Skip to main content
SpringerLink
Log in
Book cover

Fine-Tuning of RNA Functions by Modification and Editing pp 1–22Cite as

Modification and editing of RNA: historical overview and important facts to remember

Part of the Topics in Current Genetics book series (TCG,volume 12)

Abstract

RNA plays a central role in many cellular processes and several peculiarities of RNAs are probably relics of an ancient primordial RNA World. To fulfill their multiple present-day functions, these molecules need more than just four canonical bases. The numerous modified nucleosides that are formed during processing of nascent precursor RNA transcripts clearly serve this purpose. The recent discoveries of RNA-guided RNA modification machineries and of RNA editing processes leading to selected conversions of one base into another in the pre-RNA, add new dimensions to the problems surrounding the biosynthesis and functions of modified and edited nucleosides in RNA. The majority of these so-called minor or edited nucleosides appear to improve the performance of the matured RNA by working more efficiently and accurately in various steps of cellular metabolism. However, their effects can be subtle and not easy to demonstrate either in vivo or in vitro. Here, we review some basic characteristics of the modified nucleosides and of enzymes leading to such post-transcriptional modifications and editing of RNA

Keywords

These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.

This is a preview of subscription content, log in via an institution.

Preview

Unable to display preview. Download preview PDF.

Unable to display preview. Download preview PDF.

References

  • 1. Agris PF (1996) The importance of being modified: roles of modified nucleosides and Mg2+ in RNA structure and function. Prog Nucleic Acid Res Mol Biol 53:79-129

    Google Scholar 

  • 2. Agris PF (2004) Decoding the genome: a modified view. Nucleic Acids Res 32:223-238

    CrossRef  CAS  PubMed  Google Scholar 

  • 3. Anantharaman V, Koonin EV, Aravind L (2001) TRAM, a predicted RNA-binding domain, common to tRNA uracil methylation and adenine thiolation enzymes. FEMS Microbiol Lett 197:215-221

    CrossRef  Google Scholar 

  • 4. Anantharaman V, Koonin EV, Aravind L (2002) Comparative genomics and evolution of proteins involved in RNA metabolism. Nucleic Acids Res 30:1427-1464

    CrossRef  Google Scholar 

  • 5. Aravind L, Koonin EV (1999) Novel predicted RNA-binding domains associated with the translation machinery. J Mol Evol 48:291-302

    Google Scholar 

  • 6. Aravind L, Koonin EV (2001) THUMP, a predicted RNA binding domain shared by 4-thiouridine, pseudouridine synthases and RNA methylases. Trends Biochem Sci 26:215-217

    CrossRef  Google Scholar 

  • 7. Auxilien S, Crain P, Trewyn RW, Grosjean H (1996) Mechanism, specificity and general properties of the yeast enzyme catalysing the formation of inosine 34 in the anticodon of transfer RNA. J Mol Biol 262:437-458

    CrossRef  Google Scholar 

  • 8. Bachellerie JP, Nicoloso M, Balakin A, Jingwey N, Fournier MJ (1995) Antisense snoRNAs: a family of molecular RNAs with long complementarities to rRNA. Trends Biochem Sci 20:261-265

    CrossRef  Google Scholar 

  • 9. Bass BL (2001) RNA Editing. Oxford University Press, Oxford UK

    Google Scholar 

  • 10. Bass BL, Weintraub H (1988) An unwinding activity that covalently modifies its double-stranded RNA substrate. Cell 55:1089-1098

    CrossRef  CAS  PubMed  Google Scholar 

  • 11. Benne R (1994) RNA-editing in trypanosomes. European J Biochem 221:9-11

    Google Scholar 

  • 12. Benne R (1993) RNA Editing: The alteration of protein coding sequences of RNA. Ellis Horwood, Chichester UK

    Google Scholar 

  • 13. Benne R, Van den Burg D, Brakenhoff JP, Sloof P, Van Boom JH, Tromp MC (1986) Major transcript of the frameshifted coxII gene from trypanosome mitochondria contains four nucleotides that are not encoded in the DNA. Cell 46:819-826

