Nucleic Acids Are Not Boring Long Polymers of Only Four Types of Nucleotides: A Guided Tour

DNA and RNA Modification Enzymes: Structure, Mechanism, Function and Evolution

Volumn , Issue , 2009, Pages 1-18

  Grosjean, Henri ^a  

^a CNRS   (France)

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EID: 85019179237     PISSN: None     EISSN: None     Source Type: Book    
DOI: None     Document Type: Chapter

References (100)

1. Avery OT, MacLeod CM, McCarthy M. Studies on the chemical nature of the substance inducing transformation of pneumococcal types. J Exp Med 1944; 79:137-158.
2. McCarthy M, Avery OT. Studies on the chemical nature of the substance inducing transformation of pneumococcal types: II. Effect of deoxyribonuclease on the biological activity of the transforming substance. J Exp Med 1946; 83:89-96.
3. Hotchkiss ED, Marmur J. Double marker transformation as evidence of linked factors in deoxyribonu-cleate transforming agents. Proc. Natl Acad Sci USA 1954; 40:55-60.
4. Chargaff E. Structure and function of nucleic acids as cell constituents. Fed Proc 1951; 10:654-659.
5. Watson JD, Crick FHC. A structure for deoxyribose nucleic acid. Nature 1953; 171:737-738.
6. Watson JD, Crick FHC. General implications of the structure of deoxyribonucleic acid. Nature 1953; 171:964-967.
7. Meselson M, Yuan R. DNA restriction enzyme from E. coli. Nature 1968; 217:1110-1114.
8. Smith HO, Wilcox KW. A restriction enzyme from hemophilus-influenza. L Purification and general properties. J Mol Biol 1970; 51:379-391. See also the paper by Danna K, Nathans D. Specific cleavage of simian virus 40 DNA by restriction endonuclease of Hemophilus influenzae. Proc Natl Acad Sci1971; 68:2913-2917.
9. Sanger F, Nicklen S, Coulson AR. DNA sequencing with chain-terminating inhibitors. Proc Nad Acad Sci USA 1977; 4:5463-5467.
10. Maxam A, Gilbert W. A new method for sequencing DNA. Proc Natl Acad Sci USA 1977; 74:560-564
11. Berg P Dissections and reconstructions of genes and chromosomes. Science 1981; 213:296-303.
12. Roberts RJ. How restriction enzymes became the workhorses of molecular biology. Proc Nad Sci USA2005; 102:5905-5908.
13. Singh H, Lane BG. The separation, estimation and characterization of alkali-stable derived from commercial ribonucleate preparation. Can J Biochem 1964; 42:87-93.
14. Holley RW, Apgar J, Merrill SH. Evidence for the liberation of a nuclease from human fingers. J Biol Chem 1961; 236:PC42.
15. Marko AM, Buder GC. The isolation of sodium deoxyribonuclcatc with sodium dodecyl sulphate. J Biol Chem 1951; 190:165-176.
16. Colter JS, Brown RA. Preparation of nucleic acids from Ehrlich ascites tumor cells. Science 1956; 123:1077-1078.
17. Hoagland MB, Stephenson ML, Scott JF et al. A soluble RNA intermediate in Protein Synthesis. J Biol Chem 1958; 231:241-257
18. Crick FHC. On protein synthesis. Symp Soc Exp Biol 1958; 12:138-163
19. Crick FHC. Codon-Anticodon pairing: The Wobble hypothesis. J Mol Bio 1966; 19:184-191.
20. Johnson TB, Coghill RD. The discovery of 5-methyl-cytosine in tuberculinic acid, the nucleic acid of the Tubercle bacillus. J Am Chem Soc 1925; 47:2838-2844.
21. Vischer E, Zamenhof S, Chargaff E. Microbial nucleic acids: the desoxypentose nucleic acids of avian tubercle bacilli and yeast. J Biol Chem 1949; 177:429-438.
22. Hotchkiss RD. The quantitative separation of purines, pyrimidines and nucleosides by paper chromatography. J Biol Chem 1948;175:315-332.
23. Wyatt GR. Occurrence of 5-methylcytosine in nucleic acids. Nature 1950; 166:237-238.
24. Dunn DB, Smith JD. The occurrence of 6-methylaminopurinc in microbial deoxyribonucleic acids. Nature London 1955; 175:336-339, and Biochem J 1958; 68:627-636.
25. Wyatt GR, Cohen SS. The base of the nucleic acids of some bacterial and animal viruses: the occurrence of 5-hydroxymethylcytosine. Biochem J 1953; 55:774-782.
