Functions of the exosome in rRNA, snoRNA and snRNA synthesis

EMBO Journal

Volumn 18, Issue 19, 1999, Pages 5399-5410

  Allmang, Christine ^a   Kufel, Joanna ^a   Chanfreau, Guillaume ^b,c   Mitchell, Philip ^a   Petfalski, Elisabeth ^a   Tollervey, David ^a  

^a UNIVERSITY OF EDINBURGH   (United Kingdom)

^b INSTITUT PASTEUR   (France)

^c UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

Pre rRNA; RNA processing; Saccharomyces cerevisiae; SnoRNA; SnRNA

Indexed keywords

EXORIBONUCLEASE; MESSENGER RNA; RIBOSOME RNA; RNA HELICASE; SMALL NUCLEAR RNA; UNCLASSIFIED DRUG;

ARTICLE; EXOSOME; INTRON; NONHUMAN; PRIORITY JOURNAL; RNA PROCESSING; RNA SYNTHESIS; YEAST;

BASE SEQUENCE; EXODEOXYRIBONUCLEASE V; EXODEOXYRIBONUCLEASES; NUCLEIC ACID CONFORMATION; RNA PROCESSING, POST-TRANSCRIPTIONAL; RNA, RIBOSOMAL; RNA, SMALL NUCLEAR; RNA, SMALL NUCLEOLAR; SACCHAROMYCES CEREVISIAE;

SACCHAROMYCES CEREVISIAE;

EID: 0033214175     PISSN: 02614189     EISSN: None     Source Type: Journal    
DOI: 10.1093/emboj/18.19.5399     Document Type: Article

References (47)