    CrossRef  Google Scholar 

  • 14. Björk GR (1996) Stable RNA modification. In: Neidhardt FC, Curtiss III R, Ingraham JL, Lin ECC, Low KB, Magasanik B, Reznikoff WS, Riley M, Schaechter M, Umbarger HE (eds) Escherichia coli and Salmonella, Cellular and Molecular Biology 2nd ed ASM Press Washington DC, pp 861-886

    Google Scholar 

  • 15. Björk GR, Rasmuson T (1998) Links between tRNA modification and metabolisms and modified nucleosides as tumor markers. In: Grosjean H, Benne R (eds) Modification and Editing of RNA, ASM Press, Washington DC, Chap 26, pp471-491

    Google Scholar 

  • 16. Borek E, Srinivasan PR (1966) The methylation of nucleic acids. Ann Rev Biochem 35:275-298

    CrossRef  Google Scholar 

  • 17. Bratt E, Ohman M (2003) Coordination of editing and splicing of glutamate receptor pre-mRNA. RNA 9:309-318

    CrossRef  Google Scholar 

  • 18. Bujnicki, JM, Droogmans L, Grosjean H, Purushothaman SK, Lapeyre B (2004) Bioinformatics-guided identification and experimental characterization of novel RNA methyltransferases in nucleic acids. In: Bujnicki JM (ed) Practical Bioinformatics series, Springer-Verlag Berlin Heidelberg, Molecular Biol vol 5, pp 139-168

    Google Scholar 

  • 19. Chargaff E, Davidson JN (1955) The Nucleic Acids, vol 1, Academic Press Inc, New York NY

    Google Scholar 

  • 20. Chen S-H, Habib G, Yang C-Y, Gu Z-W, Lee BR Weng S-A, Silberman SR, Cai S-J, Deslypere JP, Rosseneu M (1987) Apolipoprotein B48 is the product of a messenger RNA with an organ-specific in frame-stop codon. Science 238:363-366

    CAS  PubMed  Google Scholar 

  • 21. Clouet d’Orval B, Bortolin ML, Gaspin C, Bachellerie JP (2001) Box C/D RNA guides for the ribose methylation of archaeal tRNAs: the tRNA-Trp intron guides the formation of two-ribose methylated nucleosides in the mature tRNA-Trp. Nucleic Acids Res 29:4518-4529

    CrossRef  Google Scholar 

  • 22. Cohn WE (1960) Pseudouridine, a carbon-carbon linked ribonucleoside in ribonucleic acids: isolation, structure and chemical characteristics J Biol Chem 235:1488-1498

    Google Scholar 

  • 23. Cohn WE, Volkin E (1951) Nucleoside-5’-phosphates from ribonucleic acid. Nature 167:483-484

    Google Scholar 

  • 24. Conticello SG, Thomas CJ, Petersen-Mahrt SK, Neuberger MS (2005) Evolution of the AID/APOBEC family of polynucleotide (deoxy)cytidine deaminase. Mol Biol Evol 22:367-377

    CrossRef  Google Scholar 

  • 25. Crain PF (1998) Detection and structure analysis of modified nucleosides in RNA by mass spectrometry. In: Grosjean H, Benne R (eds) Modification and Editing of RNA, ASM Press, Washington DC, Chap 3, pp 47-57

    Google Scholar 

  • 26. Crick FHC (1966) Codon-Anticodon pairing: the wobble hypothesis. J Mol Biol 19:548-555

    Google Scholar 

  • 27. Curran JF (1998) Modified nucleosides in translation. In: Grosjean H, Benne R (eds) Modification and Editing of RNA, ASM Press, Washington DC, Chap 27, pp 493-516