26. Kallen RG, Simon M, Marmur J. The occurrence of a new pyrimidine base replacing thymine in a bacteriophage DNA: 5-hydroxymethyluracil. J Mol Biol 1962; 5:248-250.
27. Takahashi I, Marmur J. Replacement of thymidylic acid by deoxyurydilic acid in the DNA of a transducing phage for B. subtilis. Nature 1963; 197:794-795.
28. Bessman MJ, Lehman IR, Adler J et al. Enzymatic synthesis of DNA. 3. The incorporation of pyrimidine and purine analogues into DNA. Proc Natl Acad Sci USA 1958; 44:633-640.
29. Lehman IR, Pratt EA. On the structure of the glucosylated hydroymethylcytosine nucleotides of co-liphagcs T2, T4 and T6. J Biol Chem I960; 235:3254-3259.
30. Takahashi I, Marmur J. Glucosylated DNA from a transducing phage for B. subtilis. Biochem Biophys Res Commun 1963; 10:289-292.
31. Warren RAJ. Modified bases in bacteriophage DNAs. Ann Rev Microbiol 1980; 34:137-158 (review).
32. Gommers-Ampt JH, Borst P. Hypermodified bases in DNA. FASEB J 1995; 9:1034-1042 (review).
33. Kimos MD, Khudyakov IY, Alexandruschkina NI et al. 2-aminoadeninc in an adenine substituting for a base in S-2L cyanophage DNA. Nature 1977; 369-370.
34. Khudyakov IY, Kirnos MD, Alexandruschkina NI et al. Cyanophage S-2L contains DNA with 2,6-di-aminopurine substituted for adenine. Virology 1978; 88:8-18.
35. Janulaitis A, Klimasauskas S, Pctrusyte M et al. Cytosine modification in DNA by Beni methylase yields N4-mcthyleytosine. FEBS Lett 1983; 161:131-134.
36. Ehrlich M, Gama-Sosa MA, Carreira LH et al. DNA méthylation in thermophilic bacteria: N4-meth-ylcytosine and N6-methyladenine. Nucl Acids Res 1985; 13:1399-1412.
37. Ehrlich M, Wilson GG, Kuo KC et al. N4-methylcytosine as a minor base in bacterial DNA. J Bact 1987; 169:939-943.
38. Grosjean H, Oshima T. How nucleic acids cope with high temperature. In: Gerday C, Glansdorff N, eds. Physiology and Biochemistry of Extremophiles. Washington, DC: ASM Press, 2007:39-56.
39. Zhou X, He X, Liang J et al. A novel DNA modification by sulphur. Mol Microbiol 2005; 57:1428-1438.
40. Wang L, Chen S, Xu T et al Phosphothioation of DNA In bacteria by dnd genes. Nature Chem Biol 2007; 3:709-710.
41. Eckstein F. News and views: Phosphorothioation of DNA in bacteria. Nature Chem Biol 2007; 3:689-670.
42. Cohn WE, Volkin E. Nucleoside-5’-phosphates from ribonucleic acid. Nature 1951; 167:483-484.
43. Davis FF, Allen FW. Ribonucleic acids from yeast which contain a fifth nucleotide. J Biol Chem 1957; 227:907-915.
44. Cohn WE. 5-Ribosyl uracil, ribofuranyl nucleoside in RNA. Biochim. Biophys Acta 1959; 32:569-571.
45. Smith JD, Dunn DB. An additional sugar component of RNA. Biochim Biophys Acta 1959; 31:573-575.
46. Lane BG, Butler GC. The isolation, identification and properties of dinucleotides from alkali hydrolyzates of RNA. Can J Biochem Physiol 1959; 37:1329-1350.
47. Littlefield JW, Dunn DB. The occurrence and distribution of thymine and three methylated adenine bases in RNA from several sources. Biochem J 1958; 70:642-651.
48. Adler M, Weissmann B, Gutman AB. Occurrence of methylated purine bases in RNA. J Biol Chem1958; 230:717-723.
49. Smith JD, Dunn DB. The occurrence of methylated guanines in ribonucleic acids from several sources. Biochem J 1959; 72:294-301.
50. Dunn DB. Additional components in RNA of rat liver fractions. Biochim Biophys Acta 1959; 34:286-288.
51. Hall RH. The Modified Nucleosides in Nucleic Acids. New York/London: Columbia University Press, 1971.
52. Limbach PA, Crain PF, McCloskey JA. Summary: the modified nucleosides of RNA. Nucl Adds Res1994; 22:2183-2196.
53. McCloskey JA, Rozenski J. The small subunit rRNA modification database. Nucleic Acids Res 2005; 33:D135-138.
