Collided ribosomes form a unique structural interface to induce Hel2‐driven quality control pathways
Ribosome stalling triggers quality control pathways targeting the mRNA (NGD: no‐go decay) and the nascent polypeptide (RQC: ribosome‐associated quality control). RQC requires Hel2‐dependent uS10 ubiquitination and the RQT complex in yeast. Here, we report that Hel2‐dependent uS10 ubiquitination and...
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| Published in: | The EMBO journal Vol. 38; no. 5 |
|---|---|
| Main Authors: | , , , , , , , , , |
| Format: | Journal Article |
| Language: | English |
| Published: |
London
Nature Publishing Group UK
01.03.2019
Springer Nature B.V John Wiley and Sons Inc |
| Subjects: | |
| ISSN: | 0261-4189, 1460-2075, 1460-2075 |
| Online Access: | Get full text |
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| Abstract | Ribosome stalling triggers quality control pathways targeting the mRNA (NGD: no‐go decay) and the nascent polypeptide (RQC: ribosome‐associated quality control). RQC requires Hel2‐dependent uS10 ubiquitination and the RQT complex in yeast. Here, we report that Hel2‐dependent uS10 ubiquitination and Slh1/Rqt2 are crucial for RQC and NGD induction within a di‐ribosome (disome) unit, which consists of the leading stalled ribosome and the following colliding ribosome. Hel2 preferentially ubiquitinated a disome over a monosome on a quality control inducing reporter mRNA in an
in vitro
translation reaction. Cryo‐EM analysis of the disome unit revealed a distinct structural arrangement suitable for recognition and modification by Hel2. The absence of the RQT complex or uS10 ubiquitination resulted in the elimination of NGD within the disome unit. Instead, we observed Hel2‐mediated cleavages upstream of the disome, governed by initial Not4‐mediated monoubiquitination of eS7 and followed by Hel2‐mediated K63‐linked polyubiquitination. We propose that Hel2‐mediated ribosome ubiquitination is required both for canonical NGD (NGD
RQC
+
) and RQC coupled to the disome and that RQC‐uncoupled NGD outside the disome (NGD
RQC
−
) can occur in a Not4‐dependent manner.
Synopsis
Ribosome stalling triggers both ribosome‐associated quality control (RQC) of nascent polypeptides and no‐go decay (NGD) of mRNA. Structural and biochemical data show that collided ribosomes form a unique structural unit allowing the Hel2 ubiquitin ligase to operate in both pathways.
Hel2‐mediated uS10 ubiquitination and Slh1/Rqt2 are crucial for RQC and NGD induction within a di‐ribosome (disome) unit.
Cryo‐EM reveals a unique composite interface between the small subunits of the stalled leading and the following colliding ribosome, which can serve as stalling‐recognition pattern for Hel2.
Hel2 preferentially ubiquitinates colliding ribosomes, where Hel2 ubiquitination targets on the respective small subunits congregate in close vicinity.
Two distinct NGD branches act differentially on or near a disome unit, one coupled to and one uncoupled from RQC.
RQC‐uncoupled NGD is characterized by Not4‐mediated mono‐ubiquitination followed by Hel2‐mediated polyubiquitination of ribosomal protein eS7, resulting in mRNA cleavage upstream of the disome unit.
