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Chapter 8 : Mechanisms of RNA-Modifying and -Editing Enzymes

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Abstract:

This chapter focuses on mechanistic issues involved in RNA-modifying enzymes. From a chemical/structural viewpoint, modified nucleosides can be divided into two groups. The first group consists of relatively "simple" modifications (e.g., methylation, thiolation, deamination, and isomerization). The second group of modified nucleosides consists of more "complex" modifications (e.g., multiple modifications and hypermodifications), involving a multi-enzyme pathway or, as is the case with queuine and archaeosine, involving biosynthetic precursors synthesized by other enzymes for this purpose alone. The X-ray crystal structure of a nucleoside adenosine deaminase has been determined, and a zinc ion and an ordered water molecule have been located in the active site. The X-ray crystal structure of cytidine deaminase complexed with uridine has also recently been determined. The miaA enzyme utilizes Δ-isopentenyl pyrophosphate (IPP, or dimethylallyl diphosphate) as the isopentenyl group donor. Δ-IsopentenyI pyrophosphate is utilized by a number of isopentenyl transferases leading to various isoprenoids and ultimately to steroids. Two reaction mechanisms have been postulated for the isopentenyl transferases, an associative mechanism and a dissociative mechanism. Technological advances in RNA generation (both by in vitro transcription and by chemical synthesis) along with advances in molecular biological approaches (to identify, clone and express modifying enzyme genes) have been predominantly responsible for the renewed activity in RNA modification and editing research.

Citation: Garcia G, Goodenough-Lashua D. 1998. Mechanisms of RNA-Modifying and -Editing Enzymes, p 135-168. In Grosjean H, Benne R (ed), Modification and Editing of RNA. ASM Press, Washington, DC. doi: 10.1128/9781555818296.ch8

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Image of Figure 1
Figure 1

Proposed chemical mechanism for RUMT.

Citation: Garcia G, Goodenough-Lashua D. 1998. Mechanisms of RNA-Modifying and -Editing Enzymes, p 135-168. In Grosjean H, Benne R (ed), Modification and Editing of RNA. ASM Press, Washington, DC. doi: 10.1128/9781555818296.ch8
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Figure 2

Chiral methyl AdoMet mechanisms. X, a nucleophile on the enzyme; Enz, enzyme.

Citation: Garcia G, Goodenough-Lashua D. 1998. Mechanisms of RNA-Modifying and -Editing Enzymes, p 135-168. In Grosjean H, Benne R (ed), Modification and Editing of RNA. ASM Press, Washington, DC. doi: 10.1128/9781555818296.ch8
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Figure 3

Stereochemistry of addition to C5-C6 of U54.

Citation: Garcia G, Goodenough-Lashua D. 1998. Mechanisms of RNA-Modifying and -Editing Enzymes, p 135-168. In Grosjean H, Benne R (ed), Modification and Editing of RNA. ASM Press, Washington, DC. doi: 10.1128/9781555818296.ch8
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Figure 4

Possible general base mechanisms for purine n1 methylation. (A) Deprotonation of guanine Ν1; (B) deprotonation of adenine N6. enz, enzyme.

Citation: Garcia G, Goodenough-Lashua D. 1998. Mechanisms of RNA-Modifying and -Editing Enzymes, p 135-168. In Grosjean H, Benne R (ed), Modification and Editing of RNA. ASM Press, Washington, DC. doi: 10.1128/9781555818296.ch8
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Figure 5

(A) X-ray crystal structure of VP39; (B) model for mRNA binding, term, terminus. Adapted from Hodel et al., 1996, with permission of the author and publisher.

Citation: Garcia G, Goodenough-Lashua D. 1998. Mechanisms of RNA-Modifying and -Editing Enzymes, p 135-168. In Grosjean H, Benne R (ed), Modification and Editing of RNA. ASM Press, Washington, DC. doi: 10.1128/9781555818296.ch8
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Figure 6

Proposed activation step for uridine thiolation.

Citation: Garcia G, Goodenough-Lashua D. 1998. Mechanisms of RNA-Modifying and -Editing Enzymes, p 135-168. In Grosjean H, Benne R (ed), Modification and Editing of RNA. ASM Press, Washington, DC. doi: 10.1128/9781555818296.ch8
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Figure 7

Proposed mechanism for sulfur transfer.

