Chromosoma

, Volume 105, Issue 7–8, pp 391–400 | Cite as

Eukaryotic ribosomal RNA: the recent excitement in the nucleotide modification problem

  • B. Edward H. Maden
  • John M. X. Hughes
Chromosoma Focus

Abstract

Eukaryotic ribosomal RNA (rRNA) contains numerous modified nucleotides: about 115 methyl groups and some 95 pseudouridines in vertebrates; about 65 methyl groups and some 45 pseudouridines inSaccharomyces cerevisiae. All but about ten of the methyl groups are ribose methylations. The remaining ten are on heterocyclic bases. The ribose methylations occur very rapidly upon the primary rRNA transcript in the nucleolus, prabably on nascent chains, and they appear to play an important role in ribosome maturation, at least in vertebrates. All of the methyl groups occur in the conserved core of rRNA. However, there is no consensus feature of sequence or secondary structure for the methylation sites; thus the nature of the signal(s) for site-specific methylations had until recently remained a mystery. The situation changed dramatically with the discovery that many of the ribose methylation sites are in regions that are precisely complementary to small nucleolar RNA (snoRNA) species. Experimental evidence indicates that structural motifs within the snoRNA species do indeed pinpoint the precise nucleotides to be methylated by the putative 2′-O-methyl transferase(s). Regarding base methylations, the geneDIM1, responsible for modification of the conserved dimethyladenosines near the 3′ end of 18S rRNA, has been shown to be essential for viability inS. cerevisiae and is suggested to play a role in the nucleocytoplasmic transport of the small ribosomal subunit. Recently nearly all of the pseudouridines have also been mapped in the rRNA of several eukaryotic species. As is the case for ribose methylations, most pseudouridine modifications occur rapidly upon precursor rRNA, within core sequences, and in a variety of local primary and secondary structure environments. In contrast to ribose methylation, no potentially unifying process has yet been identified for the enzymic recognition of the many pseudouridine modification sites. However, the new data afford the basis for a search for any potential involvement of snoRNAs in the recognition process.

Preview

Unable to display preview. Download preview PDF.

Unable to display preview. Download preview PDF.