54. Piekna-Ptzybylska D, Decatur WA, Fournier MJ. New bioinformatics tool for analysis of nudeotidc modifications in eukaryotic rRNA. RNA 2007; 13:1-8.
55. Piekna-Przybylska D, Decatur WA, Fournier MJ. The 3D rRNA modification maps database: with interactive tools for ribosome analysis. Natl Acids Res 2008; 36:D178-183.
56. Woesc CR, Kandlcr O, Wheelis ML. Towards a natural system of organisms: proposal for the domains Archaea, Bacteria and Eukarya. Proc Natl Acad Sci USA 1990; 87:4576-4579.
57. Gehrke CW, McCune RA, Gama-Sosa MA et al Quantitative reversed-phasc high-performance liquid chromatography of major and modified nudeosides in DNA. J Chromatogr 1984; 301:199-219.
58. Gehrke CW, Kuo KC. Ribonudeoside analysis by reversed-phase high-performance liquid chromatography. J Chromatogr 1989; 471:3-36.
59. Grosjean H, Keith G, Droogmans L. Detection and quantification of modified nucleotides in RNA using thin-layer chromatography. In: Gott JM, ed. RNA Interference, Editing and Modification - Methods in Molecular Biology. Totowan: Humana Press, 2004; 265:357-392.
60. Wagner TM, Nair V, Guymon R et al. A novel method for sequence placement of modified nudeotides in mixtures of tRNA. Nudeic Acids Symp Series 2004; 48:263-264.
61. Gott JM. Methods in Enzymology. Vols. 424 and 425. Academic Press-Elsevier, 2007.
62. Cermakian N, Cedegren R. Modified nucleosides always were: an evolutionary model In: Grosjean H, Benne R, eds. Modification and Editing of RNA. Washington DC: ASM Press, 1998:535-541.
63. Anantharaman V, Koonin EV, Aravind L. Comparative genomics and evolution of proteins involved in RNA metabolism. Nucl Acids Res 2002; 30:1427-1464.
64. Uurbonavicius J, Auxilien S, Walbott E et al. Acquisition of a bacterial RumA-type tRNA(uracil-54, C5)-methyltransferase by Archaea through an ancient horizontal gene transfer. Mol Microbiol 2008; 67:323-333.
65. Jühling J, Môrl M, Hartmann V et al tRNAdb 2009: compilation of tRNA sequences and tRNA genes. Nucleic Acids Res 2009; 37, Database issue: D159-D162.
66. Grosjean H, Sprinzl M, Steinberg S. Posttrancriptionally modified nucleosides in tRNA: their locations and frequencies. Biochimie 1995; 77:139-141.
67. de Crécy-Lagard V, Marck C, Grosjean H. Comparative RNomics and modomics in moUicutes: prediction of gene function and evolutionary implications. IUBMB Life 2007; 59:634-658
68. Grosjean H, Gupta R, Maxwell S. Modified nucleotides in archaeal RNAs. In: Blum P, ed. Archaea, New Models for Prokaryotic Biology. Norwich: Horizon Press, 2008:164-196; www.caister.com.
69. Grosjean H, Gaspin C, Marck C et al RNomics and Modomics in the halophilc Haloferax volcanii: identification of RNA modification genes. BMC Genomics 2008; 9:470-496.
70. Orner AD, Ziesche S, Decatur WA et al. RNA-modifying machines in archaea. Mol Microbiol 2003; 48:617-629.
71. Muller S, Charpentier B, Branlant C et al A dedicated computational approach for the identification of archaeal H/ACA sRNAs. Methods Enzymol 2007; 425:355-387.
72. Svensson I, Boman HG, Eriksson KG et al Studies on microbial RNA: Transfer of methyl groups from methionine to soluble RNA from E. coli. J Mol Biol 1963; 7:254-271.
73. Fleissner E, Borek E. A new enzyme of RNA synthesis: RNA methylase. Proc Natl Acad Sci USA 1962; 48:1199-1203.
74. Starr JL. The incorporation of methyl groups into amino acid transfer ribonucleic acid Biochem Biophys Res Comm 1963; 10:175-180.
75. Hurwitz J, Gold M, Anders M The enzymatic méthylation of RNA and DNA. 3. Purification of soluble RNA-methylating enzymes. J Biol Chem 1964; 239:3462-3473.
76. Hurwitz J, Anders M, Gold M et al The enzymatic méthylation of RNA and DNA. 7. The méthylation of ribosomal RNA. J Biol Chem 1965; 240:1256-1266.
77. Delk AS, Rabinowitz JC. Biosynthesis of ribosylthymine in the tRNA of S. faecalis: a folate-dependent méthylation not involving S-adenosylmethionine. Proc Natl Acad Sci 1975; 72:528-530.