Citation: Garcia G, Goodenough-Lashua D. 1998. Mechanisms of RNA-Modifying and -Editing Enzymes, p 135-168. In Grosjean H, Benne R (ed), Modification and Editing of RNA. ASM Press, Washington, DC. doi: 10.1128/9781555818296.ch8
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Figure 8

(A) Proposed mechanism for the nucleoside adenosine deaminase; (B) structures of its transition state analog inhibitors.

Citation: Garcia G, Goodenough-Lashua D. 1998. Mechanisms of RNA-Modifying and -Editing Enzymes, p 135-168. In Grosjean H, Benne R (ed), Modification and Editing of RNA. ASM Press, Washington, DC. doi: 10.1128/9781555818296.ch8
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Figure 9

Hypothetical nucleophilic attack at C5 mechanism for pseudouridine synthase. Nuc, enzymatic nucleophile; enz, enzyme.

Citation: Garcia G, Goodenough-Lashua D. 1998. Mechanisms of RNA-Modifying and -Editing Enzymes, p 135-168. In Grosjean H, Benne R (ed), Modification and Editing of RNA. ASM Press, Washington, DC. doi: 10.1128/9781555818296.ch8
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Figure 10

Hypothetical nucleophilic attack at C1′ (or SN2) mechanism for pseudouridine synthase. Nuc, enzymatic nucleophile; enz, enzyme.

Citation: Garcia G, Goodenough-Lashua D. 1998. Mechanisms of RNA-Modifying and -Editing Enzymes, p 135-168. In Grosjean H, Benne R (ed), Modification and Editing of RNA. ASM Press, Washington, DC. doi: 10.1128/9781555818296.ch8
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Figure 11

(A) Two proposed mechanisms for prenyl transferases; (B) trifluoromethyl analog of D2-isopentenyl pyrophosphate. Nu, prenyl acceptor nucleophile.

Citation: Garcia G, Goodenough-Lashua D. 1998. Mechanisms of RNA-Modifying and -Editing Enzymes, p 135-168. In Grosjean H, Benne R (ed), Modification and Editing of RNA. ASM Press, Washington, DC. doi: 10.1128/9781555818296.ch8
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Figure 12

Chemical steps for the carbamoyl phosphate synthetase reaction. Enz, enzyme.

Citation: Garcia G, Goodenough-Lashua D. 1998. Mechanisms of RNA-Modifying and -Editing Enzymes, p 135-168. In Grosjean H, Benne R (ed), Modification and Editing of RNA. ASM Press, Washington, DC. doi: 10.1128/9781555818296.ch8
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Figure 13

Proposed mechanism for threonylcarbamoylation of tRNA.

Citation: Garcia G, Goodenough-Lashua D. 1998. Mechanisms of RNA-Modifying and -Editing Enzymes, p 135-168. In Grosjean H, Benne R (ed), Modification and Editing of RNA. ASM Press, Washington, DC. doi: 10.1128/9781555818296.ch8
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Figure 14

Proposed mechanism for m1A deaminase.

Citation: Garcia G, Goodenough-Lashua D. 1998. Mechanisms of RNA-Modifying and -Editing Enzymes, p 135-168. In Grosjean H, Benne R (ed), Modification and Editing of RNA. ASM Press, Washington, DC. doi: 10.1128/9781555818296.ch8
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Figure 15

Biosynthetic pathway for mnm5s2U and mnm5se2U.

Citation: Garcia G, Goodenough-Lashua D. 1998. Mechanisms of RNA-Modifying and -Editing Enzymes, p 135-168. In Grosjean H, Benne R (ed), Modification and Editing of RNA. ASM Press, Washington, DC. doi: 10.1128/9781555818296.ch8
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Figure 16

Queuosine 34-tRNA biosynthesis in

Citation: Garcia G, Goodenough-Lashua D. 1998. Mechanisms of RNA-Modifying and -Editing Enzymes, p 135-168. In Grosjean H, Benne R (ed), Modification and Editing of RNA. ASM Press, Washington, DC. doi: 10.1128/9781555818296.ch8
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Figure 17

Structure of FMPP.

Citation: Garcia G, Goodenough-Lashua D. 1998. Mechanisms of RNA-Modifying and -Editing Enzymes, p 135-168. In Grosjean H, Benne R (ed), Modification and Editing of RNA. ASM Press, Washington, DC. doi: 10.1128/9781555818296.ch8
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Figure 18

Postulated nucleophilic catalysis mechanism for TGT. Nu, enzymatic nucleophile.

