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Collision-induced ribosome degradation driven by ribosome competition and translational perturbations

How translation affects ribosome stability is an intriguing question. Here, the authors uncover a collision-induced small subunit turnover pathway that selectively removes suboptimal ribosomes during ribosome competition and alters subunit abundance under stress-related translational perturbations.

Sihan Li
Okuto Shounai
Toshifumi Inada
ResearchOpen Access12 Dec 2025
Nature Communications

Volume: 16, P: 1-17
The mechanistic basis and cellular functions of UFMylation

UFMylation, a ubiquitin-like modification, regulates endoplasmic reticulum-associated ribosome quality control by conjugating UFM1 to the ribosomal subunit RPL26, preserving ribosome integrity under stress. This Review explores the structural basis of UFMylation and its emerging functional breadth, and it discusses putative UFMylation substrates.

Masaaki Komatsu
Nobuo N. Noda
Toshifumi Inada
Reviews09 Jan 2026
Nature Reviews Molecular Cell Biology

P: 1-14
Publisher Correction: Structure and function of Vms1 and Arb1 in RQC and mitochondrial proteome homeostasis

Ting Su
Toshiaki Izawa
Roland Beckmann
Amendments and Corrections25 Jun 2019
Nature

Volume: 571, P: E4
A distinct mammalian disome collision interface harbors K63-linked polyubiquitination of uS10 to trigger hRQT-mediated subunit dissociation

Collided ribosomes are marked by ubiquitination to induce quality control mechanisms. Here, authors show that mammalian disomes form a distinct structural interface, in which uS10 K63-linked polyubiquitination is critical for ribosome dissociation.

Momoko Narita
Timo Denk
Toshifumi Inada
ResearchOpen Access27 Oct 2022
Nature Communications

Volume: 13, P: 1-16
RQT complex dissociates ribosomes collided on endogenous RQC substrate SDD1

Identification of SDD1 mRNA from Saccharomyces cerevisiae as an endogenous RQC substrate allows analysis of the mechanism underlying translational stalling and Hel2-dependent polyubiquitination of collided ribosomes to provide insight into ribosome dissociation.

Yoshitaka Matsuo
Petr Tesina
Toshifumi Inada
Research23 Mar 2020
Nature Structural & Molecular Biology

Volume: 27, P: 323-332
Herpes simplex virus 1 evades APOBEC1-mediated immunity via its uracil-DNA glycosylase in mice

The herpes simplex virus 1 uracil-DNA glycosylase counters host APOBEC1 to evade genome editing and to enable viral replication that promotes encephalitis in mice.

Akihisa Kato
Hayato Harima
Yasushi Kawaguchi
Research03 Jun 2025
Nature Microbiology

Volume: 10, P: 1758-1774
Crucial roles of Grr1 in splicing and translation of HAC1 mRNA upon unfolded stress response

Ribosome ubiquitination regulates HAC1 mRNA processing during the unfolded protein response. Here, the authors show that the SCFGrr1 complex promotes HAC1 mRNA splicing and translation by degrading the deubiquitinating enzyme Ubp3, thereby maintaining eS7A monoubiquitination to facilitate HAC1i translation.

Nichika Sato
Yu Nakano
Toshifumi Inada
ResearchOpen Access04 Mar 2025
Nature Communications

Volume: 16, P: 1-16
The proteasome’s balancing act

The 26S proteasome is conventionally viewed as a destroyer of proteins. However, it is now shown to help stabilize RNAs and thus fine-tune a plant’s anti-viral defences.

Toshifumi Inada
News & Views18 Nov 2019
Nature Plants

Volume: 5, P: 1203-1204
Structural basis for clearing of ribosome collisions by the RQT complex

Ribosome collisions serve as proxy for aberrant translation to initiate rescue and quality control pathways. Here, authors elucidate the molecular mechanism of collided ribosome clearance by the ribosome quality control trigger complex.