    Google Scholar 

  • 28. Darzacq X, Jady B, Verheggen C, Kiss AM, Bertrand E, Kiss T (2002) Cajal body-specific small nuclear RNAs: a novel class of 2’-O-methylation and pseudouridylation guide RNAs. EMBO J 21:2746-2756

    CrossRef  Google Scholar 

  • 29. Davis RD (1998) Biophysical and conformational properties of modified nucleosides in RNA (nuclear magnetic resonance studies). In: Grosjean H, Benne R (eds) Modification and Editing of RNA, ASM Press, Washington DC, Chap 5, pp85-102

    Google Scholar 

  • 30. Davis FF, Allen FW (1957) Ribonucleic acid from yeast, which contain a fifth nucleotide. J Biol Chem 227:907-915

    Google Scholar 

  • 31. Decatur WA, Fournier MJ (2002) rRNA modifications and ribosome function. Trends Biochem Sci 27:344-351

    CrossRef  Google Scholar 

  • 32. Decatur WA, Fournier MJ (2003) RNA-guided nucleotide modification of ribosomal and other RNAs. J Biol Chem 278:695-698

    CrossRef  Google Scholar 

  • 33. De Crécy-Lagard V (2004) Finding Missing tRNA modification genes: a comparative genomics goldmine. In: JM Bujnicki JM (ed) Practical Bioinformatics Series, Springer-Verlag Berlin Heidelberg, Molecular Biology vol. 15, pp169-190

    Google Scholar 

  • 34. Driscoll DM, Innerarity TL (2001) RNA editing by cytidine deamination in mammals. In: Bass BL (ed) RNA Editing, Oxford University Press, Oxford UK, Chap 4, pp 61-76

    Google Scholar 

  • 35. Droogmans L, Roovers M, Bujnicki JM, Tricot C, Hartsch T, Stalon V, Grosjean H (2003) Cloning and characterization of tRNA (m1A58) TrmI from Thermus thermophilus HB27, a protein required for cell growth at extreme temperatures. Nucleic Acids Res 31:2148-2156

    CrossRef  Google Scholar 

  • 36. Emeson RB, Singh M (2001) Adenosine-to-inosine RNA editing: substrates and consequences. In: Bass BL (ed) RNA Editing, Oxford University Press, Oxford UK, Chap 6, pp 109-138

    Google Scholar 

  • 37. Estevez AM, Simpson L (1999) Uridine insertion/deletion RNA editing in trypanosome mitochondria - a review. Gene 240:247-260

    CrossRef  Google Scholar 

  • 38. Farkas WR, Hankins WD, Singh R (1973) The guanylation of transfer RNA: an enzymatic reaction. Biochim Biophys Acta 294:94-105

    Google Scholar 

  • 39. Fleissner E, Borek E (1962) A new enzyme of RNA synthesis: RNA methylase. Proc Natl Acad Sci USA 48:1199-1203

    Google Scholar 

  • 40. Förster C, Chakraburtty K, Sprinzl M (1993) Discrimination between initiation and elongation of protein biosynthesis in yeast: identity assured by a nucleotide modification in the initiator tRNA. Nucleic Acids Res 21:5679-5683

    Google Scholar 

  • 41. Ganot P, Bortolin ML, Kiss T (1997) Site-specific pseudouridine formation in preribosomal RNA is guided by small nucleolar. RNA Cell 89:799-809

    Google Scholar 

  • 42. Garcia GA, Goodenough-Lashua DEM (1998) Mechanisms of RNA-modifying and -editing enzymes. In: Grosjean H, Benne R (eds) Modification and Editing of RNA, ASM Press, Washington DC, Chap 8, pp135-168

    Google Scholar 

  • 43. Garcia GA, Kittendorf JD (2005) Transglycosylation: a mechanism for RNA modification and editing. Bioorganic Chem (in press)

    Google Scholar 

  • 44. Gerber AP, Grosjean H, Melcher T, Keller W (1998) Tad1p, a yeast tRNA-specific adenosine deaminase, is related to the mammalian pre-mRNA editing enzymes ADAR1 and ADAR2. EMBO J 17:4780-4789