References

  1. Bachellerie J-P,Michot B,Nicoloso M,Balakin A,Ni J,Fournier MJ (1995) Antisense snoRNAs: a family of nucleolar RNAs with long complementarities to rRNA. Trends Biochem Sci 20:261–264PubMedCrossRefGoogle Scholar
  2. Bakin A, Ofengand J (1993) Four newly located pseudouridylate residues inEscherichia coli 23S ribosomal RNA are all at the peptidyl transfer center: analysis by a new sequencing technique. Biochemistry 32:9754–9762PubMedCrossRefGoogle Scholar
  3. Bakin A, Kowalak JA,McCloskey JA,Ofengand J (1994a) The single pseudouridylate residue inE. coli 16S rRNA is located at position 516. Nucleic Acids Res 22:3681–3684PubMedGoogle Scholar
  4. Bakin A, Lane BG,Ofengand J (1994b) Clustering of pseudouridine residues around the peptidyl transfer center of yeast cytoplasmic and mitochondrial ribosomes. Biochemistry 33:13475–13483PubMedCrossRefGoogle Scholar
  5. Balakin AG,Schneider GS, Corbett MS, Ni JW, Fournier MJ (1993) SnR31, snR32, and snR33: three novel, nonessential snRNAs fromSaccharomyces cerevisiae. Nucleic Acids Res 21:5391–5397PubMedGoogle Scholar
  6. Balakin AG,Smith L, Fournier MJ (1996) The RNA World of the nucleolus: two major families of small RNAs defined by different box elements with related functions. Cell 86:823–834PubMedCrossRefGoogle Scholar
  7. Bally M, Hughes J, Cesareni G (1988) SnR30: a new essential small nuclear RNA fromSaccharomyces cerevisiae. Nucleic Acids Res 16:5291–5303PubMedGoogle Scholar
  8. Beltrame M, Tollervey D (1995) Base pairing between U3 and the pre-ribosomal RNA is required for 18S rRNA synthesis. EMBO J 14:4350–4356PubMedGoogle Scholar
  9. Brand RC, Klootwijk J, van Steenbergen TJM, de Kok AJ, Planta RJ (1977) Secondary methylation of yeast ribosomal precursor RNA. Eur J Biochem 75:311–318PubMedCrossRefGoogle Scholar
  10. Brand RC, Klootwijk J, Planta RJ, Maden BEH (1978) Biosynthesis of a hypermodified nucleotide inSaccharomyces carlsbergensis 17S and HeLa cell 18S ribosomal ribonucleic acid. Biochem J 169:71–77PubMedGoogle Scholar
  11. Caboche M, Bachellerie J-P (1977) RNA methylation and control of eukaryotic RNA biosynthesis. Effects of cycloleucine, a specific inhibitor of methylation, on ribosomal RNA maturation. Eur J Biochem 74:19–29PubMedCrossRefGoogle Scholar
  12. Cavaillé J, Nicoloso M, Bachellerie J-P (1996). Targeted ribose methylation of RNA in vivo directed by tailored antisense RNA guides. Nature 383:732–735PubMedCrossRefGoogle Scholar
  13. Choi YC, Busch H (1978) Modified nucleotides in T1 RNase oligonucleotides of 18S ribosomal RNA of the Novikoff Hepatoma. Biochemistry 17:2551–2560PubMedCrossRefGoogle Scholar
  14. Hadjiolov AA (1985) The nucleolus and ribosome biogenesis. In: Albert M, Beerman W, Goldstein L, Porter, KR, Sitte P (eds) Cell biology monographs. Springer, ViennaGoogle Scholar
  15. Helser TL, Davies JE, Dahlberg JE (1971) Change in methylation of 16S ribosomal RNA associated with mutation to kasugamycin resistance inEscherichia coli. Nature New Biol 233:12–14PubMedGoogle Scholar
  16. Helser TL, Davies JE, Dahlberg JE (1972) Mechanism of kasugamycin resistance inEscherichia coli. Nature New Biol 235:6–9PubMedGoogle Scholar
  17. Hughes, JMX (1991) Functional base-pairing interaction between highly conserved elements of U3 small nucleolar RNA and the small ribosomal subunit RNA. J Mol Biol 259:645–654CrossRefGoogle Scholar
