Comparison of the yeast and human nuclear exosome complexes

Biochemical Society Transactions

Volumn 40, Issue 4, 2012, Pages 850-855

  Sloan, Katherine E ^a   Schneider, Claudia ^a   Watkins, Nicholas J ^a  

^a NEWCASTLE UNIVERSITY   (United Kingdom)

Author keywords

Exonuclease; Exosome; RNA degradation; RNA processing; RNA surveillance

Indexed keywords

DIS3 PROTEIN; PROTEIN; RIBONUCLEASE; RRP44 PROTEIN; RRP6 PROTEIN; TRAMP PROTEIN; UNCLASSIFIED DRUG;

CATALYSIS; CONFERENCE PAPER; EXOSOME; HUMAN; NONHUMAN; PRIORITY JOURNAL; RNA DEGRADATION; RNA PROCESSING; RNA SPLICING; RNA STRUCTURE; YEAST;

EXOSOMES; HUMANS; RNA PROCESSING, POST-TRANSCRIPTIONAL; RNA STABILITY; SACCHAROMYCES CEREVISIAE; SACCHAROMYCES CEREVISIAE PROTEINS;

EUKARYOTA; SACCHAROMYCES CEREVISIAE;

EID: 84864383638     PISSN: 03005127     EISSN: 14708752     Source Type: Journal    
DOI: 10.1042/BST20120061     Document Type: Conference Paper

References (50)

