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. 1996 Oct 15;15(20):5701–5714.

RRP5 is required for formation of both 18S and 5.8S rRNA in yeast.

J Venema 1, D Tollervey 1
PMCID: PMC452314  PMID: 8896463

Abstract

Three of the four eukaryotic ribosomal RNA molecules (18S, 5.8S and 25-28S) are synthesized as a single precursor which is subsequently processed into the mature rRNAs by a complex series of cleavage and modification reactions. In the yeast Saccharomyces cerevisiae, the early pre-rRNA cleavages at sites A0, A1 and A2, required for the synthesis of 18S rRNA, are inhibited in strains lacking RNA or protein components of the U3, U14, snR10 and snR30 small nucleolar ribonucleoproteins (snoRNPs). The subsequent cleavage at site A3, required for formation of the major, short form of 5.8S rRNA, is carried out by another ribonucleoprotein, RNase MRP. A screen for mutations showing synthetic lethality with deletion of the non-essential snoRNA, snR10, identified a novel gene, RRP5, which is essential for viability and encodes a 193 kDa nucleolar protein. Genetic depletion of Rrp5p inhibits the synthesis of 18S rRNA and, unexpectedly, also of the major short form of 5.8S rRNA. Pre-rRNA processing is concomitantly impaired at sites A0, A1, A2 and A3. This distinctive phenotype makes Rrp5p the first cellular component simultaneously required for the snoRNP-dependent cleavage at sites A0, A1 and A2 and the RNase MRP-dependent cleavage at A3 and provides evidence for a close interconnection between these processing events. Putative RRP5 homologues from Caenorhabditis elegans and humans were also identified, suggesting that the critical function of Rrp5p is evolutionarily conserved.

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Selected References

These references are in PubMed. This may not be the complete list of references from this article.

  1. Allmang C., Henry Y., Morrissey J. P., Wood H., Petfalski E., Tollervey D. Processing of the yeast pre-rRNA at sites A(2) and A(3) is linked. RNA. 1996 Jan;2(1):63–73. [PMC free article] [PubMed] [Google Scholar]
  2. Aris J. P., Blobel G. Identification and characterization of a yeast nucleolar protein that is similar to a rat liver nucleolar protein. J Cell Biol. 1988 Jul;107(1):17–31. doi: 10.1083/jcb.107.1.17. [DOI] [PMC free article] [PubMed] [Google Scholar]
  3. Bachellerie J. P., Michot B., Nicoloso M., Balakin A., Ni J., Fournier M. J. Antisense snoRNAs: a family of nucleolar RNAs with long complementarities to rRNA. Trends Biochem Sci. 1995 Jul;20(7):261–264. doi: 10.1016/s0968-0004(00)89039-8. [DOI] [PubMed] [Google Scholar]
  4. Beltrame M., Henry Y., Tollervey D. Mutational analysis of an essential binding site for the U3 snoRNA in the 5' external transcribed spacer of yeast pre-rRNA. Nucleic Acids Res. 1994 Nov 25;22(23):5139–5147. doi: 10.1093/nar/22.23.5139. [DOI] [PMC free article] [PubMed] [Google Scholar]
