Structure and assembly pathway of the ribosome quality control complex

Molecular Cell

Volumn 57, Issue 3, 2015, Pages 433-444

  Shao, Sichen ^a   Brown, Alan ^a   Santhanam, Balaji ^a   Hegde, Ramanujan S ^a  

^a MRC LABORATORY OF MOLECULAR BIOLOGY   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

LISTERINE; AMINOACYL TRANSFER RNA; NEMF PROTEIN, HUMAN; NUCLEOCYTOPLASMIC TRANSPORT PROTEIN; TRNA, PEPTIDYL-; TUMOR ANTIGEN; UBIQUITIN PROTEIN LIGASE;

ARTICLE; CONTROLLED STUDY; GOLD STANDARD; HEK293 CELL LINE; IN VITRO STUDY; IN VIVO STUDY; MASS SPECTROMETRY; NONHUMAN; POLYSOME; PROTEIN ASSEMBLY; PROTEIN DEGRADATION; PROTEIN FUNCTION; PROTEIN QUALITY; PROTEIN SECONDARY STRUCTURE; PROTEIN STRUCTURE; RIBOSOME SUBUNIT; RING FINGER MOTIF; SEQUENCE ANALYSIS; UBIQUITINATION; BINDING SITE; CHEMICAL STRUCTURE; CHEMISTRY; CONFORMATION; CRYOELECTRON MICROSCOPY; HUMAN; METABOLISM; RIBOSOME;

ANTIGENS, NEOPLASM; BINDING SITES; CRYOELECTRON MICROSCOPY; HEK293 CELLS; HUMANS; MODELS, MOLECULAR; MOLECULAR CONFORMATION; NUCLEOCYTOPLASMIC TRANSPORT PROTEINS; RIBOSOMES; RNA, TRANSFER, AMINO ACYL; UBIQUITIN-PROTEIN LIGASES; UBIQUITINATION;

EID: 84924777167     PISSN: 10972765     EISSN: 10974164     Source Type: Journal    
DOI: 10.1016/j.molcel.2014.12.015     Document Type: Article

References (40)