    CrossRef  Google Scholar 

  • 45. Gerber AP, Keller W (2001) RNA Editing by base deamination: more enzymes, more targets, new mysteries. Trends Biochem Sci 26:376-384

    CrossRef  CAS  PubMed  Google Scholar 

  • 46. Giegé R, Sissler M, Florentz C (1998) Universal rules and idiosyncratic features in tRNA identity. Nucleic Acids Res 26:5017-5035

    CrossRef  Google Scholar 

  • 47. Gott JM, Emeson RB (2000) Functions and mechanisms of RNA editing. Ann Rev Genet 2000 34:499-531

    CrossRef  Google Scholar 

  • 48. Gray MW (2001) Speculation on the origin and evolution of editing. In: Bass BL (ed) RNA Editing, Oxford University Press, Oxford UK, Chap 8, pp160-184

    Google Scholar 

  • 49. Gregson JM, Crain PF, Edmonds CG, Gupta R, Hashizume T, Phillipson DW, McCloskey JA (1993) Structure of the Archaeal transfer RNA nucleoside G*-15 (2-amino-4,7-diohydro-4-oxo-7-B-D-ribofuranosyl-1H-pyrrolo[2,3-d]pyrimidine-5-carboximidamide (Archaeosine). J Biol Chem 268:10076-10086

    Google Scholar 

  • 50. Grosjean H, Keith G, Droogmans L (2004) Detection and quantification of modified nucleotides in RNA using thin-layer chromatography. Methods Mol Biol 265:357-391

    Google Scholar 

  • 51. Grosjean H, Motorin Y, Morin A (1998) RNA-Modifying and RNA-Editing Enzymes: Methods for their identification. In: Grosjean H, Benne R (eds) Modification and Editing of RNA, ASM Press, Washington DC, Chap 2, pp 21-46

    Google Scholar 

  • 52. Grosjean H, Sprinzl M, Steinberg S (1995) Posttranscriptionally modified nucleosides in transfer RNA: their locations and frequencies. Biochimie 77:139-141

    CrossRef  Google Scholar 

  • 53. Grosshans H, Lecointe F, Grosjean H, Hurt E, Simos G (2001) Pus1p-dependent tRNA pseudouridinylation becomes essential when tRNA biogenesis is compromised in yeast. J Biol Chem 276:46333-46339

    CrossRef  Google Scholar 

  • 54. Gutgsell NS, Del Campo M, Raychandhuri S, Ofengand J (2001) A second function for pseudouridine synthases: a point mutant of RluD unable to form pseudouridine 1911, 1915, and 1917 in Escherichia coli 23S ribosomal RNA restores normal growth to an TruD-minus strain. RNA 7:990-998

    CrossRef  Google Scholar 

  • 55. Hall RH (1971) The Modified nucleosides in nucleic Acids. Columbia University Press, New York, NY

    Google Scholar 

  • 56. Hoang C, Ferré d’Amaré (2001) Cocrystal structure of a tRNA Psi-55 pseudouridine synthase: nucleotide flipping by an RNA-modifying enzyme. Cell 71:929-939

    CrossRef  Google Scholar 

  • 57. Holley RW, Apgar J, Everett GA, Madison JT, Marquise M, Merill JR, Penswick JR, Zamir A (1965) Structure of a ribonucleic acid. Science 147:1462-1473

    Google Scholar 

  • 58. Hopper AK, Phizicky EM (2003) tRNA transfers to the limelight. Genes and Development 17:162-180

    CrossRef  Google Scholar 

  • 59. Hotchkiss RD (1948) The quantitative separation of purines, pyrimidines and nucleosides by paper chromatograhy. J Biol Chem 175:315-332

    Google Scholar 

  • 60. Hough RF, Bass BL (2001) Adenosine deaminases that act on RNA. In: Bass BL, ed, RNA Editing, Oxford University Press, Oxford UK, Chap 5, pp77-108