  5. Beltrame M., Tollervey D. Base pairing between U3 and the pre-ribosomal RNA is required for 18S rRNA synthesis. EMBO J. 1995 Sep 1;14(17):4350–4356. doi: 10.1002/j.1460-2075.1995.tb00109.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  6. Beltrame M., Tollervey D. Identification and functional analysis of two U3 binding sites on yeast pre-ribosomal RNA. EMBO J. 1992 Apr;11(4):1531–1542. doi: 10.1002/j.1460-2075.1992.tb05198.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  7. Berben G., Dumont J., Gilliquet V., Bolle P. A., Hilger F. The YDp plasmids: a uniform set of vectors bearing versatile gene disruption cassettes for Saccharomyces cerevisiae. Yeast. 1991 Jul;7(5):475–477. doi: 10.1002/yea.320070506. [DOI] [PubMed] [Google Scholar]
  8. Bergès T., Petfalski E., Tollervey D., Hurt E. C. Synthetic lethality with fibrillarin identifies NOP77p, a nucleolar protein required for pre-rRNA processing and modification. EMBO J. 1994 Jul 1;13(13):3136–3148. doi: 10.1002/j.1460-2075.1994.tb06612.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  9. Chu S., Archer R. H., Zengel J. M., Lindahl L. The RNA of RNase MRP is required for normal processing of ribosomal RNA. Proc Natl Acad Sci U S A. 1994 Jan 18;91(2):659–663. doi: 10.1073/pnas.91.2.659. [DOI] [PMC free article] [PubMed] [Google Scholar]
  10. Devereux J., Haeberli P., Smithies O. A comprehensive set of sequence analysis programs for the VAX. Nucleic Acids Res. 1984 Jan 11;12(1 Pt 1):387–395. doi: 10.1093/nar/12.1part1.387. [DOI] [PMC free article] [PubMed] [Google Scholar]
  11. Doye V., Hurt E. C. Genetic approaches to nuclear pore structure and function. Trends Genet. 1995 Jun;11(6):235–241. doi: 10.1016/s0168-9525(00)89057-5. [DOI] [PubMed] [Google Scholar]
  12. Eichler D. C., Craig N. Processing of eukaryotic ribosomal RNA. Prog Nucleic Acid Res Mol Biol. 1994;49:197–239. doi: 10.1016/s0079-6603(08)60051-3. [DOI] [PubMed] [Google Scholar]
  13. Elela S. A., Igel H., Ares M., Jr RNase III cleaves eukaryotic preribosomal RNA at a U3 snoRNP-dependent site. Cell. 1996 Apr 5;85(1):115–124. doi: 10.1016/s0092-8674(00)81087-9. [DOI] [PubMed] [Google Scholar]
  14. Gietz D., St Jean A., Woods R. A., Schiestl R. H. Improved method for high efficiency transformation of intact yeast cells. Nucleic Acids Res. 1992 Mar 25;20(6):1425–1425. doi: 10.1093/nar/20.6.1425. [DOI] [PMC free article] [PubMed] [Google Scholar]
  15. Girard J. P., Lehtonen H., Caizergues-Ferrer M., Amalric F., Tollervey D., Lapeyre B. GAR1 is an essential small nucleolar RNP protein required for pre-rRNA processing in yeast. EMBO J. 1992 Feb;11(2):673–682. doi: 10.1002/j.1460-2075.1992.tb05099.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  16. Grandi P., Doye V., Hurt E. C. Purification of NSP1 reveals complex formation with 'GLFG' nucleoporins and a novel nuclear pore protein NIC96. EMBO J. 1993 Aug;12(8):3061–3071. doi: 10.1002/j.1460-2075.1993.tb05975.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  17. Guarente L., Yocum R. R., Gifford P. A GAL10-CYC1 hybrid yeast promoter identifies the GAL4 regulatory region as an upstream site. Proc Natl Acad Sci U S A. 1982 Dec;79(23):7410–7414. doi: 10.1073/pnas.79.23.7410. [DOI] [PMC free article] [PubMed] [Google Scholar]