Graphical Abstract
Yeast Hel2 ubiquitin ligase functions in both ribosome‐associated protein quality control and canonical mRNA no‐go decay pathways coupled to disome units. |
|---|---|
| AbstractList | Ribosome stalling triggers quality control pathways targeting the mRNA (NGD: no‐go decay) and the nascent polypeptide (RQC: ribosome‐associated quality control). RQC requires Hel2‐dependent uS10 ubiquitination and the RQT complex in yeast. Here, we report that Hel2‐dependent uS10 ubiquitination and Slh1/Rqt2 are crucial for RQC and NGD induction within a di‐ribosome (disome) unit, which consists of the leading stalled ribosome and the following colliding ribosome. Hel2 preferentially ubiquitinated a disome over a monosome on a quality control inducing reporter mRNA in an in vitro translation reaction. Cryo‐EM analysis of the disome unit revealed a distinct structural arrangement suitable for recognition and modification by Hel2. The absence of the RQT complex or uS10 ubiquitination resulted in the elimination of NGD within the disome unit. Instead, we observed Hel2‐mediated cleavages upstream of the disome, governed by initial Not4‐mediated monoubiquitination of eS7 and followed by Hel2‐mediated K63‐linked polyubiquitination. We propose that Hel2‐mediated ribosome ubiquitination is required both for canonical NGD (NGDRQC
+) and RQC coupled to the disome and that RQC‐uncoupled NGD outside the disome (NGDRQC
−) can occur in a Not4‐dependent manner. Ribosome stalling triggers quality control pathways targeting the mRNA (NGD: no‐go decay) and the nascent polypeptide (RQC: ribosome‐associated quality control). RQC requires Hel2‐dependent uS10 ubiquitination and the RQT complex in yeast. Here, we report that Hel2‐dependent uS10 ubiquitination and Slh1/Rqt2 are crucial for RQC and NGD induction within a di‐ribosome (disome) unit, which consists of the leading stalled ribosome and the following colliding ribosome. Hel2 preferentially ubiquitinated a disome over a monosome on a quality control inducing reporter mRNA in an in vitro translation reaction. Cryo‐EM analysis of the disome unit revealed a distinct structural arrangement suitable for recognition and modification by Hel2. The absence of the RQT complex or uS10 ubiquitination resulted in the elimination of NGD within the disome unit. Instead, we observed Hel2‐mediated cleavages upstream of the disome, governed by initial Not4‐mediated monoubiquitination of eS7 and followed by Hel2‐mediated K63‐linked polyubiquitination. We propose that Hel2‐mediated ribosome ubiquitination is required both for canonical NGD (NGD RQC + ) and RQC coupled to the disome and that RQC‐uncoupled NGD outside the disome (NGD RQC − ) can occur in a Not4‐dependent manner. Synopsis Ribosome stalling triggers both ribosome‐associated quality control (RQC) of nascent polypeptides and no‐go decay (NGD) of mRNA. Structural and biochemical data show that collided ribosomes form a unique structural unit allowing the Hel2 ubiquitin ligase to operate in both pathways. Hel2‐mediated uS10 ubiquitination and Slh1/Rqt2 are crucial for RQC and NGD induction within a di‐ribosome (disome) unit. Cryo‐EM reveals a unique composite interface between the small subunits of the stalled leading and the following colliding ribosome, which can serve as stalling‐recognition pattern for Hel2. Hel2 preferentially ubiquitinates colliding ribosomes, where Hel2 ubiquitination targets on the respective small subunits congregate in close vicinity. Two distinct NGD branches act differentially on or near a disome unit, one coupled to and one uncoupled from RQC. RQC‐uncoupled NGD is characterized by Not4‐mediated mono‐ubiquitination followed by Hel2‐mediated polyubiquitination of ribosomal protein eS7, resulting in mRNA cleavage upstream of the disome unit. Graphical Abstract Yeast Hel2 ubiquitin ligase functions in both ribosome‐associated protein quality control and canonical mRNA no‐go decay pathways coupled to disome units. Ribosome stalling triggers quality control pathways targeting