ChemInform Abstract: Mechanisms of RNA Degradation by the Eukaryotic Exosome

Tomecki, Rafał; Drążkowska, Karolina; Dziembowski, Andrzej

doi:10.1002/chin.201029271

Cited by 2 publications

(2 citation statements)

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“…The nine-subunit core complex of the RNA exosome is found in both the cytoplasm and nucleus of all eukaryotes, and is required for degradation of a large variety of RNA substrates (Lykke-Andersen et al, 2009). In yeast, RNA degradation by the exosome depends on Rrp44p/Dis3p and Rrp6p, two ribonucleases that are associated with the core complex, and on other co-factors such as RNA helicases and RNA binding proteins (reviewed by Tomecki et al, 2010). One such co-factor of the nuclear exosome is the RNA helicase Mtr4p.…”

Section: Introductionmentioning

confidence: 99%

MTR4, a putative RNA helicase and exosome co‐factor, is required for proper rRNA biogenesis and development in Arabidopsis thaliana

Lange

Sement

Gagliardi³

2011

The Plant Journal

156

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The exosome is a conserved protein complex that is responsible for essential 3'→5' RNA degradation in both the nucleus and the cytosol. It is composed of a nine-subunit core complex to which co-factors confer both RNA substrate recognition and ribonucleolytic activities. Very few exosome co-factors have been identified in plants. Here, we have characterized a putative RNA helicase, AtMTR4, that is involved in the degradation of several nucleolar exosome substrates in Arabidopsis thaliana. We show that AtMTR4, rather than its closely related protein HEN2, is required for proper rRNA biogenesis in Arabidopsis. AtMTR4 is mostly localized in the nucleolus, a subcellular compartmentalization that is shared with another exosome co-factor, RRP6L2. AtMTR4 and RRP6L2 cooperate in several steps of rRNA maturation and surveillance, such as processing the 5.8S rRNA and removal of rRNA maturation by-products. Interestingly, degradation of the Arabidopsis 5' external transcribed spacer (5' ETS) requires cooperation of both the 5'→3' and 3'→5' exoribonucleolytic pathways. Accumulating AtMTR4 targets give rise to illegitimate small RNAs; however, these do not affect rRNA metabolism or contribute to the phenotype of mtr4 mutants. Plants lacking AtMTR4 are viable but show several developmental defects, including aberrant vein patterning and pointed first leaves. The mtr4 phenotype resembles that of several ribosomal protein and nucleolin mutants, and may be explained by delayed ribosome biogenesis, as we observed a reduced rate of rRNA accumulation in mtr4 mutants. Taken together, these data link AtMTR4 with rRNA biogenesis and development in Arabidopsis.

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Section: Introductionmentioning

confidence: 99%

MTR4, a putative RNA helicase and exosome co‐factor, is required for proper rRNA biogenesis and development in Arabidopsis thaliana

Lange

Sement

Gagliardi³

2011

The Plant Journal

156

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“…The main pathway involves decapping followed by 5′!3′ digestion performed by the Ski1p/Xrn1p exonuclease (Decker and Parker, 1993;Stevens, 2001;Parker and Song, 2004). There is a second pathway, which does not require the elimination of cap, carried out by the exosome in the 3′!5′ direction (Tomecki et al, 2010). The exosome is a multimeric complex with exonucleolytic activity located in both the cytoplasm and the nucleus.…”

Section: Introductionmentioning

confidence: 99%

Yeast RNA viruses as indicators of exosome activity: human exosome hCsl4p participates in RNA degradation in Saccharomyces cerevisiae'

Ramírez-Garrastacho

Esteban

2011

Yeast

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The exosome is an evolutionarily conserved 10-mer complex involved in RNA metabolism, located in both the nucleus and the cytoplasm. The cytoplasmic exosome plays an important role in mRNA turnover through its 3′!5′ exonucleolytic activity. The superkiller (SKI) phenotype of yeast was originally identified as an increase of killer toxin production due to elevated levels of the L-A double-stranded RNA (dsRNA) Totivirus and its satellite toxin-encoding M dsRNA. Most SKI genes were later shown to be either components of the exosome or modulators of its activity. Variations in the amount of Totivirus are, thus, good indicators of yeast exosome activity, and can be used to analyse its components. Furthermore, if exosome proteins of higher eukaryotes were functional in S. cerevisiae, these viruses would provide a simple tool to analyse their function. In this work, we have found that hCSL4, the human orthologue of SKI4 in the yeast exosome, rescues the null phenotype of the deletion mutant. hCsl4p shares with Ski4p conserved S1 RNA-binding domains, but lacks the N-terminal third of Ski4p. Nevertheless, it interacts with the Dis3p exonuclease of yeast exosome, and partially complements the superkiller phenotype of ski4-1 mutation. The elimination of the N-terminal third of Ski4p does not affect its activity, indicating that it is dispensable for RNA degradation. We have also identified the point mutation G152E in hCSL4, equivalent to the ski4-1 mutation G253E, which impairs the activity of the protein, thus validating our approach of using yeast RNA virus to analyse the exosome of higher eukaryotes.

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ChemInform Abstract: Mechanisms of RNA Degradation by the Eukaryotic Exosome

Cited by 2 publications

References 1 publication

MTR4, a putative RNA helicase and exosome co‐factor, is required for proper rRNA biogenesis and development in Arabidopsis thaliana

MTR4, a putative RNA helicase and exosome co‐factor, is required for proper rRNA biogenesis and development in Arabidopsis thaliana

Yeast RNA viruses as indicators of exosome activity: human exosome hCsl4p participates in RNA degradation in Saccharomyces cerevisiae'

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