    Google Scholar 

  • 61. Howes NK, Farkas WR (1978) Studies with a homogeneous enzyme from rabbit erythrocytes catalyzing the insertion of guanine into tRNA. J Biol Chem 253:9082-9087

    Google Scholar 

  • 62. Ishitani R, Nureki O, Nameki N, Okada N, Nishimura S, Yokoyama S (2003) Alternative tertiary structure of tRNA for recognition by a posttranscriptional modification enzyme. Cell 113:383-394

    CrossRef  Google Scholar 

  • 63. Itoh YH, Itoh T, Haruna I, Watanabe I (1977) Substitution of guanine for a specific base in tRNA by extracts of Ehrlich ascites tumour cells. Nature 267:467

    Google Scholar 

  • 64. Jady BE, Kiss T (2001) A small nucleolar guide RNA functions both in 2’-O-methylation and pseudouridylation of U5 spliceseomal RNA. EMBO J 20:541-551

    CrossRef  Google Scholar 

  • 65. Kammen HO, Spengler SJ (1970) The biosynthesis of inosinic acid in transfer RNA. Biochim Biophys Acta 213:352-364

    Google Scholar 

  • 66. Kaya Y, Del Campo M, Ofengand J, Malhotra A (2004) Crystal structure of TruD, a novel pseudouridine synthase with a new protein fold. J Biol Chem 279:18107-18110

    CrossRef  Google Scholar 

  • 67. Keller W, Wolf J, Gerber A (1999) Editing of messenger RNA precursors and of RNA by adenosine-to-inosine conversion. FEBS Letters 452:71-76

    CrossRef  Google Scholar 

  • 68. King TH, Liu B, McCully RR, Fournier MJ (2003) Ribosome structure and activity are altered in cells lacking snoRNPs that form pseudouridines in peptidyl transferases center. Mol Cell 11:425-435

    CrossRef  Google Scholar 

  • 69. Kiss-Laszlo 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 85:1077-1088

    CrossRef  Google Scholar 

  • 70. Kline LK, Söll D (1982) Nucleotide Modification in RNA. In: Boyer PD (ed) The Enzymes, vol XV, Academic Press, New York, NY, pp 567-585

    Google Scholar 

  • 71. Kowalak JA, Dalluge JJ, McCloskey JA, Stetter KO (1994) The role of posttranscriptional modification in stabilization of transfer RNA from hyperthermophiles. Biochem 33:7869-7876

    Google Scholar 

  • 72. Lafontaine D, Delcour J, Glasser AL, Desgrés J, Vandenhaute J (1994) The DIM1 gene responsible for the conserved m62m62 dimethylation in the 3’ terminal loop of 18S rRNA is essential in yeast. J Mol Biol 241:492-497

    CrossRef  Google Scholar 

  • 73. Lafontaine LJ, Tollervey D (1998) Regulatory aspects of rRNA modification and pre-rRNA processing. In: Grosjean H, Benne R (eds) Modification and Editing of RNA, ASM Press, Washington DC, Chap 15, pp 281-288

    Google Scholar 

  • 74. Limbach PA, Crain PF, Pomerantz SC, McCloskey JA (1995) Structures of posttrancriptionally modified nucleosides from RNA. Biochimie 77:135-138

    CrossRef  Google Scholar 

  • 75. Maden BEH (1998) Intracellular locations of RNA-modifying enzymes. In: Grosjean H, Benne R (eds) Modification and Editing of RNA, ASM Press, Washington DC, Chap 24, pp 421-440

    Google Scholar 

  • 76. Marchfelder A, Binder S, Brennicke A, Knoop V (1998) RNA editing by base conversion in plant organellar RNAs. In: Grosjean H, Benne R (eds) Modification and Editing of RNA, ASM Press, Washington DC, Chap 17, pp 307-323

