The Human Nuclear Exosome Targeting Complex Is Loaded onto Newly Synthesized RNA to Direct Early Ribonucleolysis

Lubas, Michał; Andersen, Peder; Schein, Aleks; Dziembowski, Andrzej; Kudla, Grzegorz; Jensen, Torben Heick

doi:10.1016/j.celrep.2014.12.026

Cited by 167 publications

(231 citation statements)

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“…In higher eukaryotes, RNA degradative functions of the exosome have started to emerge due to studies that have analyzed the phenotypes of cells depleted for various components of the exosome (Lubas et al 2015;Pefanis et al 2015). Recently, mutations affecting EXOSC3, the human homolog of Rrp40p, were shown to cause pontocerebellar hypoplasia type 1B (PCH1B, OMIM614678) (Wan et al 2012).…”

Section: Introductionmentioning

confidence: 99%

Mutations of EXOSC3/Rrp40p associated with neurological diseases impact ribosomal RNA processing functions of the exosome in S. cerevisiae

Gillespie

Gabunilas

Jen

et al. 2017

RNA

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The RNA exosome is a conserved multiprotein complex that achieves a large number of processive and degradative functions in eukaryotic cells. Recently, mutations have been mapped to the gene encoding one of the subunits of the exosome, EXOSC3 (yeast Rrp40p), which results in pontocerebellar hypoplasia with motor neuron degeneration in human patients. However, the molecular impact of these mutations in the pathology of these diseases is not well understood. To investigate the molecular consequences of mutations in EXOSC3 that lead to neurological diseases, we analyzed the effect of three of the mutations that affect conserved residues of EXOSC3/Rrp40p (G31A, G191C, and W238R; G8A, G148C, and W195R, respectively, in human and yeast) in S. cerevisiae. We show that the severity of the phenotypes of these mutations in yeast correlate with that of the disease in human patients, with the W195R mutant showing the strongest growth and RNA processing phenotypes. Furthermore, we show that these mutations affect more severely pre-ribosomal RNA processing functions of the exosome rather than other nuclear processing or surveillance functions. These results suggest that delayed or defective pre-rRNA processing might be the primary defect responsible for the pathologies detected in patients with mutations affecting EXOSC3 function in residues conserved throughout eukaryotes.

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Section: Introductionmentioning

confidence: 99%

Mutations of EXOSC3/Rrp40p associated with neurological diseases impact ribosomal RNA processing functions of the exosome in S. cerevisiae

Gillespie

Gabunilas

Jen

et al. 2017

RNA

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“…S. cerevisiae Rrp subunits correspond to human EXOSC subunits. The functions of the RNA exosome have been extensively characterized in budding yeast (Sloan et al 2012), and many are conserved in humans (Schilders et al 2005;Staals et al 2010;Lubas et al 2011Lubas et al , 2015 the RNA exosome, six subunits comprise a core ring, and three putative RNA-binding subunits, including EXOSC3, form a cap that interacts with the core ring on one side of the complex ( Figure 1A). The catalytic DIS3 subunit, which possesses both endo and exoribonuclease activities Lebreton et al 2008;), associates with the opposite side of the core ring from the cap ( Figure 1A) (Malet et al 2010;Staals et al 2010;Tomecki et al 2010;Makino et al 2013).…”

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confidence: 99%

Insight into the RNA Exosome Complex Through Modeling Pontocerebellar Hypoplasia Type 1b Disease Mutations in Yeast

