Ribosome-associated quality control

Stable Identifier
R-HSA-9948299
DOI
Type
Pathway
Species
Homo sapiens
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5/5
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Features such as damaged nucleotides, strong secondary structure, presence of stretches of more than four uninterrupted AAA codons in a mRNA coding region (designated a no-go mRNA) or the absence of a stop codon in a mRNA (a non-stop mRNA) can cause a ribosome to stall during translation and the stalled ribosome can cause collisions with trailing ribosomes on the mRNA (reviewed in Joazeiro 2017, Eisenack and Trentini 2022, Filbeck et al. 2022, McGirr et al. 2025).
In cases in which the ribosome stalls internally on the mRNA and a 3' region of the mRNA protrudes from the ribosome, ZNF598, a ubiquitin E3 ligase that is the homolog of yeast HEL2, binds the ribosome (Garzia et al. 2017, Juszkiewicz and Hegde 2017, Sundaramoorthy et al. 2017) and catalyzes the lysine-63 (K63) linked ubiquitination of the 40S subunit ribosomal proteins eS10 (RPS10) at residues K138 and K139 and uS10 (RPS20) at residues K4 and K8 to initiate splitting of the 40S and 60S ribosomal subunits (Juszkiewicz and Hegde 2017, Sundaramoorthy et al. 2017, Garzia et al. 2017, Juszkiewicz et al. 2018, Narita et al. 2022, Miścicka et al. 2024, also inferred from yeast homologs in Matsuo et al. 2017, Sitron et al. 2017, Ikeuchi et al. 2019, reviewed in Ford et al. 2024). RACK1 then stabilizes the interface between the 40S subunits of the collided ribosomes to enable the ubiquitination of ribosomal proteins by ZNF598 (Sundaramoorthy et al. 2017). RACK1 is also required for the recruitment of EDF1 which has been proposed by structural studies to stabilize the collision interface through a conserved KKW motif and an alpha-helical segment that clamps the mRNA (Sinha et al. 2020). Additionally, EDF1 recruits the 4EHP-GIGYF2 complex to the collided ribosome to mediate translational repression of aberrant mRNAs (Sinha et al. 2020, Juszkiewicz et al. 2020), a mechanism which can also be initiated by ZNF598 (Hickey et al. 2020).
The ASCC2 subunit (Narita et al. 2022) of the ribosome quality control trigger complex (ASCC, ASC-1 complex, ASCC2:ASCC3:TRIP4, homologue of the RQT complex in yeast) binds K63-linked polyubiquitin conjugated to the 40S protein uS10 (Hashimoto et al. 2020, Juszkiewicz et al. 2020, Narita et al. 2022, and inferred from yeast homologs in Matsuo et al. 2023). The ASCC3 subunit of the RQT complex splits stalled 80S ribosomes with K63-polyubiquitinated uS10 into 60S and 40S subunits (Hashimoto et al. 2020, Juszkiewicz et al. 2020, Narita et al. 2022, Miścicka et al. 2024) apparently by exerting a pulling force on the mRNA (inferred from the yeast homolog Slh1 in Best et al. 2023). The peptidyl-tRNA remains bound in the 60S subunit, with the tRNA positioned in the P site. The problematic mRNA dissociates after splitting and is thought to be degraded at this time. In the case of collided yeast ribosomes, the mRNA is first endonucleolytically cleaved and the cleavage products are exonucleolytically degraded by XRN1 and the exosome (Ikeuchi et al. 2019).