Citation: Garcia G, Goodenough-Lashua D. 1998. Mechanisms of RNA-Modifying and -Editing Enzymes, p 135-168. In Grosjean H, Benne R (ed), Modification and Editing of RNA. ASM Press, Washington, DC. doi: 10.1128/9781555818296.ch8
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Figure 19

Structures of the base of archaeosine and preQ0.

Citation: Garcia G, Goodenough-Lashua D. 1998. Mechanisms of RNA-Modifying and -Editing Enzymes, p 135-168. In Grosjean H, Benne R (ed), Modification and Editing of RNA. ASM Press, Washington, DC. doi: 10.1128/9781555818296.ch8
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Image of Figure 20
Figure 20

Wyosine from Circled carbons are derived from the methyl group of methionine. Atoms in boxes are of unknown origin. R, ribose.

Citation: Garcia G, Goodenough-Lashua D. 1998. Mechanisms of RNA-Modifying and -Editing Enzymes, p 135-168. In Grosjean H, Benne R (ed), Modification and Editing of RNA. ASM Press, Washington, DC. doi: 10.1128/9781555818296.ch8
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References

/content/book/10.1128/9781555818296.chap8
1. Abrell, J. W.,, E. E. Kaufman,, and M. N. Lipsett. 1971. The biosynthesis of 4-thiouridylate. J. Biol. Chem. 246:294301.
2. Agris, P. F. Personal communication.
3. Agris, P. F.,, D. J. Armstrong,, K. P. Schafer,, and D. Soil. 1975. Maturation of a hypermodified nucleoside in transfer RNA. Nucleic Acids Res. 2:691698.
4. Aitken, D. M.,, P. F. Lue,, and J. G. Kaplan. 1975. Kinetics and reaction mechanism of the carbamylphosphate synthetase of a multienzyme aggregate from yeast. Can. J. Biochetn. 53: 721730.
5. Ajitkumar, P.,, and J. D. Cherayil. 1988. Thionucleosides in transfer ribonucleic acid: diversity, structure, biosynthesis, and function. Microbiol. Rev. 52:103113.
6. Allaudeen, H. S.,, S. K. Yang,, and D. Soil. 1972. Leucine tRNA from hisT mutant of Salmonella typhimurium lacks two pseudouridines. FEBS Lett. 28:205208.
7. Arnold, H.,, and H. Kersten. 1975. Inhibition of the tetrahydro-folate-dependent biosynthesis of ribothymidine in tRNAs of B. subtilis and M. lysodeikticus by trimethoprim. FEBS Lett. 53: 258261.
8. Astrom, S. U.,, and A. S. Bystrom. 1994. Ritl, a tRNA backbone-modifying enzyme that mediates initiator and elongator tRNA discrimination. Cell 79:535546.
9. Auxilien, S.,, P. F. Crain,, R. W. Trewyn,, and H. Grosjean. 1996. Mechanism, specificity and general properties of the yeast enzyme catalyzing the formation of inosine 34 in the anticodon of transfer RNA.J. Mol. Biol. 262:437458.
10. Auxilien, S.,, and H. Grosjean. 1995. Edition and modification of RNA from eukaryotic cells and viruses by enzymatic deamination of adenosine to inosine. M-S (Med. Sci.) 11:10891098.
11. Bachellerie, J.-P.,, and J. Cavaille. 1997. Guiding ribose methylation of rRNA. Trends Biochem. Sci. 22:257261.
12. Bartz, J. K.,, L. K. Kline,, and D. Soil. 1970. N6-(A2-Isopentenyl)adenosine: biosynthesis in vitro in transfer RNA by an enzyme purified from Escherichia coli. Biochem. Biophys. Res. Commun. 40:14811487.
13. Bartz, J. K.,, and D. Soil. 1972. N6-(A2-Isopentenyl)adenosine: biosynthesis in vitro in transfer RNA by an enzyme purified from Escherichia coli. Biochimie 54:3139.
14. Bass, B. 1995. An I for editing. Curr. Biol. 5:598600.
15. Becker, H. F.,, Y. Motorin,, M. Sissler,, C. Florentz,, and H. Grosjean. 1997. Major identity determinants for enzymatic formation of ribothymidine and pseudouridine in the TΨ-loop of yeast tRNAs.J. Mol. Biol. 274:505518.
16. Benne, R. 1996. The long and short of it. Nature (London) 380: 391392.