78. Farkas WR, Hankins WD, Sing R. The guanylation of tRNA: an enzymatic reaction. Biochim Biophys Acta 1973; 294:94-105.
79. Okada N, Harada F, Nishimura S. Specific replacement of Q-base in the anticodon of tRNA by guanine catalyzed by a cell-free extract of rabbit reticulocytes. Nutl Acids Res 1976; 3:2593-2603.
80. Itoh YH, Itoh T, Haruna I et al. Substitution of guanine for a specific base in tRNA by extracts of Ehrlich ascites tumor cell. Nature 1977; 267:467.
81. Watanabe M, Matsuo M, Tanaka S et al. Biosynthesis of archaeosine, a novel derivative of 7-dcaza-guanosine specific to archaeal tRNA, preceeds via a pathway involving base replacement in the tRNA polynucleotide chain. J Biol Chem 1997; 272:20146-20151.
82. Kiss-Laszlo Z, Henry Y, Bachellerie JP et al. Site-specific ribose méthylation of prcribosomal RNA: a novel ¿unction for small nucleolar RNAs. Cell 1996; 85:1077-1088.
83. Nicoloso M, Qu LH, Michot B et al. Intron-encoded, antisense small nucleolar RNAs: the characterization of nine novel species points to their role as guides for 2,-0-ribose méthylation of rRNAS. J Mol Biol 1996; 260:178-195.
84. Ni J, Tien AL, Fournier MJ. Small nucleolar RNAs direct site-specific synthesis of pscudouridines in ribosomal RNA. Cell 1997; 89:565-573.
85. Ganot P, Bortolin ML, Kiss T. Site-specific pseudouridine formation in preribosomal RNA is guided by small nucleolar RNA. Cell 1997; 89:799-809.
86. Bonnerot C, Pintard L, Lutfaila G. Functional redundancy of Spblp and a snR52-dependent mechanism for the 2’-0-ribose méthylation of a conserved rRNA position in yeast. Mol Cell 2003; 12:1309-1315.
87. Renalier MH, Joseph N, Gaspin C et al. The Cm56 tRNA modification in archaea is catalyzed cither by a specific 2’-0-methylase, or a C/D sRNP..RNA 2005;11:1051-1063.
88. Ma X, Yang C, Alexandrov A et al. Pseudouridylation of yeast U2 snRNA is catalyzed by either an RNA-guided or RNA-independent mechanism. EMBO J 2005; 24:2403-2413.
89. Gurha P, Joardar A, Chaurasia P et al. Differential roles of archaeal box H/ACA proteins in guide RNA-dependent and independent pseudouridine formation. RNA Biol 2007; 4:101-109.
90. Decatur WA, Schnare MN. Different mechanisms for pseudouridine formation in yeast 5S and 5.8S rRNAs. Mol Cell Biol 2008; 28:3089-3100.
91. Gold M, Hurwitz J, Anders M. The méthylation of RNA and DNA. II. On the species specificity of the méthylation enzymes. Proc Natl Acad Sci USA 1963; 50:164-169.
92. Gold M, Hurwitz J. Enzymatic méthylation of ribonucleic acid and deoxyribonucleic acid. V. Purification and properties of DNA-methylating activity of E. coli. J Biol Chem 1964; 239:3858-386.
93. Kornberg SR, Zimmerman SB, Komberg A. Glucosylation of deoxyribonucleic acid by enzymes from bacteriophage-infected E. coli. J Biol Chem 1961; 236:1487-1493.
94. Rae P, Steele R. Modified bases in the DNAs of unicellular eukaryotes. Biosystems 1978; 10: 37-53.
95. Borst P, Sabatini R. Base J: Discovery, Biosynthesis and possible Functions. Ann Rev Microbiol 2008; 62:235-251.
96. Yu B, Yang Z, Li J et al. Méthylation as a crucial step in plant microRNA biogenesis. Science 2005; 307:932-935.
97. Ebhardt HA, Thi EP, Wang MB et al. Extensive 3’ modification of plant small RNAs is modulated by helper component-proteinase expression. Proc Natl Acad Sci 2005; 102:13398-13403.
98. Ohara T, Sakaguchi Y, Suzuki T et al. The 3’ termini of mouse Piwi-interacting RNAs arc 2′-0-meth-ylated. Nature Struct Biol 2007; 14:349-350.
99. Kawahara Y, Mcgraw M, Krcider E et al. Frequency and fate of micro-RNA editing in human brain. Nucl Acids Res 2008; 36:5270-5280.
100. Habig J, Taraka D, Bass B. mi-RNA editing, we should have inosine this coming. Molec Cell 2007; 25:712-713