Non-stop mRNAs result in ribosomal stalls proximal to the 3' end of the mRNA, which are resolved by a distinct pathway. In this case, a complex comprising PELO, a paralog of the ribosome release factor eRF1, and HBS1L:GTP, a paralog of the ribosome release factor eRF3:GTP, binds the stalled ribosome near the subunit interface and the mRNA entry site (Shao et al. 2013, and inferred from human PELO:HBS1L and rabbit ribosomes in Pisareva et al. 2011, inferred from yeast homologs DOM34:HBS1 in Shoemaker et al. 2010, Tsuboi et al. 2012, Guydosh and Green 2014, reviewed in Franckenberg et al. 2012). PELO:HBS1L preferentially acts on ribosomes that are bound to mRNAs that have fewer than 12 nucleotides extending 3' of the ribosomal P site (Pisareva et al. 2011).
HBS1L hydrolyzes GTP and dissociates from PELO and the ribosome, exposing a site on PELO to which ABCE1 binds. ABCE1 then hydrolyzes ATP to cause a conformational change that splits the ribosome into 40S and 60S subunits (Shao et al. 2013, Shao and Hegde 2014, and inferred from the yeast homologs DOM34:HBS1 and archaeal homologs in Becker et al. 2012, inferred from the yeast homologs in Saito et al. 2013). ABCE1 and possibly the mRNA remain bound to the 40S ribosomal subunit, while the peptidyl-tRNA remains bound to the 60S ribosomal subunit as in the ASCC-mediated rescue pathway (Becker et al. 2012, reviewed in Franckenberg et al. 2012).
At this stage of either pathway, the 40S subunit can be deubiquitinated [by OTUD3, USP21, or USP10] which may be necessary to license the 40S for further rounds of translation (Garshott et al. 2020, Meyer et al. 2020). In contrast, the 60S-peptidyl-tRNA complex requires additional steps to extract and destroy the nascent polypeptide before the 60S subunit can be recycled.
NEMF (the human homolog of yeast RQC2) binds the exposed peptidyl-tRNA of the isolated 60S ribosomal subunit produced by either the RQT complex or ABCE1 and transfers alanine residues from aminoacyl tRNAs to the C-terminus of the nascent peptide, a process termed Carboxy-terminal Alanine and Threonine tailing (CAT-tailing) after the alanine and threonine tails observed in yeast (Udagawa et al. 2021, Thrun et al. 2021, inferred from the yeast homolog RQC2 in Shen et al. 2015, Kostova et al. 2017, Osuna et al. 2017). Structures of CAT-tailing intermediates in yeast indicate that RQC2 positions an aminoacyl-tRNA in the A site of the 60S subunit and eIF5A enables peptidyl transfer (Shen et al. 2015, Tesina et al. 2023).
The alanine C-terminal tails are believed to push the nascent peptide through the exit tunnel of the 60S ribosomal subunit to expose lysine residues for K48-linked ubiquitination by Listerin (LTN1), however alanine tails can cause aggregation of nascent peptides (Udagawa et al. 2021, and inferred from yeast homologs in Yonashiro et al. 2016). The alanine tails can also act as degrons by binding the CRL2-KHDC10 ubiquitin E3 ligase complex (Thrun et al. 2021, Patil et al. 2023) or the RCHY1 (PIRH2) ubiquitin E3 ligase (Thrun et al. 2021, Patil et al. 2023, Wang et al. 2023) CRL2-KHDC10 and RCHY1 ubiquitinate the nascent peptide using K48 polyubiquitin linkages, targeting the nascent peptide for destruction by the 26S proteasome.
Listerin (LTN1, also called RKR1 in yeast), a ubiquitin E3 ligase, is also capable of catalyzing the K48-linked ubiquitination of the nascent peptide after NEMF recruits LTN1 to the 60S ribosomal subunit (Shao et al. 2015). The N-terminal region of LTN1 contacts the 60S ribosomal subunit and NEMF while the C-terminal region of LTN1 binds the 60S ribosomal subunit near the exit tunnel (Shao et al. 2015, inferred from yeast homologs in Lyumkis et al. 2014). TCF25 (the homolog of RQC1 in yeast) interacts with LTN1 (inferred from yeast homologs in Defenouillère et al. 2013).