17. Bokar, J. A.,, M. E. Rath-Shambaugh,, R. Ludwiczak,, P. Narayan,, and F. Rottman. 1994. Characterization and partial purification of mRNA N6-adenosine methyltransferase from HeLa cell nuclei. Internal mRNA methylation requires a multisubunit complex.J. Biol. Chem. 269:17697704.
18. Braxton, B. L.,, L. S. Mullins,, F. M. Raushel,, and G. D. Reinhart. 1992. Quantifying the allosteric properties of Escherichia coli carbamoyl-phosphate synthetase: determination of thermodynamic linked-function parameters in an ordered kinetic mechanism. Biochemistry 31:23092316.
19. Britton, H. G.,, V. Rubio,, and S. Grisolia. 1979. Mechanism of carbamoyl-phosphate synthetase. Eur.J. Biochem. 102:521530.
20. Buck, M.,, and B. Ames. 1984. A modified nucleoside in tRNA as a possible regulator of aerobiosis. Cell 36:523531.
21. Bystrom, A. S.,, and G. R. Björk. 1982a. Chromosomal location and cloning of the gene (trmD) responsible for the synthesis of tRNA (m'G) methyltransferase in Escherichia coli K-12. Mol. Gen. Genet. 188:440446.
22. Bystrom, A. S.,, and G. R. Björk. 1982b. The structural gene (trmD) for the tRNA (m'G) methyltransferase in part of a four polypeptide operon in Escherichia coli K-12. Mol. Gen. Genet. 188:447454.
23. Caillet, J.,, and L. Droogmans. 1988. Molecular cloning of the Eschericia coli miaA gene, involved in the formation of δ2 isopentenyl adenosine in tRNA.J. Bacteriol. 170:41474152.
24. Carbon, P.,, E. Haumont,, M. Fournier,, S. D. Henau,, and H. Grosjean. 1983. Site-directed in vitro replacement of nucleosides in the anticodon loop of tRNA: application to the study of structural requirements for queuine insertase activity. EMBO J. 2: 1093.
25. Chheda, G. B.,, C. I. Hong,, C. F. Piskorz,, and G. A. Harmon. 1972. Biosynthesis of N-(purin-6-ylcarbamoyl)-L-threonine riboside. Biochem. J. 127:515519.
26. Chong, S.,, A. W. Curnow,, T. J. Huston,, and G. A. Garcia. 1995. tRNA-guanine transglycosylase from Escherichia coli is a zinc metalloprotein. Site-directed mutagenesis studies to identify the zinc ligands. Biochemistry 34:36943701.
27. Connolly, D. M., and M. E. Winkler. 1989. Genetic and physiological relationships among the miaA gene, 2-methylthio-N6-(delta 2-isopentenyl)-adenosine tRNA modification, and spontaneous mutagenesis in Escherichia coli K-12.J. Bacteriol. 171: 32333246.
28. Constantinesco, F.,, and H. Grosjean. Personal communication.
29. Cortese, R.,, H. O. Kammen,, S. J. Spengler, and B. N. Ames. 1974. Biosynthesis of pseudouridine in transfer ribonucleic acid. J. Biol. Chem. 249:11031108.
30. Curnow, A. W.,, and G. A. Garcia. 1994. tRNA-guanine transglycosylase from Escherichia coli: recognition of dimeric, unmodified tRNATyr. Biochimie 76:11831191.
31. Curnow, A. W.,, and G. A. Garcia. 1995. tRNA-guanine transglycosylase from Escherichia coli—minimal tRNA structure and sequence requirements for recognition. J. Biol. Chem. 270: 1726417267.
32. Curnow, A. W.,, F. L. Rung,, K. A. Koch,, and G. A. Garcia. 1993. tRNA-guanine transglycosylase from Escherichia coli: gross tRNA structural requirements for recognition. Biochemistry 32: 52395246.
33. Delk, A. S.,, D. P. Nagle,, and J. C. Rabinowitz. 1980. Methylene-tetrahydrofolate-dependent biosynthesis of ribothymidine in transfer RNA of Streptococcus faecalis. Evidence for reduction of the 1-carbon unit by FADH2.J. Biol. Chem. 255:43874390.
34. Delk, A. S.,, J. M. Romeo,, D. P. Nagle,, and J. C. Rabinowitz. 1976. Biosynthesis of ribothymidine in the transfer RNA of Streptococcus faecalis and Bacillus subtilis. A methylation of RNA involving 5,10-methylenetetrahydrofolate. J. Biol. Chem. 251: 76497656.