Katharina Best
Ken Ikeuchi
Roland Beckmann
ResearchOpen Access17 Feb 2023
Nature Communications

Volume: 14, P: 1-12
The UFM1 system regulates ER-phagy through the ufmylation of CYB5R3

The UFM1 system, a ubiquitin-like conjugation system is crucial for endoplasmic reticulum (ER) homeostasis. Here, authors found that CYB5R3 is covalently conjugated with UFM1, which becomes a signal for ER-phagy, a selective autophagy of ER.

Ryosuke Ishimura
Afnan H. El-Gowily
Masaaki Komatsu
ResearchOpen Access21 Dec 2022
Nature Communications

Volume: 13, P: 1-16
Decoding of the ubiquitin code for clearance of colliding ribosomes by the RQT complex

The colliding ribosomes are ubiquitinated by the sensor protein Hel2, leading to noncanonical subunit dissociation by the ribosome associated quality control trigger (RQT) complex. Here the authors reveal the decoding mechanism of the ribosome ubiquitin code by the RQT complex.

Yoshitaka Matsuo
Takayuki Uchihashi
Toshifumi Inada
ResearchOpen Access10 Jan 2023
Nature Communications

Volume: 14, P: 1-12
Profiles of Extracellular miRNAs in the Aqueous Humor of Glaucoma Patients Assessed with a Microarray System

Yuji Tanaka
Satoru Tsuda
Toru Nakazawa
ResearchOpen Access28 May 2014
Scientific Reports

Volume: 4, P: 1-7
Molecular basis for recognition and deubiquitination of 40S ribosomes by Otu2

Otu2-driven deubiquitylation of ribosomal protein eS7 impacts translational efficiency. Here, the authors provide the molecular basis for recognition of monoubiquitinated eS7 on 40S and give mechanistic insights into Otu2’s role in translation reset.

Ken Ikeuchi
Nives Ivic
Roland Beckmann
ResearchOpen Access12 May 2023
Nature Communications

Volume: 14, P: 1-15
Stress- and ubiquitylation-dependent phase separation of the proteasome

Hyperosmotic stress leads to a phase separation of the proteasome, triggered by interactions between RAD23B and ubiquitylated proteins, which bring together p97 and proteasome-associated proteins into nuclear proteolytic foci.

Sayaka Yasuda
Hikaru Tsuchiya
Yasushi Saeki
Research05 Feb 2020
Nature

Volume: 578, P: 296-300
Structure and function of Vms1 and Arb1 in RQC and mitochondrial proteome homeostasis

Cryo-electron microscopy structures of the yeast 60S ribosomal subunit in complex with Vms1 provides insights into the roles of proteins in the ribosome-associated quality control pathway.

Ting Su
Toshiaki Izawa
Roland Beckmann
Research12 Jun 2019
Nature

Volume: 570, P: 538-542
FUS regulates AMPA receptor function and FTLD/ALS-associated behaviour via GluA1 mRNA stabilization

FUS is an RNA/DNA-binding protein involved in gene expression regulation and associated with amyotrophic lateral sclerosis and frontotemporal dementia (FTLD) but the disease-causing mechanisms are unclear. Here the authors show that FUS regulates the stability of GluA1mRNA and dendritic maturation and plays a role in FTLD-associated behaviours.

Tsuyoshi Udagawa
Yusuke Fujioka
Gen Sobue
ResearchOpen Access13 May 2015
Nature Communications

Volume: 6, P: 1-13
Ubiquitination of stalled ribosome triggers ribosome-associated quality control

Several protein quality control mechanisms are in place to trigger the rapid degradation of aberrant polypeptides and mRNAs. Here the authors describe a mechanism of ribosome-mediated quality control that involves the ubiquitination of ribosomal proteins by the E3 ubiquitin ligase Hel2/RQT1.

