Functions of the Cytoplasmic Exosome

Schaeffer, Daneen; Clark, Amanda; Klauer, A. Alejandra; Tsanova, Borislava; Hoof, Ambro van

doi:10.1007/978-1-4419-7841-7_7

Cited by 50 publications

(55 citation statements)

References 82 publications

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“…It is still unclear how the cytoplasmic and nuclear exosome complexes within a cell relate to each other in their assembly and functional and spatial separations [20]. Our observation that Ski7 interacts with the core exosome in a very similar fashion as Rrp6 provides new insight into the relationship between the two types of exosomes in a cell.…”

Section: Discussionmentioning

confidence: 77%

“…Rrp6 has been revealed to interact with the Exo10 complex at the top region, next to the entry site of the core [14,15,19]. In the cytoplasm, Ski7, a putative GTPase, bridges the exosome with the ribosome complex and the Ski2/3/8 complex, a cofactor complex, thus promoting recognition and degradation of aberrant mRNAs by the exosome [20]. Ski7 has been suggested to interact with Csl4 at the top of the Exo10 core [21,22].…”

Section: Introductionmentioning

confidence: 99%

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CryoEM structure of yeast cytoplasmic exosome complex

Liu

Niu

et al. 2016

Cell Res

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The eukaryotic multi-subunit RNA exosome complex plays crucial roles in 3′-to-5′ RNA processing and decay. Rrp6 and Ski7 are the major cofactors for the nuclear and cytoplasmic exosomes, respectively. In the cytoplasm, Ski7 helps the exosome to target mRNAs for degradation and turnover via a through-core pathway. However, the interaction between Ski7 and the exosome complex has remained unclear. The transaction of RNA substrates within the exosome is also elusive. In this work, we used single-particle cryo-electron microscopy to solve the structures of the Ski7-exosome complex in RNA-free and RNA-bound forms at resolutions of 4.2 Å and 5.8 Å, respectively. These structures reveal that the N-terminal domain of Ski7 adopts a structural arrangement and interacts with the exosome in a similar fashion to the C-terminal domain of nuclear Rrp6. Further structural analysis of exosomes with RNA substrates harboring 3′ overhangs of different length suggests a switch mechanism of RNA-induced exosome activation in the through-core pathway of RNA processing.

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Section: Discussionmentioning

confidence: 77%

Section: Introductionmentioning

confidence: 99%

CryoEM structure of yeast cytoplasmic exosome complex

Liu

Niu

et al. 2016

Cell Res

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“…Interestingly L-A virions used m 7 GpppG in vitro as a cap donor. Thus the virus can potentially utilize not only host mRNA but also m 7 GpppG or capped oligo fragments generated from the 3′-5′ mRNA degradation pathway carried out by the exosome (20,21), as cap donors. A substantial amount (ca.…”

Section: Discussionmentioning

confidence: 99%

Cap-snatching mechanism in yeast L-A double-stranded RNA virus

Fujimura

Esteban

2011

Proc. Natl. Acad. Sci. U.S.A.

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The 5′ cap structure (m 7 GpppX-) is an essential feature of eukaryotic mRNA required for mRNA stability and efficient translation. Influenza virus furnishes its mRNA with this structure by a capsnatching mechanism, in which the viral polymerase cleaves host mRNA endonucleolytically 10-13 nucleotides from the 5′ end and utilizes the capped fragment as a primer to synthesize viral transcripts. Here we report a unique cap-snatching mechanism by which the yeast double-stranded RNA totivirus L-A furnishes its transcript with a cap structure derived from mRNA. Unlike influenza virus, L-A transfers only m 7 Gp from the cap donor to the 5′ end of the viral transcript, thus preserving the 5′ α-and β-phosphates of the transcript in the triphosphate linkage of the final product. This in vitro capping reaction requires His154 of the coat protein Gag, a residue essential for decapping of host mRNA and known to form m 7 Gp-His adduct. Furthermore, the synthesis of capped viral transcripts in vivo and their expression were greatly compromised by the Arg154 mutation, indicating the involvement of Gag in the cap-snatching reaction. The overall reaction and the structure around the catalytic site in Gag resemble those of guanylyltransferase, a key enzyme of cellular mRNA capping, suggesting convergent evolution. Given that Pol of L-A is confined inside the virion and unable to access host mRNA in the cytoplasm, the structural protein Gag rather than Pol catalyzing this unique cap-snatching reaction exemplifies the versatility as well as the adaptability of eukaryotic RNA viruses.transcription | Saccharomyces cerevisiae | killer toxin E ukaryotic mRNA is capped at the 5′ end by a 7-methyl GMP moiety via an inverted 5′-5′ triphosphate linkage (m 7 GpppX) (1, 2). The cap structure is required for mRNA stability and efficient translation. Capping of the RNA 5′ end is accomplished in cells and for most viruses in three sequential catalytic reactions (3, 4): removal of the 5′ γ-phosphate by RNA triphosphatase, addition of GMP from GTP by guanylyltransferase, and methylation of the added GMP by methyltransferase. Influenza virus, how-

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“…The rationale for examining cytoplasmic RNA exosome function is threefold: first, the cytoplasmic functions of the RNA exosome are nonessential, and thus distinct from those tested above (Jacobs Anderson and Parker 1998; Schaeffer et al 2010); second, residue substitutions in a different RNA exosome cap protein (Csl4/EXOSC1) inactivate cytoplasmic RNA exosome function without blocking the essential (nuclear) function ; and third, the hypothesis has been put forth that PCH1b and PCH1c are the result of a defect in cytoplasmic mRNA degradation by the RNA exosome (Boczonadi et al 2014).…”

Section: Pch1b Patients Have Mutations That Alter Conserved Exosc3 Rementioning

confidence: 99%

“…The RNA exosome is present in both the nucleus and the cytoplasm. Nuclear and cytoplasmic RNA exosomes also require specific exosome cofactors (Butler and Mitchell 2010;Schaeffer et al 2010), which help to guide the degradation and/or processing of specific RNAs. In particular, the cytoplasmic cofactor, the SKI complex, is required for all known cytoplasmic functions of the RNA exosome, but not for its nuclear functions (Jacobs Anderson and Parker 1998;van Hoof et al 2000).…”

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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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Functions of the Cytoplasmic Exosome

Cited by 50 publications

References 82 publications

CryoEM structure of yeast cytoplasmic exosome complex

CryoEM structure of yeast cytoplasmic exosome complex

Cap-snatching mechanism in yeast L-A double-stranded RNA virus

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

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