1. Abou Elela, S. and Ares, M., Jr (1998) Depletion of yeast RNase III blocks correct U2 3′ end formation and results in polyadenylated but functional U2 snRNA. EMBO J., 17, 3738-3746.
2. Abou Elela, S., Igel, H. and Ares, M., Jr (1996) RNase III cleaves eukaryotic preribosomal RNA at a U3 snoRNP-dependent site. Cell, 85, 115-124.
3. 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.
4. Amberg, D.C., Goldstein, A.L. and Cole, C.N. (1992) Isolation and characterization of RATI: an essential gene of Saccharomyces cerevisiae required for the efficient nucleocytoplasmic trafficking of mRNA. Genes Dev., 6, 1173-1189.
5. Baker, R.E., Harris, K. and Zhang, K. (1998) Mutations synthetically lethal with cep1 target S.cerevisiae kinetochore components. Genetics, 149, 73-85.
6. Baudin, A., Ozier-Kalogeropoulos, O., Denouel, A., Lacroute, F. and Cullin, C. (1993) A simple and efficient method for direct gene deletion in Saccharomyces cerevisiae. Nucleic Acids Res., 21, 3329-3330.
7. Beltrame, M. and Tollervey, D. (1992) Identification and functional analysis of two U3 binding sites on yeast pre-ribosomal RNA. EMBO J., 11, 1531-1542.
8. Briggs, M.W., Burkard, K.T. and Butler, J.S. (1998) Rrp6p, the yeast homologue of the human PM-Scl 100-kDa autoantigen, is essential for efficient 5.8 S rRNA 3′ end formation. J. Biol. Chem., 273, 13255-13263.
9. Caffarelli, E., Arese, M., Santoro, B., Fragapane, P. and Bozzoni, I. (1994) In vitro study of processing of the intron-encoded U16 small nucleolar RNA in Xenopus laevis. Mol. Cell. Biol., 14, 2966-2974.
10. Caffarelli, E., De Gregorio, E., Fatica, A., Prislei, S., Fragapane, P. and Bozzoni, I. (1996) Processing of the intron-encoded U16 and U18 snoRNAs: the conserved C and D boxes control both the processing reactions and the stability of the mature snoRNAs. EMBO J., 15, 1121-1131.
11. Cavaillé, J. and Bachellerie, J.-P. (1996) Processing of fibrillarin-associated snoRNAs from pre-mRNA introns: an exonucleolytic process exclusively directed by the common stem-box terminal structure. Biochimie, 78, 443-456.
12. Cecconi, F., Mariottini, P. and Amaldi, F. (1995) The Xenopus intron-encoded U17 snoRNA is produced by exonucleolytic processing of its precursor in oocytes. Nucleic Acids Res., 23, 4670-4676.
13. Chanfreau, G., Elela, S.A., Ares, M.,Jr and Guthrie, C. (1997) Alternative 3′-end processing of U5 snRNA by RNase III. Genes Dev., 11, 2741-2751.
14. Chanfreau, G., Legrain, P. and Jacquier, A. (1998a) Yeast RNase III as a key processing enzyme in small nucleolar RNAs metabolism. J. Mol. Biol., 284, 975-988.
15. Chanfreau, G., Rotondo, G., Legrain, P. and Jacquier, A. (1998b) Processing of a dicistronic small nucleolar RNA precursor by the RNA endonuclease Rnt1. EMBO J., 17, 3726-3737.
16. 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.
17. Decker, C.J. and Parker, R. (1993) A turnover pathway for both stable and unstable mRNAs in yeast: evidence for a requirement for deadenylation. Genes Dev., 7, 1632-1643.
18. Gietz, D., St. Jean, A., Woods, R.A. and Schiestl, R.H. (1992) Improved method for high efficiency transformation of intact yeast cells. Nucleic Acids Res., 20, 1425.
19. Henry, Y., Wood, H., Morrissey, J.P., Petfalski, E., Kearsey, S. and Tollervey, D. (1994) The 5′ end of yeast 5.8S rRNA is generated by exonucleases from an upstream cleavage site. EMBO J., 13, 2452-2463.
20. Kenna, M., Stevens, A., McCammon, M. and Douglas, M.G. (1993) An essential yeast gene with homology to the exonuclease-encoding XRNIIKEMI gene also encodes a protein with exoribonuclease activity. Mol. Cell. Biol., 13, 341-350.
21. Kiss, T., Bortolini, M.-L. and Filipowicz, W. (1996) Characterization of the intron-encoded U19 RNA, a new mammalian small nucleolar RNA that is not associated with fibrillarin. Mol. Cell. Biol., 16, 1391-1400.
22. Kiss-László, Z., Henry, Y., Bachellerie, J.-P., Caizergues-Ferrer, M. and Kiss, T. (1996) Site-specific ribose methylation of preribosomal RNA: a novel function for small nucleolar RNAs. Cell, 85, 1077-1088.
23. Kretzner, L., Rymond, B.C. and Rosbash, M. (1987) S.cerevisiae U1 RNA is large and has limited primary sequence homology to metazoan U1 snRNA. Cell, 50, 593-602.
24. Kufel, J., Dichtl, B. and Tollervey, D. (1999) Yeast Rnt1p is required for cleavage of the pre-ribosomal RNA in the 3′ ETS but not the 5′ ETS. RNA, 5, 909-917.