  18. Hughes, JMX, Ares M (1991) Depletion of U3 small nucleolar RNA inhibits cleavage in the 5′ external transcribed spacer of yeast preribosomal RNA and prevents formation of 18S ribosomal RNA. EMBO J 10:4231–4239PubMedGoogle Scholar
  19. Hughes JMX, Konings DAM, Cesareni G (1987) The yeast homologue of U3 snRNA. EMBO J 6:2145–2155PubMedGoogle Scholar
  20. Jeanteur P, Amaldi F, Attardi G (1968) Partial sequence analysis of ribosomal RNA from HeLa cells. II. Evidence for sequences of non-ribosomal type in 45S and 32S ribosomal RNA precursors. J Mol Biol 33:757–775PubMedCrossRefGoogle Scholar
  21. Jeppesen C, Stebbins-Boaz B, Gerbi SA (1988) Nucleotide sequence determination and secondary structure ofXenopus U3 snRNA. Nucleic Acids Res 16:2127–2148PubMedGoogle Scholar
  22. Kass S, Tyc K, Steitz JA, Sollner-Webb B (1990) The U3 small nucleolar ribonucleoprotein functions in the first step of pre-ribosomal RNA processing. Cell 60:897–908PubMedCrossRefGoogle Scholar
  23. Kiss-László Z, Henry Y, Bachellerie J-P, Caizergues-Ferrer M, Kiss T (1996) Site-specific ribose methylation of preribosomal RNA: a novel function for small nucleolar RNAs. Cell 85:1077–1088PubMedCrossRefGoogle Scholar
  24. Lafontaine D, Delcour J, Glasser A-L, Desgrès J, Vandenhaute J (1994) TheDIM1 gene responsible for the conserved m26Am26A dimethylation in the 3′ terminal loop of 18S rRNA is essential in yeast. J Mol Biol 241:492–497PubMedCrossRefGoogle Scholar
  25. Lafontaine D, Vandenhaute J, Tollervey D (1995) The 18S rRNA dimethylase Dim1p is required for pre-ribosomal RNA processing in yeast. Genes Dev 9:2470–2481PubMedGoogle Scholar
  26. Lane BG, Ofengand J, Gray MW (1992) Pseudouridine in the large subunit (23S-like) ribosomal RNA. The site of peptidyl transfer in ribosome? FEBS Lett 302:1–4PubMedCrossRefGoogle Scholar
  27. Lane BG, Ofengand J, Gray MW (1995) Pseudouridine and 2′-O-methylated nucleosides. Significance of their selective occurrence in rRNA domains that function in ribosome-catalyzed synthesis of the peptide bonds in proteins. Biochimie 77:7–15PubMedCrossRefGoogle Scholar
  28. Li HV, Zagorski J, Fournier MJ (1990) Depletion of U14 snRNA (snR128) disrupts production of 18S ribosomal RNA synthesis inSaccharomyces cerevisiae. Mol Cell Biol 10:1145–1152PubMedGoogle Scholar
  29. Liang W-Q, Fournier MJ (1995) U14 base-pairs with 18S rRNA: a novel snoRNA interaction required for rRNA processing. Genes Dev 9:2433–2443PubMedGoogle Scholar
  30. Maden BEH (1986) Identification of the locations of the methyl groups in 18S ribosomal RNA fromXenopus laevis and man,. J Mol Biol 189:681–699PubMedCrossRefGoogle Scholar
  31. Maden BEH (1988) Locations of methyl groups in 28S rRNA ofXenopus laevis and man: clustering in the conserved core of molecule. J Mol Biol 201:289–314PubMedCrossRefGoogle Scholar
  32. Maden BEH (1990a) The modified nucleotides in ribosomal RNA of man and other eukaryotes. In: Gehrke CW, Kuo KCT (eds) Chromatography and modification of nucleosides part B: biological roles and function of modification. Elsevier, Amsterdam, pp B265–301Google Scholar
  33. Maden BEH (1990b) The numerous modified nucleotides in eukaryotic ribosomal RNA. Prog Nucleic Acid Res Mol Biol 39:241–303PubMedCrossRefGoogle Scholar
  34. Maden BEH, Salim M (1974) The methylated nucleotide sequences in HeLa cell ribosomal RNA and its precursors. J Mol Biol 88:133–164PubMedCrossRefGoogle Scholar
  35. Maden BEH, Wakeman JA (1988) Pseudouridine distribution in mammalian 18S ribosomal RNA: a major cluster in the central region of the molecule. Biochem J 249:459–464PubMedGoogle Scholar