Yoshitaka Matsuo
Ken Ikeuchi
Toshifumi Inada
ResearchOpen Access31 Jul 2017
Nature Communications

Volume: 8, P: 1-14
tRNA recycling on stalled ribosomes

In the ribosome-associated quality control (RQC) pathway, stalled ribosomes are ubiquitinated and dissociated into subunits. The nascent protein chain associated with the 60S ribosomal subunit is ubiquitinated by the E3 ligase Listerin (Ltn1) and is released from tRNA by ANKZF1 (Vms1) for proteasomal degradation. Shao and colleagues now report that ANKZF1 (Vms1)-cleaved tRNAs are recycled via a two-step process that requires the removal of a terminal 2′,3′-cyclic phosphate and the addition of CCA by TRNT1.

Toshifumi Inada
News & Views22 Apr 2019
Nature Structural & Molecular Biology

Volume: 26, P: 340-342
Ribosome-associated Asc1/RACK1 is required for endonucleolytic cleavage induced by stalled ribosome at the 3′ end of nonstop mRNA

Ken Ikeuchi
Toshifumi Inada
ResearchOpen Access17 Jun 2016
Scientific Reports

Volume: 6, P: 1-10
Identification of a novel trigger complex that facilitates ribosome-associated quality control in mammalian cells

Satoshi Hashimoto
Takato Sugiyama
Toshifumi Inada
ResearchOpen Access25 Feb 2020
Scientific Reports

Volume: 10, P: 1-12
Ribosomal protein S7 ubiquitination during ER stress in yeast is associated with selective mRNA translation and stress outcome

Yasuko Matsuki
Yoshitaka Matsuo
Toshifumi Inada
ResearchOpen Access12 Nov 2020
Scientific Reports

Volume: 10, P: 1-15
Microcrystalline array structures induced by heat treatment of friction-transferred organic semiconductor films

Yuhi Inada
Masashi Koda
Shu Hotta
ResearchOpen Access05 Jul 2019
Scientific Reports

Volume: 9, P: 1-11

Search

Collision-induced ribosome degradation driven by ribosome competition and translational perturbations

The mechanistic basis and cellular functions of UFMylation

Publisher Correction: Structure and function of Vms1 and Arb1 in RQC and mitochondrial proteome homeostasis

A distinct mammalian disome collision interface harbors K63-linked polyubiquitination of uS10 to trigger hRQT-mediated subunit dissociation

RQT complex dissociates ribosomes collided on endogenous RQC substrate SDD1

Herpes simplex virus 1 evades APOBEC1-mediated immunity via its uracil-DNA glycosylase in mice

Crucial roles of Grr1 in splicing and translation of HAC1 mRNA upon unfolded stress response

The proteasome’s balancing act

Structural basis for clearing of ribosome collisions by the RQT complex

The UFM1 system regulates ER-phagy through the ufmylation of CYB5R3

Decoding of the ubiquitin code for clearance of colliding ribosomes by the RQT complex

Profiles of Extracellular miRNAs in the Aqueous Humor of Glaucoma Patients Assessed with a Microarray System

Molecular basis for recognition and deubiquitination of 40S ribosomes by Otu2

Stress- and ubiquitylation-dependent phase separation of the proteasome

Structure and function of Vms1 and Arb1 in RQC and mitochondrial proteome homeostasis

FUS regulates AMPA receptor function and FTLD/ALS-associated behaviour via GluA1 mRNA stabilization

Ubiquitination of stalled ribosome triggers ribosome-associated quality control

tRNA recycling on stalled ribosomes

Ribosome-associated Asc1/RACK1 is required for endonucleolytic cleavage induced by stalled ribosome at the 3′ end of nonstop mRNA

Identification of a novel trigger complex that facilitates ribosome-associated quality control in mammalian cells

Ribosomal protein S7 ubiquitination during ER stress in yeast is associated with selective mRNA translation and stress outcome

Microcrystalline array structures induced by heat treatment of friction-transferred organic semiconductor films

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