1. Mitchell, P., Petfalski, E. and Tollervey, D. (1996) The 3′ end of yeast 5.8S rRNA is generated by an exonuclease processing mechanism. Genes Dev. 10, 502-513
2. Tomecki, R., Drazkowska, K. and Dziembowski, A. (2010) Mechanisms of RNA degradation by the eukaryotic exosome. ChemBioChem 11, 938-945
3. Houseley, J., LaCava, J. and Tollervey, D. (2006) RNA-quality control by the exosome. Nat. Rev. Mol. Cell Biol. 7, 529-539 (Pubitemid 44036458)
4. Vanacova, S. and Stefl, R. (2007) The exosome and RNA quality control in the nucleus. EMBO Rep. 8, 651-657 (Pubitemid 47033796)
5. Lykke-Andersen, S., Tomecki, R., Jensen, T.H. and Dziembowski, A. (2011) The eukaryotic RNA exosome: same scaffold but variable catalytic subunits. RNA Biol. 8, 61-66
6. Liu, Q., Greimann, J.C. and Lima, C.D. (2006) Reconstitution, activities and structure of the eukaryotic RNA exosome. Cell 127, 1223-1237 (Pubitemid 44894519)
7. Bonneau, F., Basquin, J., Ebert, J., Lorentzen, E. and Conti, E. (2009) The yeast exosome functions as a macromolecular cage to channel RNA substrates for degradation. Cell 139, 547-559
8. Dziembowski, A., Lorentzen, E., Conti, E. and Seraphin, B. (2007) A single subunit, Dis3, is essentially responsible for yeast exosome core activity. Nat. Struct. Mol. Biol. 14, 15-22 (Pubitemid 46067418)
9. Schneider, C., Anderson, J.T. and Tollervey, D. (2007) The exosome subunit Rrp44 plays a direct role in RNA substrate recognition. Mol. Cell 27, 324-331 (Pubitemid 47058304)
10. Brouwer, R., Allmang, C., Raijmakers, R., van Aarssen, Y., Egberts, W.V., Petfalski, E., van Venrooij, W.J., Tollervey, D. and Pruijn, G.J. (2001) Three novel components of the human exosome. J. Biol. Chem. 276, 6177-6184
11. Gelpi, C., Alguero, A., Angeles Martinez, M., Vidal, S., Juarez, C. and Rodriguez-Sanchez, J.L. (1990) Identification of protein components reactive with anti-PM/Scl autoantibodies. Clin. Exp. Immunol. 81, 59-64 (Pubitemid 20229700)
12. Staals, R.H. and Pruijn, G.J. (2011) The human exosome and disease. Adv. Exp. Med. Biol. 702, 132-142
13. Yang, X.F., Wu, C.J., Chen, L., Alyea, E.P., Canning, C., Kantoff, P., Soiffer, R.J., Dranoff, G. and Ritz, J. (2002) CML28 is a broadly immunogenic antigen, which is overexpressed in tumor cells. Cancer Res. 62, 5517-5522
14. Allmang, C., Petfalski, E., Podtelejnikov, A., Mann, M., Tollervey, D. and Mitchell, P. (1999) The yeast exosome and human PM-Scl are related complexes of 3′ → 5′ exonucleases. Genes Dev. 13, 2148-2158 (Pubitemid 29407354)
15. Mitchell, P., Petfalski, E., Shevchenko, A., Mann, M. and Tollervey, D. (1997) The exosome: a conserved eukaryotic RNA processing complex containing multiple 3′ → 5′ exoribonucleases. Cell 91, 457-466 (Pubitemid 27508235)
16. Vincent, H.A. and Deutscher, M.P. (2006) Substrate recognition and catalysis by the exoribonuclease RNase R. J. Biol. Chem. 281, 29769-29775 (Pubitemid 44536986)
17. Lebreton, A., Tomecki, R., Dziembowski, A. and Seraphin, B. (2008) Endonucleolytic RNA cleavage by a eukaryotic exosome. Nature 456, 993-996
18. Schaeffer, D., Tsanova, B., Barbas, A., Reis, F.P., Dastidar, E.G., Sanchez-Rotunno, M., Arraiano, C.M. and van Hoof, A. (2009) The exosome contains domains with specific endoribonuclease, exoribonuclease and cytoplasmic mRNA decay activities. Nat. Struct. Mol. Biol. 16, 56-62
19. Schneider, C., Leung, E., Brown, J. and Tollervey, D. (2009) The N-terminal PIN domain of the exosome subunit Rrp44 harbors endonuclease activity and tethers Rrp44 to the yeast core exosome. Nucleic Acids Res. 37, 1127-1140
20. Midtgaard, S.F., Assenholt, J., Jonstrup, A.T., Van, L.B., Jensen, T.H. and Brodersen, D.E. (2006) Structure of the nuclear exosome component Rrp6p reveals an interplay between the active site and the HRDC domain. Proc. Natl. Acad. Sci. U.S.A. 103, 11898-11903 (Pubitemid 44215783)
21. Steitz, T.A. and Steitz, J.A. (1993) A general two-metal-ion mechanism for catalytic RNA. Proc. Natl. Acad. Sci. U.S.A. 90, 6498-6502 (Pubitemid 23207240)
22. Januszyk, K., Liu, Q. and Lima, C.D. (2011) Activities of human RRP6 and structure of the human RRP6 catalytic domain. RNA 17, 1566-1577
23. Cristodero, M., Bottcher, B., Diepholz, M., Scheffzek, K. and Clayton, C. (2008) The Leishmania tarentolae exosome: purification and structural analysis by electron microscopy. Mol. Biochem. Parasitol. 159, 24-29
24. Lehner, B. and Sanderson, C.M. (2004) A protein interaction framework for human mRNA degradation. Genome Res. 14, 1315-1323 (Pubitemid 39029228)
25. Callahan, K.P. and Butler, J.S. (2008) Evidence for core exosome independent function of the nuclear exoribonuclease Rrp6p. Nucleic Acids Res. 36, 6645-6655
26. Staals, R.H., Bronkhorst, A.W., Schilders, G., Slomovic, S., Schuster, G., Heck, A.J., Raijmakers, R. and Pruijn, G.J. (2010) Dis3-like 1: a novel exoribonuclease associated with the human exosome. EMBO J. 29, 2358-2367
27. Tomecki, R., Kristiansen, M.S., Lykke-Andersen, S., Chlebowski, A., Larsen, K.M., Szczesny, R.J., Drazkowska, K., Pastula, A., Andersen, J.S., Stepien, P.P. et al. (2010) The human core exosome interacts with differentially localized processive RNases: hDIS3 and hDIS3L. EMBO J. 29, 2342-2357
