Different nuclease requirements for exosome-mediated degradation of normal and nonstop mRNAs
Daneen Schaeffer1, Ambro van Hoof
1Department of Microbiology and Molecular Genetics, University of Texas Health Science Center, Houston, TX 77030, USA.
Abstract:
Two general pathways of mRNA decay have been characterized in yeast. In one pathway, the mRNA is degraded by the cytoplasmic form of the exosome. The exosome has both 3' to 5' exoribonuclease and endoribonuclease activity, and the available evidence suggests that the exonuclease activity is required for the degradation of mRNAs. We confirm here that this is true for normal mRNAs, but that aberrant mRNAs that lack a stop codon can be efficiently degraded in the absence of the exonuclease activity of the exosome. Specifically, we show that the endo- and exonuclease activities of the exosome are both capable of rapidly degrading nonstop mRNAs and ribozyme-cleaved mRNAs. Additionally, the endonuclease activity of the exosome is not required for endonucleolytic cleavage in no-go decay. In vitro, the endonuclease domain of the exosome is active only under nonphysiological conditions, but our findings show that the in vivo activity is sufficient for the rapid degradation of nonstop mRNAs. Thus, whereas normal mRNAs are degraded by two exonucleases (Xrn1p and Rrp44p), several endonucleases contribute to the decay of many aberrant mRNAs, including transcripts subject to nonstop and no-go decay. Our findings suggest that the nuclease requirements for general and nonstop mRNA decay are different, and describe a molecular function of the core exosome that is not disrupted by inactivating its exonuclease activity.
Insights
Aberrant mRNAs lacking stop codons are degraded by the exosome
Area of Science:
- Molecular Biology
- Yeast Genetics
Background:
- mRNA decay pathways are crucial for gene regulation.
- The exosome complex plays a key role in degrading various RNA molecules.
- Distinct mechanisms govern the decay of normal versus aberrant mRNAs.
Purpose of the Study:
- To investigate the role of exosome nuclease activities in the decay of aberrant mRNAs.
- To differentiate the decay mechanisms of normal mRNAs from nonstop and no-go mRNAs.
- To elucidate the specific contributions of exosome endo- and exonuclease activities.
Main Methods:
- In vitro assays using nonstop and ribozyme-cleaved mRNAs.
- Analysis of mRNA degradation in yeast mutants lacking exosome exonuclease activity.
- Characterization of exosome endonuclease activity in vivo and in vitro.
Main Results:
- Aberrant mRNAs lacking stop codons are rapidly degraded by the exosome, even without its exonuclease activity.
- Both endo- and exonuclease activities of the exosome contribute to nonstop mRNA degradation.
- Exosome endonuclease activity is sufficient for nonstop mRNA decay under physiological conditions.
- The decay of aberrant mRNAs involves multiple endonucleases, unlike normal mRNA decay.
Conclusions:
- Nuclease requirements for general and aberrant mRNA decay differ significantly.
- The exosome's endonuclease activity plays a vital role in degrading specific aberrant transcripts.
- This study reveals a distinct molecular function of the exosome in managing non-functional mRNAs.
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