et al. 2017

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Pontocerebellar hypoplasia type 1b (PCH1b) is an autosomal recessive disorder that causes cerebellar hypoplasia and spinal motor neuron degeneration, leading to mortality in early childhood. PCH1b is caused by mutations in the RNA exosome subunit gene, EXOSC3. The RNA exosome is an evolutionarily conserved complex, consisting of nine different core subunits, and one or two 39-59 exoribonuclease subunits, that mediates several RNA degradation and processing steps. The goal of this study is to assess the functional consequences of the amino acid substitutions that have been identified in EXOSC3 in PCH1b patients. To analyze these EXOSC3 substitutions, we generated the corresponding amino acid substitutions in the Saccharomyces cerevisiae ortholog of EXOSC3, Rrp40. We find that the rrp40 variants corresponding to EXOSC3-G31A and -D132A do not affect yeast function when expressed as the sole copy of the essential Rrp40 protein. In contrast, the rrp40-W195R variant, corresponding to EXOSC3-W238R in PCH1b patients, impacts cell growth and RNA exosome function when expressed as the sole copy of Rrp40. The rrp40-W195R protein is unstable, and does not associate efficiently with the RNA exosome in cells that also express wild-type Rrp40. Consistent with these findings in yeast, the levels of mouse EXOSC3 variants are reduced compared to wild-type EXOSC3 in a neuronal cell line. These data suggest that cells possess a mechanism for optimal assembly of functional RNA exosome complex that can discriminate between wildtype and variant exosome subunits. Budding yeast can therefore serve as a useful tool to understand the molecular defects in the RNA exosome caused by PCH1b-associated amino acid substitutions in EXOSC3, and potentially extending to disease-associated substitutions in other exosome subunits.KEYWORDS pontocerebellar hypoplasia type 1b; RNA exosome; EXOSC3; Rrp40; EXOSC2; RNA processing/degradation T HE RNA exosome is an evolutionarily conserved ribonuclease complex that is responsible for several essential RNA processing and degradation steps (Mitchell et al. 1997;Allmang et al. 1999;Schneider and Tollervey 2013). Major exosome substrates include mRNA, rRNA, and small RNAs. In addition to degrading aberrant and unneeded transcripts, the RNA exosome also trims precursor RNAs, including 5.8S rRNA (Mitchell et al. 1996). The RNA exosome thus plays critical roles in both RNA degradation and maturation.The subunits of the RNA exosome complex are evolutionarily conserved and many were first identified in Saccharomyces cerevisiae in a screen for ribosomal RNA processing (rrp) mutants (Mitchell et al. 1996(Mitchell et al. , 1997Allmang et al. 1999). S. cerevisiae Rrp subunits correspond to human EXOSC subunits. The functions of the RNA exosome have been extensively characterized in budding yeast (Sloan et al. 2012), and many are conserved in humans (Schilders et al. 2005;Staals et al. 2010;Lubas et al. 2011Lubas et al. , 2015 the RNA exosome, six subunits comprise a core ring, and three putative RNA-binding sub...

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“…Depletion of CBCA, NEXT components, or ZC3H18, results in accumulation of PROMPTs [10,11] . RBM7 associates with newly synthesized RNA, is enriched at regions close to the 5'-cap, and RBM7-RNA interaction is disrupted following CBC KD [85] . These data indicate that ARS2 and the CBC recruit the NEXT complex to newly synthesized RNAP II transcripts that are destined for exosomal destruction (Figure 4).…”

Section: Ars2 and The Exosomementioning

confidence: 99%

“…ARS2 KD results in accumulation of mRNA in nuclear speckle domains [121] . Interestingly, Zinc-knuckle protein ZC3H18, which interacts with ARS2 as part of the CBC-NEXT complex [11,84,85] , also interacts with the TREX complex [121] . ZC3H18 KD prevents efficient TREX recruitment to RNA and also results in an accumulation of mRNA in nuclear speckle domains [121] .…”

Section: Ars2 and Exportmentioning

confidence: 99%

“…Recently, ARS2 was shown to participate in targeting transcripts to the nuclear RNA exosome through interaction with the human nuclear exosome targeting (NEXT) complex [11,84] . This complex recruits the exosome to degrade PROMPTs and 3'-extended snRNA [11,[84][85][86][87] . NEXT is composed of the RNA helicase hMTR4, the zinc-knuckle ZCCHC8, and the RRM-containing RBM7 [11,84] .…”

Section: Ars2 and The Exosomementioning

confidence: 99%

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The Diverse Requirements of ARS2 in nuclear cap-binding complex-dependent RNA Processing

O’Sullivan

Howard

2016

RNA Dis

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ARS2 is a stable component of the nuclear cap-binding complex (CBC) and is critical for RNA Polymerase II transcript processing. Moreover, ARS2, and its orthologue SERRATE in plants, has been implicated in having a role in most established CBC-dependent functions. This review will provide insight into the functions of ARS2/SERRATE in numerous RNA Polymerase II transcript processing events, which happen co-transcriptionally from initiation to termination, and post-transcriptionally during maturation and export into the cytoplasm. Additionally, we will discuss what is known regarding ARS2/SERRATE structure in plants and in mammals.

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The Human Nuclear Exosome Targeting Complex Is Loaded onto Newly Synthesized RNA to Direct Early Ribonucleolysis

Cited by 167 publications

References 52 publications

Mutations of EXOSC3/Rrp40p associated with neurological diseases impact ribosomal RNA processing functions of the exosome in S. cerevisiae

Mutations of EXOSC3/Rrp40p associated with neurological diseases impact ribosomal RNA processing functions of the exosome in S. cerevisiae

Insight into the RNA Exosome Complex Through Modeling Pontocerebellar Hypoplasia Type 1b Disease Mutations in Yeast

The Diverse Requirements of ARS2 in nuclear cap-binding complex-dependent RNA Processing

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