  36. Maden BEH, Vaughan MH, Warner JR, Darnell JE (1969) Effects of valine deprivation on ribosome formation in HeLa cells. J Mol Biol 45:265–275PubMedCrossRefGoogle Scholar
  37. Maden BEH, Corbett ME, Heeney PA, Pugh K, Ajuh PM (1995) Classical and novel approaches to the detection and localization of the numerous modified nucleotides in eukaryotic ribosomal RNA. Biochimie 72:22–29CrossRefGoogle Scholar
  38. Maxwell ES, Fournier ML (1995) The small nucleolar RNAs. Annu Rev Biochem 35:897–934CrossRefGoogle Scholar
  39. McCallum FS, Maden BEH (1985) Human 18S ribosomal RNA sequence inferred from DNA sequence: variations in 18S sequences and secondary modification patterns between vertebrates. Biochem J 232:725–733PubMedGoogle Scholar
  40. Morrissey JP, Tollervey D (1993) Yeast snR30 is a small nucleolar RNA required for 18S rRNA synthesis. Mol Cell Biol 13:2469–2477PubMedGoogle Scholar
  41. Morrissey JP, Tollervey D (1995) Birth of the snoRNPs: the evolution of RNase MRP and the eukaryotic pre-rRNA processing system. Trends Biochem Sci 20:78–82PubMedCrossRefGoogle Scholar
  42. Mougey EB, Pape LK, Sollner-Webb B (1993) A U3 small nuclear ribonucleoprotein-requiring processing event in the 5′ external transcribed spacer ofXenopus precursor rRNA. Mol Cell Biol 13:5990–5998PubMedGoogle Scholar
  43. Négre D, Weitzmann C, Ofengand J (1989a) In vitro methylation ofE. coli 16S ribosomal RNA. Proc Natl Acad Sci USA 86:4902–4906PubMedCrossRefGoogle Scholar
  44. Négre D, Weitzman, C, Ofengand J (1989b) In vitro methylation ofEscherichia coli 16S RNA, 23S RNA, and 30S ribosomes by homologous cell-free extracts. In Jones PA, Clawson GA, Willis DB, Weisbach A (eds) Nucleic acid methylation. Willey-Liss. New York, pp 1–17Google Scholar
  45. Nicoloso M, Liang-Hu Q, Michot B, Bachellerie J-P (1996) Intron-encoded, antisense small nucleolar RNAs: the characterization of nine novel species points to their direct role as guides for the 2′-ribose methylation of rRNAs. J Mol Biol 260:178–195PubMedCrossRefGoogle Scholar
  46. Ofengand J, Bakin A (1997) Mapping to nucleotide resolution of pseudouridine residues in large subunit ribosomal RNAs from representative eukaryotes, prokaryotes, archaebacteria, mitochondria and chloroplasts. J Mol Biol 266:246–268PubMedCrossRefGoogle Scholar
  47. Parker R, Simmons T, Shuster EO, Siliciano PG, Guthrie C (1988) Genetic analysis of small nuclear RNAs inSaccharomyces cerevisiae: viable sextuple mutant. Mol Cell Biol 8:3150–3159PubMedGoogle Scholar
  48. Peculis BA, Steitz JA (1993) Disruption of U8 nucleolar snRNA inhibits 5.8S and 28S rRNA processing in theXenopus oocyte. Cell 73:1233–1245PubMedCrossRefGoogle Scholar
  49. Raué HA, Klootwijk J, Musters W (1988) Evolutionary conservation of structure and function of high molecular weight ribosomal RNA. Prog Biophys Mol Biol 51:77–129PubMedCrossRefGoogle Scholar
  50. Rimoldi OJ, Raghu B, Nag MK, Eliceiri GL (1993) Three new small nucleolar RNAs that are cross-linked in vivo to unique regions of pre-rRNA. Mol Cell Biol 13:4382–4390PubMedGoogle Scholar
  51. Salim M, Maden BEH (1981) Nucleotide sequence ofXenopus laevis RNA inferred from gene sequence. Nature 291:205–208PubMedCrossRefGoogle Scholar
  52. Samarsky DA, Balakin AG, Fournier MJ (1995) Characterization of three new snRNAs fromSaccharomyces cerevisiae: snr34, snR35 and snR36. Nucleic Acids Res 23:2548–2554PubMedGoogle Scholar