  18. Henry Y., Wood H., Morrissey J. P., Petfalski E., Kearsey S., Tollervey D. The 5' end of yeast 5.8S rRNA is generated by exonucleases from an upstream cleavage site. EMBO J. 1994 May 15;13(10):2452–2463. doi: 10.1002/j.1460-2075.1994.tb06530.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  19. Hughes J. M., Ares M., Jr Depletion of U3 small nucleolar RNA inhibits cleavage in the 5' external transcribed spacer of yeast pre-ribosomal RNA and impairs formation of 18S ribosomal RNA. EMBO J. 1991 Dec;10(13):4231–4239. doi: 10.1002/j.1460-2075.1991.tb05001.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  20. Jansen R. P., Hurt E. C., Kern H., Lehtonen H., Carmo-Fonseca M., Lapeyre B., Tollervey D. Evolutionary conservation of the human nucleolar protein fibrillarin and its functional expression in yeast. J Cell Biol. 1991 May;113(4):715–729. doi: 10.1083/jcb.113.4.715. [DOI] [PMC free article] [PubMed] [Google Scholar]
  21. Jansen R., Tollervey D., Hurt E. C. A U3 snoRNP protein with homology to splicing factor PRP4 and G beta domains is required for ribosomal RNA processing. EMBO J. 1993 Jun;12(6):2549–2558. doi: 10.1002/j.1460-2075.1993.tb05910.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  22. Jarmolowski A., Zagorski J., Li H. V., Fournier M. J. Identification of essential elements in U14 RNA of Saccharomyces cerevisiae. EMBO J. 1990 Dec;9(13):4503–4509. doi: 10.1002/j.1460-2075.1990.tb07901.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  23. Kondo K., Inouye M. Yeast NSR1 protein that has structural similarity to mammalian nucleolin is involved in pre-rRNA processing. J Biol Chem. 1992 Aug 15;267(23):16252–16258. [PubMed] [Google Scholar]
  24. Kondo K., Kowalski L. R., Inouye M. Cold shock induction of yeast NSR1 protein and its role in pre-rRNA processing. J Biol Chem. 1992 Aug 15;267(23):16259–16265. [PubMed] [Google Scholar]
  25. Koshland D., Kent J. C., Hartwell L. H. Genetic analysis of the mitotic transmission of minichromosomes. Cell. 1985 Feb;40(2):393–403. doi: 10.1016/0092-8674(85)90153-9. [DOI] [PubMed] [Google Scholar]
  26. Kranz J. E., Holm C. Cloning by function: an alternative approach for identifying yeast homologs of genes from other organisms. Proc Natl Acad Sci U S A. 1990 Sep;87(17):6629–6633. doi: 10.1073/pnas.87.17.6629. [DOI] [PMC free article] [PubMed] [Google Scholar]
  27. Lafontaine D., Tollervey D. Trans-acting factors in yeast pre-rRNA and pre-snoRNA processing. Biochem Cell Biol. 1995 Nov-Dec;73(11-12):803–812. doi: 10.1139/o95-088. [DOI] [PubMed] [Google Scholar]
  28. Lafontaine D., Vandenhaute J., Tollervey D. The 18S rRNA dimethylase Dim1p is required for pre-ribosomal RNA processing in yeast. Genes Dev. 1995 Oct 15;9(20):2470–2481. doi: 10.1101/gad.9.20.2470. [DOI] [PubMed] [Google Scholar]
  29. Lee W. C., Zabetakis D., Mélèse T. NSR1 is required for pre-rRNA processing and for the proper maintenance of steady-state levels of ribosomal subunits. Mol Cell Biol. 1992 Sep;12(9):3865–3871. doi: 10.1128/mcb.12.9.3865. [DOI] [PMC free article] [PubMed] [Google Scholar]
  30. Li H. D., Zagorski J., Fournier M. J. Depletion of U14 small nuclear RNA (snR128) disrupts production of 18S rRNA in Saccharomyces cerevisiae. Mol Cell Biol. 1990 Mar;10(3):1145–1152. doi: 10.1128/mcb.10.3.1145. [DOI] [PMC free article] [PubMed] [Google Scholar]
  31. Liang W. Q., Fournier M. J. U14 base-pairs with 18S rRNA: a novel snoRNA interaction required for rRNA processing. Genes Dev. 1995 Oct 1;9(19):2433–2443. doi: 10.1101/gad.9.19.2433. [DOI] [PubMed] [Google Scholar]