25. Lafontaine, D. and Tollervey, D. (1996) One-step PCR mediated strategy for the construction of conditionally expressed and epitope tagged yeast proteins. Nucleic Acids Res., 24, 3469-3472.
26. Larimer, F.W., Hsu, C.L., Maupin, M.K. and Stevens, A. (1992) Characterization of the XRNI gene encoding a 5′→3′ exoribonuclease: sequence data and analysis of disparate protein and mRNA levels of gene-disrupted yeast cells. Gene, 120, 51-57.
27. Li, Z., Pandit, S. and Deutscher, M.P. (1998) 3′ exoribonucleolytic trimming is a common feature of the maturation of small, stable RNAs in Escherichia coli. Proc. Natl Acad. Sci. USA, 95, 2856-2861.
28. Maxwell, E.S. and Fournier, M.J. (1995) The small nucleolar RNAs. Annu. Rev. Biochem., 35, 897-934.
29. Mian, I.S. (1997) Comparative sequence analysis of ribonucleases HII, III, II PH and D. Nucleic Acids Res., 25, 3187-3195.
30. 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.
31. Mitchell, P., Petfalski, E., Shevchenko, A., Mann, M. and Tollervey, D. (1997) The exosome; a conserved eukaryotic RNA processing complex containing multiple 3′→5′ exoribonuclease activities. Cell, 91, 457-466.
32. Moser, M.J., Holley, W.R., Chatterjee, A. and Mian, I.S. (1997) The proofreading domain of Escherichia coli DNA polymerase I and other DNA and/or RNA exonuclease domains. Nucleic Acids Res., 25, 5110-5118.
33. Noguchi, E. et al. (1996) Dis3, implicated in mitotic control, binds directly to Ran and enhances the GEF activity of RCC1. EMBO J., 15, 5595-5605.
34. Ooi, S.L., Samarsky, D.A., Fournier, M.J. and Boeke, J.D. (1998) Intronic snoRNA biosynthesis in Saccharomyces cerevisiae depends on the lariat-debranching enzyme: intron length effects and activity of a precursor snoRNA. RNA, 4, 1096-1110.
35. Patterson, B. and Guthrie, C. (1987) An essential yeast snRNA with a U5-like domain is required for splicing in vivo. Cell, 49, 613-624.
36. Petfalski, E., Dandekar, T., Henry, Y. and Tollervey, D. (1998) Processing of the precursors to small nucleolar RNAs and rRNAs requires common components. Mol. Cell. Biol., 18, 1181-1189.
37. Qu, L.H., Henry, Y., Nicoloso, M., Michot, B., Azum, M.C., Renalier, M.H., Caizergues-Ferrer, M. and Bachellerie, J.P. (1995) U24, a novel intron-encoded small nucleolar RNA with two 12 nt long, phylogenetically conserved complementarities to 28S rRNA. Nucleic Acids Res., 23, 2669-2676.
38. Qu, L.H. et al. (1999) Seven novel methylation guide small nucleolar RNAs are processed from a common polycistronic transcript by Rat1p and RNase III in yeast. Mol. Cell. Biol., 19, 1144-1158.
39. Seipelt, R.L., Zheng, B., Asuru, A. and Rymond, B.C. (1999) U1 snRNA is cleaved by RNase III and processed through an Sm site-dependent pathway. Nucleic Acids Res., 27, 587-595.
40. Siliciano, P.G., Jones, M.H. and Guthrie, C. (1987) Saccharomyces cerevisiae has a U1-like small nuclear RNA with unexpected properties. Science, 237, 1484-1487.
41. Tollervey, D. (1987) A yeast small nuclear RNA is required for normal processing of pre-ribosomal RNA. EMBO J., 6, 4169-4175.
42. Tollervey, D. and Mattaj, I.W. (1987) Fungal small nuclear ribonucleoproteins share properties with plant and vertebrate U-snRNPs. EMBO J., 6, 469-476.
43. Veldman, G.M., Klootwijk, J., van Heerihuizen, H. and Planta, R.J. (1981) The nucleotide sequence of the intergenic region between the 5.8S and 26S rRNA genes of the yeast ribosomal RNA operon. Possible implications for the interaction between 5.8S and 26S rRNA and the processing of the primary transcript. Nucleic Acids Res., 9, 4847-4862.
44. Villa, T., Ceradini, F., Presutti, C. and Bozzoni, I. (1998) Processing of the intron-encoded U18 small nucleolar RNA in the yeast Saccharomyces cerevisiae relies on both exo- and endonucleolytic activities. Mol. Cell. Biol., 18, 3376-3383.
45. Yeh, L.C. and Lee, J.C. (1990) Structural analysis of the internal transcribed spacer 2 of the precursor ribosomal RNA from Saccharomyces cerevisiae. J. Mol. Biol., 211, 699-712.
46. Yoo, C.J. and Wolin, S.L. (1997) The yeast La protein is required for the 3′ endonucleolytic cleavage that matures tRNA precursors. Cell, 89, 393-402.
47. Zagorski, J., Tollervey, D. and Fournier, M.J. (1988) Characterization of an SNR gene locus in Saccharomyces cerevisiae that specifies both dispensable and essential small nuclear RNAs. Mol. Cell. Biol., 8, 3282-3290.