Distinct elongation stalls during translation are linked with distinct pathways for mRNA degradation
Key protein adapters couple translation to mRNA decay on specific classes of problematic mRNAs in eukaryotes. Slow decoding on non-optimal codons leads to codon-optimality-mediated decay (COMD) and prolonged arrest at stall sites leads to no-go decay (NGD). The identities of the decay factors underl...
| Main Authors: | , , , , , |
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| Format: | Article |
| Language: | English |
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eLife Sciences Publications Ltd
2022-07-01
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| Series: | eLife |
| Subjects: | |
| Online Access: | https://elifesciences.org/articles/76038 |
| _version_ | 1811253464326471680 |
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| author | Anthony J Veltri Karole N D'Orazio Laura N Lessen Raphael Loll-Krippleber Grant W Brown Rachel Green |
| author_facet | Anthony J Veltri Karole N D'Orazio Laura N Lessen Raphael Loll-Krippleber Grant W Brown Rachel Green |
| author_sort | Anthony J Veltri |
| collection | DOAJ |
| description | Key protein adapters couple translation to mRNA decay on specific classes of problematic mRNAs in eukaryotes. Slow decoding on non-optimal codons leads to codon-optimality-mediated decay (COMD) and prolonged arrest at stall sites leads to no-go decay (NGD). The identities of the decay factors underlying these processes and the mechanisms by which they respond to translational distress remain open areas of investigation. We use carefully designed reporter mRNAs to perform genetic screens and functional assays in Saccharomyces cerevisiae. We characterize the roles of Hel2, Syh1, and Smy2 in coordinating translational repression and mRNA decay on NGD reporter mRNAs, finding that Syh1 and, to a lesser extent its paralog Smy2, act in a distinct pathway from Hel2. This Syh1/Smy2-mediated pathway acts as a redundant, compensatory pathway to elicit NGD when Hel2-dependent NGD is impaired. Importantly, we observe that these NGD factors are not involved in the degradation of mRNAs enriched in non-optimal codons. Further, we establish that a key factor previously implicated in COMD, Not5, contributes modestly to the degradation of an NGD-targeted mRNA. Finally, we use ribosome profiling to reveal distinct ribosomal states associated with each reporter mRNA that readily rationalize the contributions of NGD and COMD factors to degradation of these reporters. Taken together, these results provide new insight into the role of Syh1 and Smy2 in NGD and into the ribosomal states that correlate with the activation of distinct pathways targeting mRNAs for degradation in yeast. |
| first_indexed | 2024-04-12T16:51:21Z |
| format | Article |
| id | doaj.art-f6b1be037f56465d89e22d9c4d7f534c |
| institution | Directory Open Access Journal |
| issn | 2050-084X |
| language | English |
| last_indexed | 2024-04-12T16:51:21Z |
| publishDate | 2022-07-01 |
| publisher | eLife Sciences Publications Ltd |
| record_format | Article |
| series | eLife |
| spelling | doaj.art-f6b1be037f56465d89e22d9c4d7f534c2022-12-22T03:24:23ZengeLife Sciences Publications LtdeLife2050-084X2022-07-011110.7554/eLife.76038Distinct elongation stalls during translation are linked with distinct pathways for mRNA degradationAnthony J Veltri0https://orcid.org/0000-0002-7067-1796Karole N D'Orazio1Laura N Lessen2Raphael Loll-Krippleber3Grant W Brown4https://orcid.org/0000-0002-9002-5003Rachel Green5https://orcid.org/0000-0001-9337-2003Department of Molecular Biology and Genetics, Howard Hughes Medical Institute, Johns Hopkins University School of Medicine, Baltimore, United StatesDepartment of Molecular Biology and Genetics, Howard Hughes Medical Institute, Johns Hopkins University School of Medicine, Baltimore, United StatesDepartment of Molecular Biology and Genetics, Howard Hughes Medical Institute, Johns Hopkins University School of Medicine, Baltimore, United StatesDepartment of Biochemistry and Donnelly Centre, University of Toronto, Toronto, CanadaDepartment of Biochemistry and Donnelly Centre, University of Toronto, Toronto, CanadaDepartment of Molecular Biology and Genetics, Howard Hughes Medical Institute, Johns Hopkins University School of Medicine, Baltimore, United StatesKey protein adapters couple translation to mRNA decay on specific classes of problematic mRNAs in eukaryotes. Slow decoding on non-optimal codons leads to codon-optimality-mediated decay (COMD) and prolonged arrest at stall sites leads to no-go decay (NGD). The identities of the decay factors underlying these processes and the mechanisms by which they respond to translational distress remain open areas of investigation. We use carefully designed reporter mRNAs to perform genetic screens and functional assays in Saccharomyces cerevisiae. We characterize the roles of Hel2, Syh1, and Smy2 in coordinating translational repression and mRNA decay on NGD reporter mRNAs, finding that Syh1 and, to a lesser extent its paralog Smy2, act in a distinct pathway from Hel2. This Syh1/Smy2-mediated pathway acts as a redundant, compensatory pathway to elicit NGD when Hel2-dependent NGD is impaired. Importantly, we observe that these NGD factors are not involved in the degradation of mRNAs enriched in non-optimal codons. Further, we establish that a key factor previously implicated in COMD, Not5, contributes modestly to the degradation of an NGD-targeted mRNA. Finally, we use ribosome profiling to reveal distinct ribosomal states associated with each reporter mRNA that readily rationalize the contributions of NGD and COMD factors to degradation of these reporters. Taken together, these results provide new insight into the role of Syh1 and Smy2 in NGD and into the ribosomal states that correlate with the activation of distinct pathways targeting mRNAs for degradation in yeast.https://elifesciences.org/articles/76038no-go decaycodon-optimality-mediated decaySYH1quality controltranslationmRNA decay |
| spellingShingle | Anthony J Veltri Karole N D'Orazio Laura N Lessen Raphael Loll-Krippleber Grant W Brown Rachel Green Distinct elongation stalls during translation are linked with distinct pathways for mRNA degradation eLife no-go decay codon-optimality-mediated decay SYH1 quality control translation mRNA decay |
| title | Distinct elongation stalls during translation are linked with distinct pathways for mRNA degradation |
| title_full | Distinct elongation stalls during translation are linked with distinct pathways for mRNA degradation |
| title_fullStr | Distinct elongation stalls during translation are linked with distinct pathways for mRNA degradation |
| title_full_unstemmed | Distinct elongation stalls during translation are linked with distinct pathways for mRNA degradation |
| title_short | Distinct elongation stalls during translation are linked with distinct pathways for mRNA degradation |
| title_sort | distinct elongation stalls during translation are linked with distinct pathways for mrna degradation |
| topic | no-go decay codon-optimality-mediated decay SYH1 quality control translation mRNA decay |
| url | https://elifesciences.org/articles/76038 |
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