  32. Lindahl L., Archer R. H., Zengel J. M. A new rRNA processing mutant of Saccharomyces cerevisiae. Nucleic Acids Res. 1992 Jan 25;20(2):295–301. doi: 10.1093/nar/20.2.295. [DOI] [PMC free article] [PubMed] [Google Scholar]
  33. Lygerou Z., Allmang C., Tollervey D., Séraphin B. Accurate processing of a eukaryotic precursor ribosomal RNA by ribonuclease MRP in vitro. Science. 1996 Apr 12;272(5259):268–270. doi: 10.1126/science.272.5259.268. [DOI] [PubMed] [Google Scholar]
  34. Lygerou Z., Mitchell P., Petfalski E., Séraphin B., Tollervey D. The POP1 gene encodes a protein component common to the RNase MRP and RNase P ribonucleoproteins. Genes Dev. 1994 Jun 15;8(12):1423–1433. doi: 10.1101/gad.8.12.1423. [DOI] [PubMed] [Google Scholar]
  35. Maxwell E. S., Fournier M. J. The small nucleolar RNAs. Annu Rev Biochem. 1995;64:897–934. doi: 10.1146/annurev.bi.64.070195.004341. [DOI] [PubMed] [Google Scholar]
  36. Mitchell P., Petfalski E., Tollervey D. The 3' end of yeast 5.8S rRNA is generated by an exonuclease processing mechanism. Genes Dev. 1996 Feb 15;10(4):502–513. doi: 10.1101/gad.10.4.502. [DOI] [PubMed] [Google Scholar]
  37. Morrissey J. P., Tollervey D. Birth of the snoRNPs: the evolution of RNase MRP and the eukaryotic pre-rRNA-processing system. Trends Biochem Sci. 1995 Feb;20(2):78–82. doi: 10.1016/s0968-0004(00)88962-8. [DOI] [PubMed] [Google Scholar]
  38. Morrissey J. P., Tollervey D. Yeast snR30 is a small nucleolar RNA required for 18S rRNA synthesis. Mol Cell Biol. 1993 Apr;13(4):2469–2477. doi: 10.1128/mcb.13.4.2469. [DOI] [PMC free article] [PubMed] [Google Scholar]
  39. Mélèse T., Xue Z. The nucleolus: an organelle formed by the act of building a ribosome. Curr Opin Cell Biol. 1995 Jun;7(3):319–324. doi: 10.1016/0955-0674(95)80085-9. [DOI] [PubMed] [Google Scholar]
  40. Nogi Y., Vu L., Nomura M. An approach for isolation of mutants defective in 35S ribosomal RNA synthesis in Saccharomyces cerevisiae. Proc Natl Acad Sci U S A. 1991 Aug 15;88(16):7026–7030. doi: 10.1073/pnas.88.16.7026. [DOI] [PMC free article] [PubMed] [Google Scholar]
  41. Parker R., Simmons T., Shuster E. O., Siliciano P. G., Guthrie C. Genetic analysis of small nuclear RNAs in Saccharomyces cerevisiae: viable sextuple mutant. Mol Cell Biol. 1988 Aug;8(8):3150–3159. doi: 10.1128/mcb.8.8.3150. [DOI] [PMC free article] [PubMed] [Google Scholar]
  42. Robzyk K., Kassir Y. A simple and highly efficient procedure for rescuing autonomous plasmids from yeast. Nucleic Acids Res. 1992 Jul 25;20(14):3790–3790. doi: 10.1093/nar/20.14.3790. [DOI] [PMC free article] [PubMed] [Google Scholar]
  43. Schimmang T., Tollervey D., Kern H., Frank R., Hurt E. C. A yeast nucleolar protein related to mammalian fibrillarin is associated with small nucleolar RNA and is essential for viability. EMBO J. 1989 Dec 20;8(13):4015–4024. doi: 10.1002/j.1460-2075.1989.tb08584.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  44. Schmitt M. E., Clayton D. A. Nuclear RNase MRP is required for correct processing of pre-5.8S rRNA in Saccharomyces cerevisiae. Mol Cell Biol. 1993 Dec;13(12):7935–7941. doi: 10.1128/mcb.13.12.7935. [DOI] [PMC free article] [PubMed] [Google Scholar]
