OTUD1 is a deubiquitinating enzyme involved in many cellular processes including cancer and innate, immune signaling pathways. Here, we perform a proximity labeling-based interactome study that identifies OTUD1 largely present in the translation and RNA metabolism protein complexes. Biochemical analysis validates OTUD1 association with ribosome subunits, elongation factors and the E3 ubiquitin ligase ZNF598 but not with the translation initiation machinery. OTUD1 catalytic activity suppresses polyA triggered ribosome stalling through inhibition of ZNF598-mediated RPS10 ubiquitination and stimulates formation of polysomes. Finally, analysis of gene expression suggests that OTUD1 regulates the stability of rare codon rich mRNAs by antagonizing ZNF598.

Department of Hematooncology University Hospital Ostrava Ostrava Czech Republic

Faculty of Medicine University of Ostrava Ostrava Czech Republic

Faculty of Science University of Ostrava Ostrava Czech Republic

Zobrazit více v PubMed

Bonderoff JM, Lloyd RE. 2010. Time-dependent increase in ribosome processivity. Nucleic Acids Res 38:7054–7067. 10.1093/nar/gkq566. PubMed DOI PMC

Roux PP, Topisirovic I. 2018. Signaling pathways involved in the regulation of mRNA translation. Mol Cell Biol 38:e00070-18. 10.1128/MCB.00070-18. PubMed DOI PMC

Sonenberg N, Hinnebusch AG. 2009. Regulation of translation initiation in eukaryotes: mechanisms and biological targets. Cell 136:731–745. 10.1016/j.cell.2009.01.042. PubMed DOI PMC

Shoemaker CJ, Green R. 2012. Translation drives mRNA quality control. Nat Struct Mol Biol 19:594–601. 10.1038/nsmb.2301. PubMed DOI PMC

Döring K, Ahmed N, Riemer T, Suresh HG, Vainshtein Y, Habich M, Riemer J, Mayer MP, O'Brien EP, Kramer G, Bukau B. 2017. Profiling ssb-nascent chain interactions reveals principles of hsp70-assisted folding. Cell 170:298–311. 10.1016/j.cell.2017.06.038. PubMed DOI PMC

Hudson BH, Zaher HS. 2015. O 6-Methylguanosine leads to position-dependent effects on ribosome speed and fidelity. RNA 21:1648–1659. 10.1261/rna.052464.115. PubMed DOI PMC

Chandrasekaran V, Juszkiewicz S, Choi J, Puglisi JD, Brown A, Shao S, Ramakrishnan V, Hegde RS. 2019. Mechanism of ribosome stalling during translation of a poly(A) tail. Nat Struct Mol Biol 26:1132–1140. 10.1038/s41594-019-0331-x. PubMed DOI PMC

Arpat AB, Liechti A, de Matos M, Dreos R, Janich P, Gatfield D. 2020. Transcriptome-wide sites of collided ribosomes reveal principles of translational pausing. Genome Res 30:985–999. 10.1101/gr.257741.119. PubMed DOI PMC

Yan LL, Zaher HS. 2021. Ribosome quality control antagonizes the activation of the integrated stress response on colliding ribosomes. Mol Cell 81:614–628. 10.1016/j.molcel.2020.11.033. PubMed DOI PMC

Yang Q, Yu C-H, Zhao F, Dang Y, Wu C, Xie P, Sachs MS, Liu Y. 2019. eRF1 mediates codon usage effects on mRNA translation efficiency through premature termination at rare codons. Nucleic Acids Res 47:9243–9258. 10.1093/nar/gkz710. PubMed DOI PMC

Ikeuchi K, Izawa T, Inada T. 2018. Recent progress on the molecular mechanism of quality controls induced by ribosome stalling. Front Genet 9:743. 10.3389/fgene.2018.00743. PubMed DOI PMC

Juszkiewicz S, Hegde RS. 2017. Initiation of quality control during poly(A) translation requires site-specific ribosome ubiquitination. Mol Cell 65:743–750. 10.1016/j.molcel.2016.11.039. PubMed DOI PMC

van Hoof A, Frischmeyer PA, Dietz HC, Parker R. 2002. Exosome-mediated recognition and degradation of mRNAs lacking a termination codon. Science 295:2262–2264. 10.1126/science.1067272. PubMed DOI