  53. Savino R, Gerbi S (1990) In vivo disruption ofXenopus U3 snRNA affects ribosomal RNA processing. EMBO J 9:2299–2308PubMedGoogle Scholar
  54. Schmitt ME, Clayton DA (1992) Yeast site-specific ribonucleo-protein endoribonuclease MRP contains an RNA component homologous to mammalian Rnase MRP RNA and essential for viability. Genes Dev 6:1975–1985PubMedGoogle Scholar
  55. Schmitt ME, Clayton DA (1993) Nuclear RNase MRP is required for correct processing of pre-5.8S rRNA inSaccharomyces cerevisiae. Mol Cell Biol 13:7935–7941PubMedGoogle Scholar
  56. Schmitt ME, Bennet JL, Dairaghi DJ, Clayton DA (1993) Secondary structure of RNase MRP RNA as predicted by phylogenetic comparison. FASEB J 7:208–213PubMedGoogle Scholar
  57. Segal DM, Eichler DC (1991) A nucleolar 2′-0-methyltransferase: specificity and evidence for its role in the methylation of mouse 28S precursor ribosomal RNA. J Biol Chem 266:24385–24389PubMedGoogle Scholar
  58. Swann PF, Peacock AC, Bunting S (1975) Carcinogenesis and cellular injury. The effect, of ethionine on ribonucleic acid synthesis in rat liver. Biochem J 150:335–344PubMedGoogle Scholar
  59. Tollervey D (1987) A yeast small nuclear RNA is required for normal processing of pre-ribosomal RNA. EMBO J 6:4169–4175PubMedGoogle Scholar
  60. Tollervey D, Guthrie C (1985) Deletion of a yeast small nuclear RNA gene impairs growth. EMBO J 4:3873–3878PubMedGoogle Scholar
  61. Tollervey D, Lehtonen H, Jansen R, Kern H, Hurt EC (1993) Temperature-sensitive mutations demonstrate roles for yeast fibrillarin in pre-rRNA processing, pre-rRNA processing, pre-rRNA methylation and ribosome assembly. Cell 72:443–457PubMedCrossRefGoogle Scholar
  62. Tyc K, Steitz JA (1989) U3, U8 and U13 comprise a new class of mammalian snRNAs localized in the cell nucleolus. EMBO J 8:3113–3119PubMedGoogle Scholar
  63. Tycowski KT, Shu M-D, Steitz JA (1993) A small nucleolar RNA is processed from an intron of the human gene encoding ribosomal protein S3. Genes Dev 7:1176–1190PubMedGoogle Scholar
  64. Tycowski KT, Shu M-D, Steitz JA (1994) Requirement for intron-encoded U22 small nucleolar RNA in 18S ribosomal RNA maturation. Science 266:1558–1561PubMedCrossRefGoogle Scholar
  65. Van Knippenberg PH (1986) Structural and functional aspects of the N6, N6 dimethyladenosine in 16S ribosomal RNA. In: Hardersty B, Kramer G (eds) Structure, function and genetics of ribosomes. Springer, Berlin Heidelberg New York, pp 412–424Google Scholar
  66. Vaughan MH, Soeiro R, Warner JR, Darnell JE (1967) The effects of methionine deprivation on ribosome synthesis in HeLa cells. Proc Natl Acad Sci USA 58: 1527–1534PubMedCrossRefGoogle Scholar
  67. Wise JA, Weiner AM (1980)Dictyostelium small nuclear RNA D2 is homologous to rat nucleolar RNA U3 and is encoded by a disperse multigene family. Cell 22:109–118PubMedCrossRefGoogle Scholar
  68. Wolf SF, Schlesinger D (1977) Nuclear metabolism of ribosomal RNA in growing, methionine-limited and ethionine-treated HeLa cells. Biochemistry 16:2783–2791PubMedCrossRefGoogle Scholar
  69. Zagorski J, Tollervey D, Fournier MJ (1988) Characterization of an SNR gene locus inSaccharomyces cerevisiae that specifies both dispensible and essential small nuclear RNAs. Mol Cell Biol 8:3282–3290PubMedGoogle Scholar

Copyright information

© Springer-Verlag 1997

Authors and Affiliations

  • B. Edward H. Maden
    • 1
  • John M. X. Hughes
    • 1
  1. 1.School of Biological SciencesUniversity of LiverpoolLiverpoolUK

Personalised recommendations