the mRNA (NGD: no‐go decay) and the nascent polypeptide (RQC: ribosome‐associated quality control). RQC requires Hel2‐dependent uS10 ubiquitination and the RQT complex in yeast. Here, we report that Hel2‐dependent uS10 ubiquitination and Slh1/Rqt2 are crucial for RQC and NGD induction within a di‐ribosome (disome) unit, which consists of the leading stalled ribosome and the following colliding ribosome. Hel2 preferentially ubiquitinated a disome over a monosome on a quality control inducing reporter mRNA in an in vitro translation reaction. Cryo‐EM analysis of the disome unit revealed a distinct structural arrangement suitable for recognition and modification by Hel2. The absence of the RQT complex or uS10 ubiquitination resulted in the elimination of NGD within the disome unit. Instead, we observed Hel2‐mediated cleavages upstream of the disome, governed by initial Not4‐mediated monoubiquitination of eS7 and followed by Hel2‐mediated K63‐linked polyubiquitination. We propose that Hel2‐mediated ribosome ubiquitination is required both for canonical NGD (NGDRQC+) and RQC coupled to the disome and that RQC‐uncoupled NGD outside the disome (NGDRQC−) can occur in a Not4‐dependent manner. Synopsis Ribosome stalling triggers both ribosome‐associated quality control (RQC) of nascent polypeptides and no‐go decay (NGD) of mRNA. Structural and biochemical data show that collided ribosomes form a unique structural unit allowing the Hel2 ubiquitin ligase to operate in both pathways. Hel2‐mediated uS10 ubiquitination and Slh1/Rqt2 are crucial for RQC and NGD induction within a di‐ribosome (disome) unit. Cryo‐EM reveals a unique composite interface between the small subunits of the stalled leading and the following colliding ribosome, which can serve as stalling‐recognition pattern for Hel2. Hel2 preferentially ubiquitinates colliding ribosomes, where Hel2 ubiquitination targets on the respective small subunits congregate in close vicinity. Two distinct NGD branches act differentially on or near a disome unit, one coupled to and one uncoupled from RQC. RQC‐uncoupled NGD is characterized by Not4‐mediated mono‐ubiquitination followed by Hel2‐mediated polyubiquitination of ribosomal protein eS7, resulting in mRNA cleavage upstream of the disome unit. Yeast Hel2 ubiquitin ligase functions in both ribosome‐associated protein quality control and canonical mRNA no‐go decay pathways coupled to disome units. Ribosome stalling triggers quality control pathways targeting the mRNA (NGD: no-go decay) and the nascent polypeptide (RQC: ribosome-associated quality control). RQC requires Hel2-dependent uS10 ubiquitination and the RQT complex in yeast. Here, we report that Hel2-dependent uS10 ubiquitination and Slh1/Rqt2 are crucial for RQC and NGD induction within a di-ribosome (disome) unit, which consists of the leading stalled ribosome and the following colliding ribosome. Hel2 preferentially ubiquitinated a disome over a monosome on a quality control inducing reporter mRNA in an in vitro translation reaction. Cryo-EM analysis of the disome unit revealed a distinct structural arrangement suitable for recognition and modification by Hel2. The absence of the RQT complex or uS10 ubiquitination resulted in the elimination of NGD within the disome unit. Instead, we observed Hel2-mediated cleavages upstream of the disome, governed by initial Not4-mediated monoubiquitination of eS7 and followed by Hel2-mediated K63-linked polyubiquitination. We propose that Hel2-mediated ribosome ubiquitination is required both for canonical NGD (NGDRQC+) and RQC coupled to the disome and that RQC-uncoupled NGD outside the disome (NGDRQC-) can occur in a Not4-dependent manner.Ribosome stalling triggers quality control pathways targeting the mRNA (NGD: no-go decay) and the nascent polypeptide (RQC: ribosome-associated quality control). RQC requires Hel2-dependent uS10 ubiquitination and the RQT complex in yeast. Here, we report that Hel2-dependent uS10 ubiquitination and Slh1/Rqt2 are crucial for RQC and NGD induction