  45. Shuai K., Warner J. R. A temperature sensitive mutant of Saccharomyces cerevisiae defective in pre-rRNA processing. Nucleic Acids Res. 1991 Sep 25;19(18):5059–5064. doi: 10.1093/nar/19.18.5059. [DOI] [PMC free article] [PubMed] [Google Scholar]
  46. Sikorski R. S., Hieter P. A system of shuttle vectors and yeast host strains designed for efficient manipulation of DNA in Saccharomyces cerevisiae. Genetics. 1989 May;122(1):19–27. doi: 10.1093/genetics/122.1.19. [DOI] [PMC free article] [PubMed] [Google Scholar]
  47. Teigelkamp S., Newman A. J., Beggs J. D. Extensive interactions of PRP8 protein with the 5' and 3' splice sites during splicing suggest a role in stabilization of exon alignment by U5 snRNA. EMBO J. 1995 Jun 1;14(11):2602–2612. doi: 10.1002/j.1460-2075.1995.tb07258.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  48. Teigelkamp S., Whittaker E., Beggs J. D. Interaction of the yeast splicing factor PRP8 with substrate RNA during both steps of splicing. Nucleic Acids Res. 1995 Feb 11;23(3):320–326. doi: 10.1093/nar/23.3.320. [DOI] [PMC free article] [PubMed] [Google Scholar]
  49. Tollervey D. A yeast small nuclear RNA is required for normal processing of pre-ribosomal RNA. EMBO J. 1987 Dec 20;6(13):4169–4175. doi: 10.1002/j.1460-2075.1987.tb02763.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  50. Tollervey D., Guthrie C. Deletion of a yeast small nuclear RNA gene impairs growth. EMBO J. 1985 Dec 30;4(13B):3873–3878. doi: 10.1002/j.1460-2075.1985.tb04160.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  51. Tollervey D., Lehtonen H., Carmo-Fonseca M., Hurt E. C. The small nucleolar RNP protein NOP1 (fibrillarin) is required for pre-rRNA processing in yeast. EMBO J. 1991 Mar;10(3):573–583. doi: 10.1002/j.1460-2075.1991.tb07984.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  52. Umen J. G., Guthrie C. A novel role for a U5 snRNP protein in 3' splice site selection. Genes Dev. 1995 Apr 1;9(7):855–868. doi: 10.1101/gad.9.7.855. [DOI] [PubMed] [Google Scholar]
  53. Umen J. G., Guthrie C. Prp16p, Slu7p, and Prp8p interact with the 3' splice site in two distinct stages during the second catalytic step of pre-mRNA splicing. RNA. 1995 Aug;1(6):584–597. [PMC free article] [PubMed] [Google Scholar]
  54. Venema J., Dirks-Mulder A., Faber A. W., Raué H. A. Development and application of an in vivo system to study yeast ribosomal RNA biogenesis and function. Yeast. 1995 Feb;11(2):145–156. doi: 10.1002/yea.320110206. [DOI] [PubMed] [Google Scholar]
  55. Venema J., Henry Y., Tollervey D. Two distinct recognition signals define the site of endonucleolytic cleavage at the 5'-end of yeast 18S rRNA. EMBO J. 1995 Oct 2;14(19):4883–4892. doi: 10.1002/j.1460-2075.1995.tb00169.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  56. Venema J., Tollervey D. Processing of pre-ribosomal RNA in Saccharomyces cerevisiae. Yeast. 1995 Dec;11(16):1629–1650. doi: 10.1002/yea.320111607. [DOI] [PubMed] [Google Scholar]
  57. Wimmer C., Doye V., Grandi P., Nehrbass U., Hurt E. C. A new subclass of nucleoporins that functionally interact with nuclear pore protein NSP1. EMBO J. 1992 Dec;11(13):5051–5061. doi: 10.1002/j.1460-2075.1992.tb05612.x. [DOI] [PMC free article] [PubMed] [Google Scholar]

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