LTN1 ubiquitinates exposed lysine residues on the nascent peptide after the residues have emerged from the exit tunnel of the 60S ribosomal subunit (Osuna et al. 2017, Kuroha et al. 2018, Abaeva et al. 2025, inferred from yeast homologs in Bengtson and Joazeiro 2010, Shao et al. 2013, Shao and Hegde 2014, reviewed in Mishra et al. 2021). TCF25, the human homolog of RQC1 in yeast, interacts with the RING domain of LTN1 to orient the ubiquitin substrate molecules to produce lysine-48 (K48) linkages in the polyubiquitin product (Kuroha et al. 2018, Abaeva et al. 2025).
A hexamer of VCP subunits plus a heterodimer of UFDL1 (UFD1) and NPLOC4 bind polyubiquitin that contains lysine-48 linkages (K48polyUb) and is conjugated to the nascent peptide emerging from the exit tunnel of the 60S ribosomal subunit (Tsuchiya et al. 2017, Sato et al. 2019, Williams et al. 2023, and inferred from CDC48, the yeast orthologue of VCP, in Brandman et al. 2012, Defenouillère et al. 2013, Verma et al. 2013). In yeast, the Npl4:Ufd1 heterodimer (homolog of NPLOC4:UFD1L) acts as an adapter that binds K48-linked polyubiquitin and inserts it into the pore of the VCP hexamer (inferred from rat p97 and Ufd1:Npl4 in Meyer et al. 2000, reviewed in Meyer and van den Boom 2023).
ANKZF1, which interacts with VCP, cleaves the C-terminal 3 nucleotides, CCA, of the tRNA in the peptidyl-tRNA bound to the 60S ribosomal subunit, yielding a free tRNA and the nascent peptide covalently bound to the CCA sequence (Verma et al. 2018, Yip et al. 2019, and inferred from the yeast homolog, VMS1, in Verma et al. 2018, Yip et al. 2019). In yeast, Arb1 (mammalian ABCF2) occupies the E-site of the collided ribosome, extending a domain towards the peptidyl-tRNA that may help position it for release by Vms1/ANKZF1 (SU et al. 2019).
The VCP hexamer then extracts the ubiquitinated nascent peptide from the 60S ribosomal subunit. Six subunits of VCP surround the substrate protein, which is located in the central pore of the hexamer. Hydrolysis of ATP by a subunit causes it to disengage from the hexamer. Release of ADP and binding of ATP causes the subunit to rebind the hexamer more proximally to the 60S ribosomal subunit (reviewed in Meyer and van den Boom 2023). The result is a ratcheting effect that withdraws the nascent peptide from the 60S subunit. The extracted nascent peptide remains bound to the ribosome-associated quality control complex (RQC complex, LTN1:NEMF:TCF25:VCP hexamer) which dissociates from the 60S ribosomal subunit and escorts the nascent peptide to the proteasome (inferred from yeast homologs in Defenouillère et al. 2017). The region of the nascent peptide that is unfolded by the VCP hexamer is able to enter the proteasome, resulting in degradation of the nascent peptide (inferred from the yeast homolog CDC48 in Olszewski et al. 2019). After removal of the ubiquitinated nascent peptide and tRNA, and mRNA, the 60S subunit is able to be re-used in translation. The 40 S subunit is deubiquitinated by OTUD3 and USP21.
Literature References
PubMed ID Title Journal Year
32099016 Identification of a novel trigger complex that facilitates ribosome-associated quality control in mammalian cells