    Google Scholar 

  • 77. Marck C, Grosjean H (2002) RNomics: analysis of tRNA genes from 50 genomes of Eukarya, Archaea and Bacteria reveals anticodon-sparing strategies and domain-specific features. RNA 8:1189-1232

    CrossRef  Google Scholar 

  • 78. Marck C, Grosjean H (2003) Identification of BHB splicing motif in intron-containing tRNA from 18 achaeons: evolutionary implications. RNA 9:1516-1531

    CrossRef  Google Scholar 

  • 79. Mass S, Gerber AP, Rich A (1999) Identification and characterization of a human tRNA-specific adenosine deaminase related to the ADAR family of pre-mRNA editing enzyme. Proc Natl Acad Sci USA 96:8895-8900

    CrossRef  Google Scholar 

  • 80. Masson T (1998) Functional aspects of the three modified nucleotides in yeast mitochondrial large-subunit rRNA. In Grosjean H, Benne R (eds) Modification and Editing of RNA, ASM Press, Washington DC, Chap 14, pp 273-280

    Google Scholar 

  • 81. Mol CD, Parikhi SS, Putman CD, Lo TP, Tainer JA (1999) DNA repair mechanisms for the recognition and removal of damaged DNA bases. Ann Rev Biophys Biomol Struct 28:101-128

    CrossRef  Google Scholar 

  • 82. Mueller EG (2002) Chips off the old block. Nature Structural Biol 9:320-322

    Google Scholar 

  • 83. Murphy FV, Ramakrishnan V (2004) Structure of a purine-purine wobble base pair in the decoding center of the ribosome. Nat Struct Biol 11:1251-1252

    CrossRef  Google Scholar 

  • 84. Navaratnam N, Bhattacharya S, Fujino T, Patel D, Jarmuz AL, Scott J (1995) Evolutionary origins of apoB mRNA Editing: catalysis by a cytidine deaminase that has acquired a novel RNA-binding motif at its active site. Cell 81:187-195

    CrossRef  Google Scholar 

  • 85. Navaratnam N, Fujino T, Bayliss J, Jarmuz A, How A, Richardson N, Somasekaram A, Bhattacharya S, Carter C, Scott J (1998) Escherichia coli cytidine deaminase provides a molecular model for apoB RNA editing and a mechanism for RNA substrate recognition. J Mol Biol 275:695-714

    CrossRef  Google Scholar 

  • 86. Navaratnam N, Morrison JR, Bhattacharya S, Patel D, Funahashi T, Giannoni F, Teng B-B, Davidson NO, Scott J (1993) The p27 catalytic subunit of the apolipoprotein B mRNA editing enzyme is a cytidine deaminase. J Biol Chem 268:20709-20712

    Google Scholar 

  • 87. Ni J, Tien AL, Fournier MJ (1997) Small nucleolar RNAs direct site-specific synthesis of pseudouridines in ribosomal RNA. Cell 89:565-573

    CrossRef  Google Scholar 

  • 88. Nicoloso M, QU LH, Michot B, Bachellerie JP (1996) Intron-encoded, antisense small nucleolar RNAs: the characterisation of nine novel species points to their role as guides for the 2’-O-ribose methylation of rRNAs. J Mol Biol 260:178-195

    CrossRef  Google Scholar 

  • 89. Nishimura S (1983) Structure, biosynthesis and function of queuosine in transfer RNA. Prog Nucl Acid Res Mol Biol 28:49-73

    Google Scholar 

  • 90. Ofengand J, Rudd KE (2000) Bacterial, Archaeal, and organellar rRNA pseudouridines and methylated nucleosides and their enzymes. In: The Ribosomes: Structure, Function, Antibiotics and Cellular Interactions, Garrett RA, Douthwaie SR, Liljas A, Matheson AT, Moore PB, Noller HF (eds) ASM Press, Washington DC, pp 175-189