Kurosaki T, Popp MW, Maquat LE. 2019. Quality and quantity control of gene expression by nonsense-mediated mRNA decay. Nat Rev Mol Cell Biol 20:406–420. 10.1038/s41580-019-0126-2. PubMed DOI PMC

Kontos H, Napthine S, Brierley I. 2001. Ribosomal pausing at a frameshifter RNA pseudoknot is sensitive to reading phase but shows little correlation with frameshift efficiency. Mol Cell Biol 21:8657–8670. 10.1128/MCB.21.24.8657-8670.2001. PubMed DOI PMC

Doma MK, Parker R. 2006. Endonucleolytic cleavage of eukaryotic mRNAs with stalls in translation elongation. Nature 440:561–564. 10.1038/nature04530. PubMed DOI PMC

Karamyshev AL, Karamysheva ZN. 2018. Lost in translation: ribosome-associated mRNA and protein quality controls. Front Genet 9:431. 10.3389/fgene.2018.00431. PubMed DOI PMC

Morris C, Cluet D, Ricci EP. 2021. Ribosome dynamics and mRNA turnover, a complex relationship under constant cellular scrutiny. Wiley Interdiscip Rev RNA 12. 10.1002/wrna.1658. PubMed DOI PMC

Juszkiewicz S, Chandrasekaran V, Lin Z, Kraatz S, Ramakrishnan V, Hegde RS. 2018. ZNF598 is a quality control sensor of collided ribosomes. Mol Cell 72:469–481. 10.1016/j.molcel.2018.08.037. PubMed DOI PMC

Meyer C, Garzia A, Morozov P, Molina H, Tuschl T. 2020. The G3BP1-family-USP10 deubiquitinase complex rescues ubiquitinated 40S subunits of ribosomes stalled in translation from lysosomal degradation. Mol Cell 77:1193–1205. 10.1016/j.molcel.2019.12.024. PubMed DOI

Shao S, Brown A, Santhanam B, Hegde RS. 2015. Structure and assembly pathway of the ribosome quality control complex. Mol Cell 57:433–444. 10.1016/j.molcel.2014.12.015. PubMed DOI PMC

Garzia A, Jafarnejad SM, Meyer C, Chapat C, Gogakos T, Morozov P, Amiri M, Shapiro M, Molina H, Tuschl T, Sonenberg N. 2017. The E3 ubiquitin ligase and RNA-binding protein ZNF598 orchestrates ribosome quality control of premature polyadenylated mRNAs. Nat Commun 8:16056. 10.1038/ncomms16056. PubMed DOI PMC

Joazeiro CAP. 2017. Ribosomal stalling during translation: providing substrates for ribosome-associated protein quality control. Annu Rev Cell Dev Biol 33:343–368. 10.1146/annurev-cellbio-111315-125249. PubMed DOI

Clague MJ, Urbé S, Komander D. 2019. Breaking the chains: deubiquitylating enzyme specificity begets function. Nat Rev Mol Cell Biol 20:338–352. 10.1038/s41580-019-0099-1. PubMed DOI

Garshott DM, Sundaramoorthy E, Leonard M, Bennett EJ. 2020. Distinct regulatory ribosomal ubiquitylation events are reversible and hierarchically organized. Elife 9:e54023. 10.7554/eLife.54023. PubMed DOI PMC

Zhang Z, Fan Y, Xie F, Zhou H, Jin K, Shao L, Shi W, Fang P, Yang B, van Dam H, ten Dijke P, Zheng X, Yan X, Jia J, Zheng M, Jin J, Ding C, Ye S, Zhou F, Zhang L. 2017. Breast cancer metastasis suppressor OTUD1 deubiquitinates SMAD7. Nat Commun 8. 10.1038/s41467-017-02029-7. PubMed DOI PMC

Carneiro AP, Reis CF, Morari EC, Maia YCP, Nascimento R, Bonatto JMC, de Souza MA, Goulart LR, Ward LS. 2014. A putative OTU domain-containing protein 1 deubiquitinating enzyme is differentially expressed in thyroid cancer and identifies less-aggressive tumours. Br J Cancer 111:551–558. 10.1038/bjc.2014.331. PubMed DOI PMC