Hashimoto, S, Sugiyama, T, Yamazaki, R, Nobuta, R, Inada, T

Sci Rep 2020
36736315 The Ufd1 cofactor determines the linkage specificity of polyubiquitin chain engagement by the AAA+ ATPase Cdc48

Williams, C, Dong, KC, Arkinson, C, Martin, A

Mol Cell 2023
20835226 Role of a ribosome-associated E3 ubiquitin ligase in protein quality control

Bengtson, MH, Joazeiro, CA

Nature 2010
36302773 A distinct mammalian disome collision interface harbors K63-linked polyubiquitination of uS10 to trigger hRQT-mediated subunit dissociation

Narita, M, Denk, T, Matsuo, Y, Sugiyama, T, Kikuguchi, C, Ito, S, Sato, N, Suzuki, T, Hashimoto, S, Machová, I, Tesina, P, Beckmann, R, Inada, T

Nat Commun 2022
25554787 Protein synthesis. Rqc2p and 60S ribosomal subunits mediate mRNA-independent elongation of nascent chains

Shen, PS, Park, J, Qin, Y, Li, X, Parsawar, K, Larson, MH, Cox, J, Cheng, Y, Lambowitz, AM, Weissman, JS, Brandman, O, Frost, A

Science 2015
24581494 Dom34 rescues ribosomes in 3' untranslated regions

Guydosh, NR, Green, R

Cell 2014
36825201 Targeting of client proteins to the VCP/p97/Cdc48 unfolding machine

Meyer, H, van den Boom, J

Front Mol Biosci 2023
28715909 Ribosomal Stalling During Translation: Providing Substrates for Ribosome-Associated Protein Quality Control

Joazeiro, CAP

Annu Rev Cell Dev Biol 2017
28223409 Asc1, Hel2, and Slh1 couple translation arrest to nascent chain degradation

Sitron, CS, Park, JH, Brandman, O

RNA 2017
30293783 ZNF598 Is a Quality Control Sensor of Collided Ribosomes

Juszkiewicz, S, Chandrasekaran, V, Lin, Z, Kraatz, S, Ramakrishnan, V, Hegde, RS

Mol Cell 2018
36804914 Molecular basis of eIF5A-dependent CAT tailing in eukaryotic ribosome-associated quality control

Tesina, P, Ebine, S, Buschauer, R, Thoms, M, Matsuo, Y, Inada, T, Beckmann, R

Mol Cell 2023
28685749 The E3 ubiquitin ligase and RNA-binding protein ZNF598 orchestrates ribosome quality control of premature polyadenylated mRNAs

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Nat Commun 2017
23178123 A ribosome-bound quality control complex triggers degradation of nascent peptides and signals translation stress

Brandman, O, Stewart-Ornstein, J, Wong, D, Larson, A, Williams, CC, Li, GW, Zhou, S, King, D, Shen, PS, Weibezahn, J, Dunn, JG, Rouskin, S, Inada, T, Frost, A, Weissman, JS

Cell 2012
35452614 Ribosome-associated quality-control mechanisms from bacteria to humans

Filbeck, S, Cerullo, F, Pfeffer, S, Joazeiro, CAP

Mol Cell 2022
28525741 In Vivo Ubiquitin Linkage-type Analysis Reveals that the Cdc48-Rad23/Dsk2 Axis Contributes to K48-Linked Chain Specificity of the Proteasome

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Mol Cell 2017
31011209 Mechanism for recycling tRNAs on stalled ribosomes

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Nat Struct Mol Biol 2019
32569528 Detection and Degradation of Stalled Nascent Chains via Ribosome-Associated Quality Control

Sitron, CS, Brandman, O

Annu Rev Biochem 2020
37676773 Mechanism and evolutionary origins of alanine-tail C-degron recognition by E3 ligases Pirh2 and CRL2-KLHDC10

Patil, PR, Burroughs, AM, Misra, M, Cerullo, F, Costas-Insua, C, Hung, HC, Dikic, I, Aravind, L, Joazeiro, CAP

Cell Rep 2023
22503425 Dom34:hbs1 plays a general role in quality-control systems by dissociation of a stalled ribosome at the 3' end of aberrant mRNA

Tsuboi, T, Kuroha, K, Kudo, K, Makino, S, Inoue, E, Kashima, I, Inada, T

Mol Cell 2012
38366554 Ribosomal collision is not a prerequisite for ZNF598-mediated ribosome ubiquitination and disassembly of ribosomal complexes by ASCC

Miścicka, A, Bulakhov, AG, Kuroha, K, Zinoviev, A, Hellen, CUT, Pestova, TV

Nucleic Acids Res 2024
22358840 Structural basis of highly conserved ribosome recycling in eukaryotes and archaea

