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The Sm complex is required for the processing of non-coding RNAs by the exosome.

Coy S, Volanakis A, Shah S, Vasiljeva L - PLoS ONE (2013)

Bottom Line: Additionally, we demonstrate that the same pathway is involved in the maturation of snRNAs.We also show that telomerase RNA accumulates in Schizosaccharomyces pombe exosome mutants, suggesting a conserved role for the exosome in processing and degradation of telomerase RNA.In summary, our data provide important mechanistic insight into the regulation of exosome dependent RNA processing as well as telomerase RNA biogenesis.

View Article: PubMed Central - PubMed

Affiliation: Department of Biochemistry, University of Oxford, Oxford, United Kingdom.

ABSTRACT
A key question in the field of RNA regulation is how some exosome substrates, such as spliceosomal snRNAs and telomerase RNA, evade degradation and are processed into stable, functional RNA molecules. Typical feature of these non-coding RNAs is presence of the Sm complex at the 3'end of the mature RNA molecule. Here, we report that in Saccharomyces cerevisiae presence of intact Sm binding site is required for the exosome-mediated processing of telomerase RNA from a polyadenylated precursor into its mature form and is essential for its function in elongating telomeres. Additionally, we demonstrate that the same pathway is involved in the maturation of snRNAs. Furthermore, the insertion of an Sm binding site into an unstable RNA that is normally completely destroyed by the exosome, leads to its partial stabilization. We also show that telomerase RNA accumulates in Schizosaccharomyces pombe exosome mutants, suggesting a conserved role for the exosome in processing and degradation of telomerase RNA. In summary, our data provide important mechanistic insight into the regulation of exosome dependent RNA processing as well as telomerase RNA biogenesis.

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A hypothetical model describing possible role for Sm binding in the exosome-mediated processing of non-coding RNAs.Non-coding RNA transcripts recognized by the nuclear exosome are degraded from their 3′ end (1). In the case of substrates that contain an Sm binding site the exosome trims along the RNA until it encounters the bound Sm complex. The Sm complex blocks the progression of the exosome (2) resulting in a processed, mature RNA. When the pathway is functional, binding of the Sm complex defines the processing mode of the exosome and protects Sm-containing RNA substrates from degradation. Removal of the Sm site or of Sm proteins results in a non-functional pathway: the blockade of the exosome progression is compromised, resulting in RNA degradation.
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pone-0065606-g006: A hypothetical model describing possible role for Sm binding in the exosome-mediated processing of non-coding RNAs.Non-coding RNA transcripts recognized by the nuclear exosome are degraded from their 3′ end (1). In the case of substrates that contain an Sm binding site the exosome trims along the RNA until it encounters the bound Sm complex. The Sm complex blocks the progression of the exosome (2) resulting in a processed, mature RNA. When the pathway is functional, binding of the Sm complex defines the processing mode of the exosome and protects Sm-containing RNA substrates from degradation. Removal of the Sm site or of Sm proteins results in a non-functional pathway: the blockade of the exosome progression is compromised, resulting in RNA degradation.

Mentions: Previous studies have implicated the exosome complex to function in multiple RNA processing reactions raising an important question: how does the exosome trim these RNAs to produce precise 3′ ends rather than degrading RNA to completion? A likely explanation is that the composition of RNP particles contributes to RNA fate determination by regulating access to the RNA by the exosome complex. We have presented evidence supporting the previously proposed hypothesis that yeast telomerase RNA is processed from the precursor RNA. Indeed, if the processing is blocked by mutating exosome activity there is an accumulation of the longer poly(A)+ TLC1 RNA. We also demonstrate that the Sm complex may play a role in preventing Sm site containing non-coding RNAs such as telomerase RNA and snRNAs from being fully degraded by the exosome and thereby regulates the processing of these RNAs (Figure 6). The high affinity of the Sm proteins to the Sm site was shown to be important for the formation of the thermodynamically stable complex on RNA [50], [51], [52] and we speculate that this enables the Sm complex to serve as a block for the degradation machinery. Also in support of the proposed model, our unpublished data show that the Sm complex is found on the precursor and mature forms of the telomerase RNA and snRNAs (manuscript in preparation). The precursor-product relationship for longer and shorter forms of TCL1 RNA is consistent with our biochemical data demonstrating that the purified exosome trims the TLC1 precursor only when it is bound by the Sm complex, otherwise degrading it to completion. Moreover, study from the Tollervey lab (personal communication) reporting the in vivo kinetics of TLC1 RNA accumulation nicely demonstrate a precursor-product relationship initially suggested in the earlier work of others using an inducible system for TLC1 expression [12]. The processing appears to mainly require activity of the core exosome assisted by Rrp47 and leads to generation of the 3′ end of mature TLC1 7 nucleotides downstream of the Sm binding site. Recent biochemical and structural studies support the view that the exosome substrates pass through the exosome channel to reach the Dis3 catalytic site [53], [54], [55]. If this is the case for substrates that are processed by the exosome, trimming should stop more than 7 nucleotides downstream of the potential block, or else the final trimming may require additional exonucleolytic activity. Indeed, it has been shown that for some RNAs such as 5.8S rRNA the final trimming is performed by Rrp6 [29], [56]. Rrp6 does not appear to be as important as the exosome core for the initial processing step of TLC1 maturation. However, further analysis is required to test whether Rrp6 or/and other exonucleolytic activities are required for subsequent trimming to produce the fully mature form.


The Sm complex is required for the processing of non-coding RNAs by the exosome.