1. Amunts A., Brown A., Bai X.-C., Llácer J.L., Hussain T., Emsley P., Long F., Murshudov G., Scheres S.H.W., Ramakrishnan V. Structure of the yeast mitochondrial large ribosomal subunit. Science 2014, 343:1485-1489.
2. Anger A.M., Armache J.-P., Berninghausen O., Habeck M., Subklewe M., Wilson D.N., Beckmann R. Structures of the human and Drosophila 80S ribosome. Nature 2013, 497:80-85.
3. Bai X.-C., Fernandez I.S., McMullan G., Scheres S.H. Ribosome structures to near-atomic resolution from thirty thousand cryo-EM particles. Elife 2013, 2. e00461-e00461.
4. Beckmann R., Spahn C.M., Eswar N., Helmers J., Penczek P.A., Sali A., Frank J., Blobel G. Architecture of the protein-conducting channel associated with the translating 80S ribosome. Cell 2001, 107:361-372.
5. Bengtson M.H., Joazeiro C.A.P. Role of a ribosome-associated E3 ubiquitin ligase in protein quality control. Nature 2010, 467:470-473.
6. Bi X., Jones T., Abbasi F., Lee H., Stultz B., Hursh D.A., Mortin M.A. Drosophila caliban, a nuclear export mediator, can function as a tumor suppressor in human lung cancer cells. Oncogene 2005, 24:8229-8239.
7. Brandman O., Stewart-Ornstein J., Wong D., Larson A., Williams C.C., Li G.-W., Zhou S., King D., Shen P.S., Weibezahn J., et al. A ribosome-bound quality control complex triggers degradation of nascent peptides and signals translation stress. Cell 2012, 151:1042-1054.
8. Burroughs A.M., Aravind L. A highly conserved family of domains related to the DNA-glycosylase fold helps predict multiple novel pathways for RNA modifications. RNA Biol. 2014, 11:360-372.
9. Carbonnelle D., Liehr T., Jacquot C., Masson D., Lustenberger P., Denis M.G., Roussakis C. Assignment of the serologically defined colon cancer antigen 1 gene (SDCCAG1) to human chromosome band 14q22 by insitu hybridization. Cytogenet. Cell Genet. 1999, 86:248-249.
10. Chiabudini M., Tais A., Zhang Y., Hayashi S., Wölfle T., Fitzke E., Rospert S. Release factor eRF3 mediates premature translation termination on polylysine-stalled ribosomes in Saccharomyces cerevisiae. Mol. Cell. Biol. 2014, 34:4062-4076.
11. Defenouillère Q., Yao Y., Mouaikel J., Namane A., Galopier A., Decourty L., Doyen A., Malabat C., Saveanu C., Jacquier A., Fromont-Racine M. Cdc48-associated complex bound to 60S particles is required for the clearance of aberrant translation products. Proc. Natl. Acad. Sci. USA 2013, 110:5046-5051.
12. Dimitrova L.N., Kuroha K., Tatematsu T., Inada T. Nascent peptide-dependent translation arrest leads to Not4p-mediated protein degradation by the proteasome. J.Biol. Chem. 2009, 284:10343-10352.
13. Doma M.K., Parker R. Endonucleolytic cleavage of eukaryotic mRNAs with stalls in translation elongation. Nature 2006, 440:561-564.
14. Emsley P., Lohkamp B., Scott W.G., Cowtan K. Features and development of Coot. Acta Crystallogr. D Biol. Crystallogr. 2010, 66:486-501.
15. Frischmeyer P.A., van Hoof A., O'Donnell K., Guerrerio A.L., Parker R., Dietz H.C. An mRNA surveillance mechanism that eliminates transcripts lacking termination codons. Science 2002, 295:2258-2261.
16. Gartmann M., Blau M., Armache J.-P., Mielke T., Topf M., Beckmann R. Mechanism of eIF6-mediated inhibition of ribosomal subunit joining. J.Biol. Chem. 2010, 285:14848-14851.
17. Hegde R.S., Ploegh H.L. Quality and quantity control at the endoplasmic reticulum. Curr. Opin. Cell Biol. 2010, 22:437-446.
18. Hessa T., Sharma A., Mariappan M., Eshleman H.D., Gutierrez E., Hegde R.S. Protein targeting and degradation are coupled for elimination of mislocalized proteins. Nature 2011, 475:394-397.
19. Izawa T., Tsuboi T., Kuroha K., Inada T., Nishikawa S.-I., Endo T. Roles of dom34:hbs1 in nonstop protein clearance from translocators for normal organelle protein influx. Cell Rep. 2012, 2:447-453.
20. Kramer G., Rauch T., Rist W., Vorderwülbecke S., Patzelt H., Schulze-Specking A., Ban N., Deuerling E., Bukau B. L23 protein functions as a chaperone docking site on the ribosome. Nature 2002, 419:171-174.
21. Kuroha K., Akamatsu M., Dimitrova L., Ito T., Kato Y., Shirahige K., Inada T. Receptor for activated C kinase 1 stimulates nascent polypeptide-dependent translation arrest. EMBO Rep. 2010, 11:956-961.
22. Lykke-Andersen J., Bennett E.J. Protecting the proteome: Eukaryotic cotranslational quality control pathways. J.Cell Biol. 2014, 204:467-476.
23. Lyumkis D., Doamekpor S.K., Bengtson M.H., Lee J.-W., Toro T.B., Petroski M.D., Lima C.D., Potter C.S., Carragher B., Joazeiro C.A.P. Single-particle EM reveals extensive conformational variability of the Ltn1 E3 ligase. Proc. Natl. Acad. Sci. USA 2013, 110:1702-1707.
24. Lyumkis D., Oliveira Dos Passos D., Tahara E.B., Webb K., Bennett E.J., Vinterbo S., Potter C.S., Carragher B., Joazeiro C.A.P. Structural basis for translational surveillance by the large ribosomal subunit-associated protein quality control complex. Proc. Natl. Acad. Sci. USA 2014, 111:15981-15986.
25. Pettersen E.F., Goddard T.D., Huang C.C., Couch G.S., Greenblatt D.M., Meng E.C., Ferrin T.E. UCSF Chimera-a visualization system for exploratory research and analysis. J.Comput. Chem. 2004, 25:1605-1612.
26. Pisareva V.P., Skabkin M.A., Hellen C.U.T., Pestova T.V., Pisarev A.V. Dissociation by Pelota, Hbs1 and ABCE1 of mammalian vacant 80S ribosomes and stalled elongation complexes. EMBO J. 2011, 30:1804-1817.
27. Pool M.R., Stumm J., Fulga T.A., Sinning I., Dobberstein B. Distinct modes of signal recognition particle interaction with the ribosome. Science 2002, 297:1345-1348.
28. Rodrigo-Brenni M.C., Hegde R.S. Design principles of protein biosynthesis-coupled quality control. Dev. Cell 2012, 23:896-907.
29. Scheres S.H.W. RELION: implementation of a Bayesian approach to cryo-EM structure determination. J.Struct. Biol. 2012, 180:519-530.
30. Shao S., Hegde R.S. Reconstitution of a minimal ribosome-associated ubiquitination pathway with purified factors. Mol. Cell 2014, 55:880-890.
31. Shao S., von der Malsburg K., Hegde R.S. Listerin-dependent nascent protein ubiquitination relies on ribosome subunit dissociation. Mol. Cell 2013, 50:637-648.
32. Shoemaker C.J., Green R. Translation drives mRNA quality control. Nat. Struct. Mol. Biol. 2012, 19:594-601.
33. Shoemaker C.J., Eyler D.E., Green R. Dom34:Hbs1 promotes subunit dissociation and peptidyl-tRNA drop-off to initiate no-go decay. Science 2010, 330:369-372.
34. Tang G., Peng L., Baldwin P.R., Mann D.S., Jiang W., Rees I., Ludtke S.J. EMAN2: an extensible image processing suite for electron microscopy. J.Struct. Biol. 2007, 157:38-46.
35. van Hoof A., Frischmeyer P.A., Dietz H.C., Parker R. Exosome-mediated recognition and degradation of mRNAs lacking a termination codon. Science 2002, 295:2262-2264.
36. Verma R., Oania R.S., Kolawa N.J., Deshaies R.J. Cdc48/p97 promotes degradation of aberrant nascent polypeptides bound to the ribosome. Elife 2013, 2. 10.7554/eLife.00308.
37. Voorhees R.M., Fernández I.S., Scheres S.H.W., Hegde R.S. Structure of the mammalian ribosome-Sec61 complex to 3.4Å resolution. Cell 2014, 157:1632-1643.
38. Wolff S., Weissman J.S., Dillin A. Differential scales of protein quality control. Cell 2014, 157:52-64.
39. Zhang Y. I-TASSER server for protein 3D structure prediction. BMC Bioinformatics 2008, 9:40.
40. Zhang Z.-R., Bonifacino J.S., Hegde R.S. Deubiquitinases sharpen substrate discrimination during membrane protein degradation from the ER. Cell 2013, 154:609-622.