28. Astuti, D., Morris, M.R., Cooper, W.N., Staals, R.H., Wake, N.C., Fews, G.A., Gill, H., Gentle, D., Shuib, S., Ricketts, C.J. et al. (2012) Germline mutations in DIS3L2 cause the Perlman syndrome of overgrowth and Wilms tumor susceptibility. Nat. Genet. 44, 277-284
29. Smith, S.B., Kiss, D.L., Turk, E., Tartakoff, A.M. and Andrulis, E.D. (2011) Pronounced and extensive microtubule defects in a Saccharomyces cerevisiae DIS3 mutant. Yeast 28, 755-769
30. van Dijk, E.L., Schilders, G. and Pruijn, G.J. (2007) Human cell growth requires a functional cytoplasmic exosome, which is involved in various mRNA decay pathways. RNA 13, 1027-1035 (Pubitemid 46984893)
31. LaCava, J., Houseley, J., Saveanu, C., Petfalski, E., Thompson, E., Jacquier, A. and Tollervey, D. (2005) RNA degradation by the exosome is promoted by a nuclear polyadenylation complex. Cell 121, 713-724 (Pubitemid 40797594)
32. Vanacova, S., Wolf, J., Martin, G., Blank, D., Dettwiler, S., Friedlein, A., Langen, H., Keith, G. and Keller, W. (2005) A new yeast poly(A) polymerase complex involved in RNA quality control. PLoS Biol. 3, e189
33. Houseley, J. and Tollervey, D. (2006) Yeast Trf5p is a nuclear poly(A) polymerase. EMBO Rep. 7, 205-211
34. Jia, H., Wang, X., Liu, F., Guenther, U.P., Srinivasan, S., Anderson, J.T. and Jankowsky, E. (2011) The RNA helicase Mtr4p modulates polyadenylation in the TRAMP complex. Cell 145, 890-901
35. Wlotzka, W., Kudla, G., Granneman, S. and Tollervey, D. (2011) The nuclear RNA polymerase II surveillance system targets polymerase III transcripts. EMBO J. 30, 1790-1803
36. Wery, M., Ruidant, S., Schillewaert, S., Lepore, N. and Lafontaine, D.L. (2009) The nuclear poly(A) polymerase and Exosome cofactor Trf5 is recruited cotranscriptionally to nucleolar surveillance. RNA 15, 406-419
37. Callahan, K.P. and Butler, J.S. (2010) TRAMP complex enhances RNA degradation by the nuclear exosome component Rrp6. J. Biol. Chem. 285, 3540-3547
38. Jackson, R.N., Klauer, A.A., Hintze, B.J., Robinson, H., van Hoof, A. and Johnson, S.J. (2010) The crystal structure of Mtr4 reveals a novel arch domain required for rRNA processing. EMBO J. 29, 2205-2216
39. Weir, J.R., Bonneau, F., Hentschel, J. and Conti, E. (2010) Structural analysis reveals the characteristic features of Mtr4, a DExH helicase involved in nuclear RNA processing and surveillance. Proc. Natl. Acad. Sci. U.S.A. 107, 12139-12144
40. de la Cruz, J., Kressler, D., Tollervey, D. and Linder, P. (1998) Dob1p (Mtr4p) is a putative ATP-dependent RNA helicase required for the 3′ end formation of 5.8S rRNA in Saccharomyces cerevisiae. EMBO J. 17, 1128-1140 (Pubitemid 28077666)
41. Lange, H., Sement, F.M. and Gagliardi, D. (2011) MTR4, a putative RNA helicase and exosome co-factor, is required for proper rRNA biogenesis and development in Arabidopsis thaliana. Plant J. 68, 51-63
42. Milligan, L., Decourty, L., Saveanu, C., Rappsilber, J., Ceulemans, H., Jacquier, A. and Tollervey, D. (2008) A yeast exosome cofactor, Mpp6, functions in RNA surveillance and in the degradation of noncoding RNA transcripts. Mol. Cell. Biol. 28, 5446-5457
43. Mitchell, P., Petfalski, E., Houalla, R., Podtelejnikov, A., Mann, M. and Tollervey, D. (2003) Rrp47p is an exosome-associated protein required for the 3′ processing of stable RNAs. Mol. Cell. Biol. 23, 6982-6992 (Pubitemid 37214665)
44. Stead, J.A., Costello, J.L., Livingstone, M.J. and Mitchell, P. (2007) The PMC2NT domain of the catalytic exosome subunit Rrp6p provides the interface for binding with its cofactor Rrp47p, a nucleic acid-binding protein. Nucleic Acids Res. 35, 5556-5567 (Pubitemid 47430457)
45. Costello, J.L., Stead, J.A., Feigenbutz, M., Jones, R.M. and Mitchell, P. (2011) The C-terminal region of the exosome-associated protein Rrp47 is specifically required for box C/D small nucleolar RNA 3′-maturation. J. Biol. Chem. 286, 4535-4543
46. Thiebaut, M., Kisseleva-Romanova, E., Rougemaille, M., Boulay, J. and Libri, D. (2006) Transcription termination and nuclear degradation of cryptic unstable transcripts: a role for the nrd1-nab3 pathway in genome surveillance. Mol. Cell 23, 853-864 (Pubitemid 44344521)
47. Schilders, G., van Dijk, E. and Pruijn, G.J. (2007) C1D and hMtr4p associate with the human exosome subunit PM/Scl-100 and are involved in pre-rRNA processing. Nucleic Acids Res. 35, 2564-2572 (Pubitemid 47073670)
48. Fasken, M.B., Leung, S.W., Banerjee, A., Kodani, M.O., Chavez, R., Bowman, E.A., Purohit, M.K., Rubinson, M.E., Rubinson, E.H. and Corbett, A.H. (2011) Air1 zinc knuckles 4 and 5 and a conserved IWRxY motif are critical for the function and integrity of the TRAMP RNA quality control complex. J. Biol. Chem. 286, 37429-37445
49. Lubas, M., Christensen, M.S., Kristiansen, M.S., Domanski, M., Falkenby, L.G., Lykke-Andersen, S., Andersen, J.S., Dziembowski, A. and Jensen, T.H. (2011) Interaction profiling identifies the human nuclear exosome targeting complex. Mol. Cell 43, 624-637
50. Schilders, G., Raijmakers, R., Raats, J.M. and Pruijn, G.J. (2005) MPP6 is an exosome-associated RNA-binding protein involved in 5.8S rRNA maturation. Nucleic Acids Res. 33, 6795-6804 (Pubitemid 41830485)