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: Ikeuchi, Ken, Tesina, Petr, Matsuo, Yoshitaka, Sugiyama, Takato, Cheng, Jingdong, Saeki, Yasushi, Tanaka, Keiji, Becker, Thomas, Beckmann, Roland, Inada, Toshifumi
Format: Journal Article
Language:English
Published: London Nature Publishing Group UK 01.03.2019
Springer Nature B.V
John Wiley and Sons Inc
Subjects:
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
no‐go mRNA decay
ribosome quality control
RQT complex
ubiquitination
ribosome collision
ISSN:0261-4189, 1460-2075, 1460-2075
Online Access:Get full text
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Summary: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.
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See also: LL Yan & HS Zaher (March 2019)
These authors contributed equally to this work
ISSN:0261-4189
1460-2075
1460-2075
DOI:10.15252/embj.2018100276