Piao S, Pei HZ, Huang B, Baek S-H. 2017. Ovarian tumor domain-containing protein 1 deubiquitinates and stabilizes p53. Cell Signal 33:22–29. 10.1016/j.cellsig.2017.02.011. PubMed DOI

Yao F, Zhou Z, Kim J, Hang Q, Xiao Z, Ton BN, Chang L, Liu N, Zeng L, Wang W, Wang Y, Zhang P, Hu X, Su X, Liang H, Sun Y, Ma L. 2018. SKP2- and OTUD1-regulated non-proteolytic ubiquitination of YAP promotes YAP nuclear localization and activity. Nat Commun 9. 10.1038/s41467-018-04620-y. PubMed DOI PMC

Song J, Liu T, Yin Y, Zhao W, Lin Z, Yin Y, Lu D, You F. 2021. The deubiquitinase OTUD1 enhances iron transport and potentiates host antitumor immunity. EMBO Rep 22. 10.15252/embr.202051162. PubMed DOI PMC

Chen X, Zhang H, Wang X, Shao Z, Li Y, Zhao G, Liu F, Liu B, Zheng Y, Chen T, Zheng H, Zhang L, Gao C. 2021. OTUD1 regulates antifungal innate immunity through deubiquitination of CARD9. J Immunol 206:1832–1843. 10.4049/jimmunol.2001253. PubMed DOI

Oikawa D, Gi M, Kosako H, Shimizu K, Takahashi H, Shiota M, Hosomi S, Komakura K, Wanibuchi H, Tsuruta D, Sawasaki T, Tokunaga F. 2022. OTUD1 deubiquitinase regulates NF-κB- and KEAP1-mediated inflammatory responses and reactive oxygen species-associated cell death pathways. Cell Death & Dis 13. 10.1038/s41419-022-05145-5. PubMed DOI PMC

Varenne S, Buc J, Lloubes R, Lazdunski C. 1984. Translation is a non-uniform process. J Mol Biol 180:549–576. 10.1016/0022-2836(84)90027-5. PubMed DOI

Cardinaud S, Starck SR, Chandra P, Shastri N. 2010. The synthesis of truncated polypeptides for immune surveillance and viral evasion. PLoS One 5:e8692. 10.1371/journal.pone.0008692. PubMed DOI PMC

Cho KF, Branon TC, Udeshi ND, Myers SA, Carr SA, Ting AY. 2020. Proximity labeling in mammalian cells with TurboID and split-TurboID. Nat Protoc 15:3971–3999. 10.1038/s41596-020-0399-0. PubMed DOI

Thomas PD, Campbell MJ, Kejariwal A, Mi H, Karlak B, Daverman R, Diemer K, Muruganujan A, Narechania A. 2003. PANTHER: a library of protein families and subfamilies indexed by function. Genome Res 13:2129–2141. 10.1101/gr.772403. PubMed DOI PMC

Morrow ME, Morgan MT, Clerici M, Growkova K, Yan M, Komander D, Sixma TK, Simicek M, Wolberger C. 2018. Active site alanine mutations convert deubiquitinases into high-affinity ubiquitin-binding proteins. EMBO Rep 19. 10.15252/embr.201745680. PubMed DOI PMC

Sundaramoorthy E, Leonard M, Mak R, Liao J, Fulzele A, Bennett EJ. 2017. ZNF598 and RACK1 regulate mammalian ribosome-associated quality control function by mediating regulatory 40S ribosomal ubiquitylation. Mol Cell 65:751–760. 10.1016/j.molcel.2016.12.026. PubMed DOI PMC

Frischmeyer PA, van Hoof A, O'Donnell K, Guerrerio AL, Parker R, Dietz HC. 2002. An mRNA surveillance mechanism that eliminates transcripts lacking termination codons. Science 295:2258–2261. 10.1126/science.1067338. PubMed DOI

Ozsolak F, Kapranov P, Foissac S, Kim SW, Fishilevich E, Monaghan AP, John B, Milos PM. 2010. Comprehensive polyadenylation site maps in yeast and human reveal pervasive alternative polyadenylation. Cell 143:1018–1029. 10.1016/j.cell.2010.11.020. PubMed DOI PMC