within a di-ribosome (disome) unit, which consists of the leading stalled ribosome and the following colliding ribosome. Hel2 preferentially ubiquitinated a disome over a monosome on a quality control inducing reporter mRNA in an in vitro translation reaction. Cryo-EM analysis of the disome unit revealed a distinct structural arrangement suitable for recognition and modification by Hel2. The absence of the RQT complex or uS10 ubiquitination resulted in the elimination of NGD within the disome unit. Instead, we observed Hel2-mediated cleavages upstream of the disome, governed by initial Not4-mediated monoubiquitination of eS7 and followed by Hel2-mediated K63-linked polyubiquitination. We propose that Hel2-mediated ribosome ubiquitination is required both for canonical NGD (NGDRQC+) and RQC coupled to the disome and that RQC-uncoupled NGD outside the disome (NGDRQC-) can occur in a Not4-dependent manner. Ribosome stalling triggers quality control pathways targeting the mRNA (NGD: no-go decay) and the nascent polypeptide (RQC: ribosome-associated quality control). RQC requires Hel2-dependent uS10 ubiquitination and the RQT complex in yeast. Here, we report that Hel2-dependent uS10 ubiquitination and Slh1/Rqt2 are crucial for RQC and NGD induction within a di-ribosome (disome) unit, which consists of the leading stalled ribosome and the following colliding ribosome. Hel2 preferentially ubiquitinated a disome over a monosome on a quality control inducing reporter mRNA in an translation reaction. Cryo-EM analysis of the disome unit revealed a distinct structural arrangement suitable for recognition and modification by Hel2. The absence of the RQT complex or uS10 ubiquitination resulted in the elimination of NGD within the disome unit. Instead, we observed Hel2-mediated cleavages upstream of the disome, governed by initial Not4-mediated monoubiquitination of eS7 and followed by Hel2-mediated K63-linked polyubiquitination. We propose that Hel2-mediated ribosome ubiquitination is required both for canonical NGD (NGD ) and RQC coupled to the disome and that RQC-uncoupled NGD outside the disome (NGD ) can occur in a Not4-dependent manner. Ribosome stalling triggers quality control pathways targeting the mRNA (NGD: no‐go decay) and the nascent polypeptide (RQC: ribosome‐associated quality control). RQC requires Hel2‐dependent uS10 ubiquitination and the RQT complex in yeast. Here, we report that Hel2‐dependent uS10 ubiquitination and Slh1/Rqt2 are crucial for RQC and NGD induction within a di‐ribosome (disome) unit, which consists of the leading stalled ribosome and the following colliding ribosome. Hel2 preferentially ubiquitinated a disome over a monosome on a quality control inducing reporter mRNA in an in vitro translation reaction. Cryo‐EM analysis of the disome unit revealed a distinct structural arrangement suitable for recognition and modification by Hel2. The absence of the RQT complex or uS10 ubiquitination resulted in the elimination of NGD within the disome unit. Instead, we observed Hel2‐mediated cleavages upstream of the disome, governed by initial Not4‐mediated monoubiquitination of eS7 and followed by Hel2‐mediated K63‐linked polyubiquitination. We propose that Hel2‐mediated ribosome ubiquitination is required both for canonical NGD (NGDRQC+) and RQC coupled to the disome and that RQC‐uncoupled NGD outside the disome (NGDRQC−) can occur in a Not4‐dependent manner. |
| Author | Inada, Toshifumi Tanaka, Keiji Beckmann, Roland Ikeuchi, Ken Cheng, Jingdong Sugiyama, Takato Becker, Thomas Tesina, Petr Saeki, Yasushi Matsuo, Yoshitaka |
| AuthorAffiliation | 1 Graduate School of Pharmaceutical Sciences Tohoku University Sendai Japan 2 Department of Biochemistry Gene Center and Center for Integrated Protein Science Munich University of Munich Munich Germany 3 Laboratory of Protein Metabolism Tokyo Metropolitan Institute of Medical Science Setagaya‐ku, Tokyo Japan |