35. Desgres, J.,, G. Keith,, K. C. Kuo,, and C. W. Gehrke. 1989. Presence of phosphorylated O-ribosyl-adenosine in T-Ψ-stem of yeast methionine initiator tRNA. Nucleic Acids Res. 17: 865882.
36. Deshpande, K. L.,, P. H. Seubert,, D. M. Tillman,, W. R. Farkas,, and J. R. Katze. 1996. Cloning and characterization of cDNA encoding the rabbit tRNA-guanine transglycosylase 60-kilodalton subunit. Arch. Biochem. Biophys. 326:17.
37. Droogmans, L.,, and H. Grosjean. 1987. Enzymatic conversion of guanosine 3' adjacent to the anticodon of tRNAPhe to N1-methylguanosine and the wye nucleoside: dependence on the anticodon sequence. EMBO J. 6:477483.
38. Droogmans, L.,, E. Haumont,, S. deHenau,, and H. Grosjean. 1986. Enzymatic 2'-O-methylation of the wobble nucleoside of eukaryotic tRNAPhe: specificity depends on structural elements outside the anticodon loop. EMBOJ. 5:11051109.
39. Edqvist, J.,, K. Blomqvist,, and K. B. Straby. 1994. Structural elements in yeast tRNAs required for homologous modification of guanosine-26 into dimethylguanosine-26 by the yeast Trm1 tRNA-modifying enzyme. Biochemistry 33:95469551.
40. Edqvist, J.,, H. Grosjean,, and K. B. Straby. 1992. Identity elements for N2-dimethylation of guanosine-26 in yeast tRNAs. Nucleic Acids Res. 20:65756581.
41. Edqvist, J.,, K. B. Straby,, and H. Grosjean. 1995. Enzymatic formation of N2,N2-dimethylguanosine in eukaryotic tRNA: importance of the tRNA architecture. Biochimie 77:5461.
42. Edqvist, J.,, K. B. Straby,, and H. Grosjean. 1993. Pleiotrophic effects of point mutation in yeast tRNAAsp on the base modification pattern. Nucleic Acids Res. 21:413417.
43. Eichler, D. C. 1994. Characterization of a nucleolar 2'-O-meth-yltransferase and its involvement in the methylation of mouse precursor ribosomal RNA. Biochimie 76:11151122.
44. Elkins, B. N.,, and E. B. Keller. 1974. The enzymatic synthesis of N-(purin-6-ylcarbamoyl)threonine, an anticodon-adjacent base in transfer ribonucleic acid. Biochemistry 13:46224628.
45. Elliott, M. S.,, and R. W. Trewyn. 1984. Inosine biosynthesis in transfer RNA by an enzymatic insertion of hypoxanthine.J. Biol. Chem. 259:24072410.
46. Ellis, S. R.,, M. J. Morales,, J. M. Li,, A. K. Hopper,, and N. C. Martin. 1986. Isolation and characterization of the TRM1 locus, a gene essential for the N2,N2-dimethylguanosine modification of both mitochondrial and cytoplasmic tRNA in Saccharomyces cerevisiae. J. Biol. Chem. 261:97039709.
47. Erdmann, V. A.,, E. Huysmans,, A. Vandenbergh,, and R. DeWachter. 1983. Collection of published 5S and 5.8S ribosomal RNA sequences. Nucleic Acids Res. Il:rl05rl33.
48. Fittler, F.,, L. K. Kline,, and R. H. Hall. 1968. N6-(δ2-Isopentenyl)adenosine: biosynthesis in vitro by an enzyme extract from yeast and rat liver. Biochem. Biophys. Res. Commun. 31:571576.
49. Frendewey, D. A.,, D. M. Kladianos,, V. G. Moore,, and I. I. Kaiser. 1982. Loss of tRNA 5-methyluridinemethyltransferase and pseudouridine synthase activities in 5-fluorouracil and l-(tetrahydro-2-furanyl)-5-fluoouracil (FTORAFUR) treated Escherichia coli. Biochim. Biophys. Acta 697:3140.
50. Frey, B.,, J. McCloskey,, W. Kersten,, and H. Kersten. 1988. New function of vitamin Bl2: cobamide-dependent reduction of epoxyqueuosine to queuosine in tRNAs of Escherichia coli and Salmonella typhimurium. J. Bacteriol. 170:20782082.