Yoshikawa H, Larance M, Harney DJ, Sundaramoorthy R, Ly T, Owen-Hughes T, Lamond AI. 2018. Efficient analysis of mammalian polysomes in cells and tissues using Ribo Mega-SEC. Elife 7:e36530. 10.7554/eLife.36530. PubMed DOI PMC

Li X, Hirano R, Tagami H, Aiba H. 2006. Protein tagging at rare codons is caused by tmRNA action at the 3′ end of nonstop mRNA generated in response to ribosome stalling. RNA 12:248–255. 10.1261/rna.2212606. PubMed DOI PMC

Vdovin A, Jelinek T, Hrdinka M, Bago JR, Sevcikova T, Hajek R, Simicek M. 2019. Identification of deubiquitinase OTUD1 as a novel player in resistance of multiple myeloma to bortezomib. Blood 134:5526–5526. 10.1182/blood-2019-127930. DOI

Mishima Y, Han P, Ishibashi K, Kimura S, Iwasaki S. 2022. Ribosome slowdown triggers codon-mediated mRNA decay independently of ribosome quality control. EMBO J 41:e109256. 10.15252/embj.2021109256. PubMed DOI PMC

Lemm I, Ross J. 2002. Regulation of c- myc mRNA decay by translational pausing in a coding region instability determinant. Mol Cell Biol 22:3959–3969. 10.1128/MCB.22.12.3959-3969.2002. PubMed DOI PMC

Simms CL, Yan LL, Qiu JK, Zaher HS. 2019. Ribosome collisions result in +1 frameshifting in the absence of no-go decay. Cell Rep 28:1679–1689. 10.1016/j.celrep.2019.07.046. PubMed DOI PMC

Presnyak V, Alhusaini N, Chen Y-H, Martin S, Morris N, Kline N, Olson S, Weinberg D, Baker KE, Graveley BR, Coller J. 2015. Codon optimality is a major determinant of mRNA stability. Cell 160:1111–1124. 10.1016/j.cell.2015.02.029. PubMed DOI PMC

Radhakrishnan A, Chen Y-H, Martin S, Alhusaini N, Green R, Coller J. 2016. The DEAD-box protein dhh1p couples mRNA decay and translation by monitoring codon optimality. Cell 167:122–132. 10.1016/j.cell.2016.08.053. PubMed DOI PMC

Mauger DM, Cabral BJ, Presnyak V, Su SV, Reid DW, Goodman B, Link K, Khatwani N, Reynders J, Moore MJ, McFadyen IJ. 2019. mRNA structure regulates protein expression through changes in functional half-life. Proc Natl Acad Sci USA 116:24075–24083. 10.1073/pnas.1908052116. PubMed DOI PMC

Subramanian A, Tamayo P, Mootha VK, Mukherjee S, Ebert BL, Gillette MA, Paulovich A, Pomeroy SL, Golub TR, Lander ES, Mesirov JP. 2005. Gene set enrichment analysis: a knowledge-based approach for interpreting genome-wide expression profiles. Proc Natl Acad Sci USA 102:15545–15550. 10.1073/pnas.0506580102. PubMed DOI PMC

Mootha VK, Lindgren CM, Eriksson K-F, Subramanian A, Sihag S, Lehar J, Puigserver P, Carlsson E, Ridderstråle M, Laurila E, Houstis N, Daly MJ, Patterson N, Mesirov JP, Golub TR, Tamayo P, Spiegelman B, Lander ES, Hirschhorn JN, Altshuler D, Groop LC. 2003. PGC-1α-responsive genes involved in oxidative phosphorylation are coordinately downregulated in human diabetes. Nat Genet 34:267–273. 10.1038/ng1180. PubMed DOI

Jansen R, Bussemaker HJ, Gerstein M. 2003. Revisiting the codon adaptation index from a whole-genome perspective: analyzing the relationship between gene expression and codon occurrence in yeast using a variety of models. Nucleic Acids Res 31:2242–2251. 10.1093/nar/gkg306. PubMed DOI PMC