| AuthorAffiliation_xml | – name: 1 Graduate School of Pharmaceutical Sciences Tohoku University Sendai Japan – name: 3 Laboratory of Protein Metabolism Tokyo Metropolitan Institute of Medical Science Setagaya‐ku, Tokyo Japan – name: 2 Department of Biochemistry Gene Center and Center for Integrated Protein Science Munich University of Munich Munich Germany |
| Author_xml | – sequence: 1 givenname: Ken orcidid: 0000-0002-9578-7920 surname: Ikeuchi fullname: Ikeuchi, Ken organization: Graduate School of Pharmaceutical Sciences, Tohoku University – sequence: 2 givenname: Petr orcidid: 0000-0002-5227-1799 surname: Tesina fullname: Tesina, Petr organization: Department of Biochemistry, Gene Center and Center for Integrated Protein Science Munich, University of Munich – sequence: 3 givenname: Yoshitaka surname: Matsuo fullname: Matsuo, Yoshitaka organization: Graduate School of Pharmaceutical Sciences, Tohoku University – sequence: 4 givenname: Takato orcidid: 0000-0001-8364-7050 surname: Sugiyama fullname: Sugiyama, Takato organization: Graduate School of Pharmaceutical Sciences, Tohoku University – sequence: 5 givenname: Jingdong surname: Cheng fullname: Cheng, Jingdong organization: Department of Biochemistry, Gene Center and Center for Integrated Protein Science Munich, University of Munich – sequence: 6 givenname: Yasushi orcidid: 0000-0002-9202-5453 surname: Saeki fullname: Saeki, Yasushi organization: Laboratory of Protein Metabolism, Tokyo Metropolitan Institute of Medical Science – sequence: 7 givenname: Keiji surname: Tanaka fullname: Tanaka, Keiji organization: Laboratory of Protein Metabolism, Tokyo Metropolitan Institute of Medical Science – sequence: 8 givenname: Thomas orcidid: 0000-0001-8458-2738 surname: Becker fullname: Becker, Thomas organization: Department of Biochemistry, Gene Center and Center for Integrated Protein Science Munich, University of Munich – sequence: 9 givenname: Roland orcidid: 0000-0003-4291-3898 surname: Beckmann fullname: Beckmann, Roland email: beckmann@genzentrum.lmu.de organization: Department of Biochemistry, Gene Center and Center for Integrated Protein Science Munich, University of Munich – sequence: 10 givenname: Toshifumi orcidid: 0000-0002-2695-588X surname: Inada fullname: Inada, Toshifumi email: tinada@m.tohoku.ac.jp organization: Graduate School of Pharmaceutical Sciences, Tohoku University |
| BackLink | https://www.ncbi.nlm.nih.gov/pubmed/30609991$$D View this record in MEDLINE/PubMed |
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| Snippet | Ribosome stalling triggers quality control pathways targeting the mRNA (NGD: no‐go decay) and the nascent polypeptide (RQC: ribosome‐associated quality... Ribosome stalling triggers quality control pathways targeting the mRNA (NGD: no-go decay) and the nascent polypeptide (RQC: ribosome-associated quality... |
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| SubjectTerms | Cryoelectron Microscopy Decay EMBO31 EMBO32 EMBO40 mRNA mRNA turnover no‐go mRNA decay Pattern recognition Polypeptides Protein Biosynthesis Proteins Quality control Ribosomal Proteins - genetics Ribosomal Proteins - metabolism ribosome collision ribosome quality control Ribosomes Ribosomes - metabolism Ribosomes - ultrastructure RNA Stability RNA, Messenger - genetics RNA, Messenger - metabolism RQT complex Saccharomyces cerevisiae - genetics Saccharomyces cerevisiae - metabolism Saccharomyces cerevisiae Proteins - genetics Saccharomyces cerevisiae Proteins - metabolism Stalling Ubiquitin Ubiquitin - metabolism Ubiquitin-protein ligase Ubiquitin-Protein Ligases - genetics Ubiquitin-Protein Ligases - metabolism Ubiquitination Upstream Yeast |
| Title | Collided ribosomes form a unique structural interface to induce Hel2‐driven quality control pathways |
| URI | https://link.springer.com/article/10.15252/embj.2018100276 https://onlinelibrary.wiley.com/doi/abs/10.15252%2Fembj.2018100276 https://www.ncbi.nlm.nih.gov/pubmed/30609991 https://www.proquest.com/docview/2186968044 https://www.proquest.com/docview/2164104426 https://pubmed.ncbi.nlm.nih.gov/PMC6396155 |
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