 820-826 ◽  
Author(s):  
Nicola Meola ◽  
Torben Heick Jensen
Keyword(s):  
Binding Proteins ◽  
Nuclear Rna ◽  
Rna Exosome
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