    Google Scholar 

  • 91. Okada N, Harada F, Nishimura S (1976) Specific replacement of Q base in the anticodon of tRNA by guanine catalyzed by a cell-free extract of rabbit reticulocytes. Nucleic Acids Res 3:2593-2603

    Google Scholar 

  • 92. Okada N, Nishimura S (1979) Isolation and characterization of a guanine insertion enzyme, a specific tRNA transglycosylase from Escherichia coli. J Biol Chem 254:3061-3066

    Google Scholar 

  • 93. Omer AD, Ziesche S, Decatur WA, Fournier MJ, Dennis PP (2003) RNA-modifying machines in archaea. Mol Microbiol 48:617-629

    CrossRef  Google Scholar 

  • 94. Persson BC (1993) Modification of tRNA as a regulatory device. Mol Microbiol 8:1011-1016

    Google Scholar 

  • 95. Persson BC, Gustafsson C, Berg DE, Björk GR (1992) The gene for a tRNA modifying enzyme, m5U54-methyltransferase, is essential for viability in Escherichia coli. Proc Natl Acad Sci USA 89:3995-3998

    Google Scholar 

  • 96. Pintard L, Kressler D, Lapeyre B (2000) Spp1p is a yeast nucleolar protein associated with Nop1p and Nop58p that is able to bind S-adenosyl-L-methionine in vitro. Mol Cell Biol 20:1370-1381

    CrossRef  Google Scholar 

  • 97. Powel LM, Wallis SC, Pease RJ Edwards, YH Knott TJ, Scott J (1987) A novel form of tissue-specific RNA processing produces apolipoprotein-B48 in intestine. Cell 50:831-840

    CrossRef  CAS  PubMed  Google Scholar 

  • 98. Rozenski J, Crain PF, McCloskey JA (1999) The RNA modification database: 1999 update. Nucleic Acids Res 27:196-197

    CrossRef  Google Scholar 

  • 99. Savva S, McAuley-Hecht K, Brown T, Pearl I (1995) The structural basis of specific base excision repair by uracil-DNA glycosylase. Nature 373:487-493

    Google Scholar 

  • 100. Shigi N, Suzuki T, Tamakoshi M, Oshima T, Watanabe K (2002) Conserved bases in the T-Psi-C loop of tRNA are determinants for thermophile-specific 2-thiouridylation at position 54. J Biol Chem 277:39128-39135

    CrossRef  Google Scholar 

  • 101. Singh SK, Gurha P, Tran EJ, Maxwell ES, Gupta R (2004) Sequential 2’-O-methylation of archaeal pre-tRNATrp nucleotides id guided by the intron-encoded but trans-acting box C/D ribonucleoprotein of pre-tRNA. J Biol Chem 279:47661-47671

    CrossRef  Google Scholar 

  • 102. Söll D, Kline LK 1982 RNA methylation. In: Boyer PD (ed) The Enzymes, vol XV, Academic Press, New York, NY, pp 557-566

    Google Scholar 

  • 103. Spedaliere CJ, Ginter JM, Johnston MW, Mueller EG (2004) The pseudouridine synthases: revisiting a mechanism that seemed settled. J Am Chem Soc 126:12758-12759

    Google Scholar 

  • 104. Sprinzl M, Horn C, Brown M, Ioudovitch A, Steinberg S (1998) Compilation of tRNA sequences and sequences of tRNA genes. Nucleic Acids Res 26:148-153

    CrossRef  Google Scholar 

  • 105. Stuart K, Panigrahi AK (2002) RNA Editing: complexity and complications. Mol Microbiol 45:591-596

    Google Scholar 

  • 106. Svensson I, Boman HG, Eriksson KG, Kjellin K (1963) Studies on microbial RNA I Transfer of methyl groups from methionine to soluble RNA from Escherichia coli. J Mol Biol 7:254-271

    Google Scholar 

  • 107. Tang TH, Rozhdestvensky TS, Clouet d’Orval BC, Bortolin ML, Huber H, Charpentier B, Branlant C, Bachellerie JP, Brosius J, Huttenhöfer A (2002) RNomics in Archaea reveals a further link between splicing of archaeal introns and rRNA processing. Nucleic Acids Res 30:921-930