Coy S, Volanakis A, Shah S, Vasiljeva L - PLoS ONE (2013)

A hypothetical model describing possible role for Sm binding in the exosome-mediated processing of non-coding RNAs.Non-coding RNA transcripts recognized by the nuclear exosome are degraded from their 3′ end (1). In the case of substrates that contain an Sm binding site the exosome trims along the RNA until it encounters the bound Sm complex. The Sm complex blocks the progression of the exosome (2) resulting in a processed, mature RNA. When the pathway is functional, binding of the Sm complex defines the processing mode of the exosome and protects Sm-containing RNA substrates from degradation. Removal of the Sm site or of Sm proteins results in a non-functional pathway: the blockade of the exosome progression is compromised, resulting in RNA degradation.
© Copyright Policy
Related In: Results  -  Collection

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getmorefigures.php?uid=PMC3675052&req=5

pone-0065606-g006: A hypothetical model describing possible role for Sm binding in the exosome-mediated processing of non-coding RNAs.Non-coding RNA transcripts recognized by the nuclear exosome are degraded from their 3′ end (1). In the case of substrates that contain an Sm binding site the exosome trims along the RNA until it encounters the bound Sm complex. The Sm complex blocks the progression of the exosome (2) resulting in a processed, mature RNA. When the pathway is functional, binding of the Sm complex defines the processing mode of the exosome and protects Sm-containing RNA substrates from degradation. Removal of the Sm site or of Sm proteins results in a non-functional pathway: the blockade of the exosome progression is compromised, resulting in RNA degradation.
Mentions: Previous studies have implicated the exosome complex to function in multiple RNA processing reactions raising an important question: how does the exosome trim these RNAs to produce precise 3′ ends rather than degrading RNA to completion? A likely explanation is that the composition of RNP particles contributes to RNA fate determination by regulating access to the RNA by the exosome complex. We have presented evidence supporting the previously proposed hypothesis that yeast telomerase RNA is processed from the precursor RNA. Indeed, if the processing is blocked by mutating exosome activity there is an accumulation of the longer poly(A)+ TLC1 RNA. We also demonstrate that the Sm complex may play a role in preventing Sm site containing non-coding RNAs such as telomerase RNA and snRNAs from being fully degraded by the exosome and thereby regulates the processing of these RNAs (Figure 6). The high affinity of the Sm proteins to the Sm site was shown to be important for the formation of the thermodynamically stable complex on RNA [50], [51], [52] and we speculate that this enables the Sm complex to serve as a block for the degradation machinery. Also in support of the proposed model, our unpublished data show that the Sm complex is found on the precursor and mature forms of the telomerase RNA and snRNAs (manuscript in preparation). The precursor-product relationship for longer and shorter forms of TCL1 RNA is consistent with our biochemical data demonstrating that the purified exosome trims the TLC1 precursor only when it is bound by the Sm complex, otherwise degrading it to completion. Moreover, study from the Tollervey lab (personal communication) reporting the in vivo kinetics of TLC1 RNA accumulation nicely demonstrate a precursor-product relationship initially suggested in the earlier work of others using an inducible system for TLC1 expression [12]. The processing appears to mainly require activity of the core exosome assisted by Rrp47 and leads to generation of the 3′ end of mature TLC1 7 nucleotides downstream of the Sm binding site. Recent biochemical and structural studies support the view that the exosome substrates pass through the exosome channel to reach the Dis3 catalytic site [53], [54], [55]. If this is the case for substrates that are processed by the exosome, trimming should stop more than 7 nucleotides downstream of the potential block, or else the final trimming may require additional exonucleolytic activity. Indeed, it has been shown that for some RNAs such as 5.8S rRNA the final trimming is performed by Rrp6 [29], [56]. Rrp6 does not appear to be as important as the exosome core for the initial processing step of TLC1 maturation. However, further analysis is required to test whether Rrp6 or/and other exonucleolytic activities are required for subsequent trimming to produce the fully mature form.

Bottom Line: Additionally, we demonstrate that the same pathway is involved in the maturation of snRNAs.We also show that telomerase RNA accumulates in Schizosaccharomyces pombe exosome mutants, suggesting a conserved role for the exosome in processing and degradation of telomerase RNA.In summary, our data provide important mechanistic insight into the regulation of exosome dependent RNA processing as well as telomerase RNA biogenesis.

View Article: PubMed Central - PubMed

Affiliation: Department of Biochemistry, University of Oxford, Oxford, United Kingdom.

ABSTRACT
A key question in the field of RNA regulation is how some exosome substrates, such as spliceosomal snRNAs and telomerase RNA, evade degradation and are processed into stable, functional RNA molecules. Typical feature of these non-coding RNAs is presence of the Sm complex at the 3'end of the mature RNA molecule. Here, we report that in Saccharomyces cerevisiae presence of intact Sm binding site is required for the exosome-mediated processing of telomerase RNA from a polyadenylated precursor into its mature form and is essential for its function in elongating telomeres. Additionally, we demonstrate that the same pathway is involved in the maturation of snRNAs. Furthermore, the insertion of an Sm binding site into an unstable RNA that is normally completely destroyed by the exosome, leads to its partial stabilization. We also show that telomerase RNA accumulates in Schizosaccharomyces pombe exosome mutants, suggesting a conserved role for the exosome in processing and degradation of telomerase RNA. In summary, our data provide important mechanistic insight into the regulation of exosome dependent RNA processing as well as telomerase RNA biogenesis.

Show MeSH
Related in: MedlinePlus