Becker, T, Franckenberg, S, Wickles, S, Shoemaker, CJ, Anger, AM, Armache, JP, Sieber, H, Ungewickell, C, Berninghausen, O, Daberkow, I, Karcher, A, Thomm, M, Hopfner, KP, Green, R, Beckmann, R

Nature 2012
26943317 The Rqc2/Tae2 subunit of the ribosome-associated quality control (RQC) complex marks ribosome-stalled nascent polypeptide chains for aggregation

Yonashiro, R, Tahara, EB, Bengtson, MH, Khokhrina, M, Lorenz, H, Chen, KC, Kigoshi-Tansho, Y, Savas, JN, Yates, JR, Kay, SA, Craig, EA, Mogk, A, Bukau, B, Joazeiro, CA

Elife 2016
37120596 Recognition of an Ala-rich C-degron by the E3 ligase Pirh2

Wang, X, Li, Y, Yan, X, Yang, Q, Zhang, B, Zhang, Y, Yuan, X, Jiang, C, Chen, D, Liu, Q, Liu, T, Mi, W, Yu, Y, Dong, C

Nat Commun 2023
30675527 The Cdc48 unfoldase prepares well-folded protein substrates for degradation by the 26S proteasome

Olszewski, MM, Williams, C, Dong, KC, Martin, A

Commun Biol 2019
28065601 Initiation of Quality Control during Poly(A) Translation Requires Site-Specific Ribosome Ubiquitination

Juszkiewicz, S, Hegde, RS

Mol Cell 2017
33406423 Failure to Degrade CAT-Tailed Proteins Disrupts Neuronal Morphogenesis and Cell Survival

Udagawa, T, Seki, M, Okuyama, T, Adachi, S, Natsume, T, Noguchi, T, Matsuzawa, A, Inada, T

Cell Rep 2021
20947765 Dom34:Hbs1 promotes subunit dissociation and peptidyl-tRNA drop-off to initiate no-go decay

Shoemaker, CJ, Eyler, DE, Green, R

Science 2010
23685075 Listerin-dependent nascent protein ubiquitination relies on ribosome subunit dissociation

Shao, S, von der Malsburg, K, Hegde, RS

Mol Cell 2013
28751611 CAT-tailing as a fail-safe mechanism for efficient degradation of stalled nascent polypeptides

Kostova, KK, Hickey, KL, Osuna, BA, Hussmann, JA, Frost, A, Weinberg, DE, Weissman, JS

Science 2017
28298488 The ribosome-bound quality control complex remains associated to aberrant peptides during their proteasomal targeting and interacts with Tom1 to limit protein aggregation

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Mol Biol Cell 2017
32579943 The ASC-1 Complex Disassembles Collided Ribosomes

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Mol Cell 2020
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J Biol Chem 2013
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Mol Cell 2018
28132843 ZNF598 and RACK1 Regulate Mammalian Ribosome-Associated Quality Control Function by Mediating Regulatory 40S Ribosomal Ubiquitylation

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Mol Cell 2017
38949989 Dysregulated ribosome quality control in human diseases

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FEBS J 2025
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Elife 2020
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Mol Cell 2015
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Cell Rep 2024
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Mol Cell 2020
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Eisenack, TJ, Trentini, DB

Front Mol Biosci 2022
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Mol Cell 2014
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Nature 2018
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Mol Cell 2021
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Elife 2020
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Genes Dev 2025
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Nat Commun 2023
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Nat Commun 2017
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Nat Commun 2019
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Nature 2019
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Nat Commun 2023
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Elife 2013
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Hickey, KL, Dickson, K, Cogan, JZ, Replogle, JM, Schoof, M, D'Orazio, KN, Sinha, NK, Hussmann, JA, Jost, M, Frost, A, Green, R, Weissman, JS, Kostova, KK

Mol Cell 2020
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