    CrossRef  Google Scholar 

  • 108. Teng B, Burant CF, Davidson NO (1993) Molecular cloning of an apolipoprotein B messenger RNA editing protein. Science 260:1816-1819

    Google Scholar 

  • 109. Terns M, Terns R (2002) Small nucleolar RNAs:versatile trans-acting molecules of ancient evolutionary origin. Gene Expression 10:17-39

    Google Scholar 

  • 110. Tran E, Brown J, Maxwell ES (2004) Evolutionary origins of the RNA-guided nucleotide-modification complexes: from the primitive translation apparatus? Trends Biochem Sci 29:343-350

    CrossRef  Google Scholar 

  • 111. Wagner LP, Ofengand J (1970) Chemical evidence for the presence of inosinic acid in the anticodon of an arginine tRNA of Escherichia coli. Biochem Biophys Acta 204:620-623

    Google Scholar 

  • 112. Wagner RW, Smith JE, Cooperman BS, Nishikura K (1989) A double-stranded RNA unwinding activity introduces structural alterations by means of adenosine to inosine conversion in mammalian cells and Xenopus eggs. Proc Natl Acad Sci USA 86:2647-2651

    Google Scholar 

  • 113. Watanabe M, Matsuo M, Tanaka S, Akimoto H, Ashahi S, Nishimura S, Katze JR, Hasizume T, Crain PF, McCloskey JA, Okada N (1997) Biosynthesis of archaeosine, a novel derivative of 7-deazaguanozine specific to archael tRNA, proceeds via a pathway involving base replacement in the tRNA polynucleotide chain. J Biol Chem 272:20146-20151

    CrossRef  Google Scholar 

  • 114. Widerak M, Kern R, Malki A, Richarme G (2005) U2552 methylation at the ribosomal A-site is a negative modulator of translational accuracy. Gene (in press)

    Google Scholar 

  • 115. Winkler ME (1998) Genetics and regulation of base modification in the tRNA and rRNA of prokaryotes and eukaryotes. In: Grosjean H, Benne R (eds) Modification and Editing of RNA, ASM Press, Washington DC, Chap 25, pp 441-469

    Google Scholar 

  • 116. Wolf J, Gerber AP, Keller W (2002) TadA, an essential tRNA-specific adenosine deaminase from Escherichia coli. EMBO J 21:3841-3851

    CrossRef  Google Scholar 

  • 117. Wyatt GR (1950) Occurrence of 5-methyl-cytosine in nucleic acid. Nature (London) 166:237-238

    Google Scholar 

  • 118. Zalkin H (1985) CTP synthase. Methods Enzymol 113:282-287

    Google Scholar 

  • 119. Zimmermann RA, Gait MJ, Moore MJ (1998) Incorporation of modified nucleotides into RNA for studies on RNA structure, function and intermolecular interactions. In: Grosjean H, Benne R (eds) Modification and Editing of RNA, ASM Press, Washington DC, Chap. 4 pp 59- 84

    Google Scholar 

Download references

Author information

Authors and Affiliations

  1. Laboratoire d’Enzymologie et Biochimie Structurales, Bldg 34, CNRS, F-91198 Gif-sur-Yvette, France

    Henri Grosjean

Authors
  1. Henri Grosjean
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Henri Grosjean .

Editor information

Henri Grosjean

Rights and permissions

Reprints and permissions

About this chapter

Cite this chapter

Grosjean, H. Modification and editing of RNA: historical overview and important facts to remember. In: Grosjean, H. (eds) Fine-Tuning of RNA Functions by Modification and Editing. Topics in Current Genetics, vol 12. Springer, Berlin, Heidelberg. https://doi.org/10.1007/b106848

Download citation

Publish with us

Policies and ethics

search

Navigation