51. Frick, L.,, R. Wolfenden,, E. Smal,, and D. Baker. 1986. Transition-state stabilization by adenosine deaminase: structural studies of its inhibitory complex with deoxycoformycin. Biochemistry 25: 16161621.
52. Garcia, G. A.,, and S. R. Chong. 1997. Cysteine 265 is in the active site of, but is not essential for catalysis by tRNA-guanine transglycosylase (TGT) from Escherichia coli. J. Protein Chem. 16: 1117.
53. Garcia, G. A.,, D. L. Tierney,, S. R. Chong,, K. Clark,, and J. E. Penner-Hahn. 1996. X-ray absorption spectroscopy of the zinc site in tRNA-guanine transglycosylase from Escherichia coli. Biochemistry 35:31333139.
54. Garrett, C. E.,, J. A. Coderre,, T. D. Meek,, E. P. Garvey,, D. M. Claman,, S. M. Beverley,, and D. V. Santi. 1984. A bifunctional thymidylate synthetase-dihydrofolate reductase in protozoa. Mol. Biochem. Parasitol. 11:257265.
55. Gerlt, J. A.,, and P. G. Gassman. 1993. Understanding the rates of certain enzyme-catalyzed reactions: proton abstraction from carbon acids, acyl-transfer reactions, and displacement reactions of phosphodiesters. Biochemistry 32:1194311952.
56. Gershon, P. D.,, B. Y. Ahn,, M. Garfield,, and B. Moss. 1991. Poly(A) polymerase and a dissociable polyadenylation stimulatory factor encoded by vaccinia virus. Cell66:12691278.
57. Gershon, P. D.,, and B. Moss. 1993. Stimulation of poly (A) tail elongation by the VP39 subunit of the vaccinia virus-encoded poly(A) polymerase.J. Biol. Chem. 268:22032210.
58. Giorgianni, F.,, S. Beranova,, C. Wesdimiotis,, and R. E. Viola. 1995. Elimination of the sensitivity of L-aspartase to active-site-directed inactivation without alteration of the catalytic activity. Biochemistry 34:35293535.
59. Glasser, A.-L.,, J. Desgres,, J. Heitzler,, C. W. Gehrke,, and G. Keith. 1991. O-Rtbosyl-phosphate purine as a constant modified nucleotide located at position 64 in cytoplasmic initiator tRNAs of yeasts. Nucleic Acids Res. 19:51995203.
60. Green, C. J.,, H. O. Kammen, and E. E. Penhoet. 1982. Purification and properties of a mammalian tRNA pseudouridine synthase. J. Biol. Chem. 257:30453052.
61. Gregson, J. M.,, P. F. Crain,, C. G. Edmonds,, R. Gupta,, T. Hashizume,, D. W. Phillipson,, and J. A. McCloskey. 1993. Structure of the archaeal transfer RNA nucleoside G*-15 (2-amino-4,7-dihydro-4-oxo-β-D-ribofuranosyl-1H-pyrrolo[2,3-d]pyrimi-dine-5-carboximidamide (archaeosine). J. Biol. Chem. 268: 1007610086.
62. Grosjean, H.,, S. Auxilien,, F. Constantinesco,, C. Simon,, Y. Corda,, H. F. Becker,, D. Foiret,, A. Morin, Y. X. Jin, M. Fournier, and J. L. Fourrey. 1996a. Enzymatic conversion of adenosine to inosine and to N-1-methylinosine in transfer RNAs: a review. Biochimie 78:488501.
63. Grosjean, H.,, F. Constantinesco,, D. Foiret,, and N. Benachenhou. 1995a. A novel enzymatic pathway leading to 1-methylinosine modification in Haloferax volcanii tRNA. Nucleic Acids Res. 23: 43124319.
64. Grosjean, H.,, S. De Henau,, T. Doi,, A. Yamane,, E. Ohtsuka,, M. Ikehara,, N. Beauchemin,, K. Nicoghosian,, and R. Cedergren. 1987. The in vivo stability, maturation and aminoacylation of anticodon-substituted Escherichia coli initiator methionine tRNAs. Eur. J. Biochem. 166:325332.
65. Grosjean, H.,, L. Droogmans,, R. Giege,, and O. C. Uhlenbeck. 1990. Guanosine modifications in runoff transcripts of synthetic transfer RNA-Phe genes microinjected into Xenopus oocytes. Biochim. Biophys. Acta 1050:267273.
66. Grosjean, H.,, J. Edqvist,, K. B. Straby,, and R. Giege. 1996b. Enzymatic formation of modified nucleosides in tRNA: dependence on tRNA architecture.J. Mol. Biol. 255:6785.
67. Grosjean, H.,, M. Sprinzl,, and S. Steinberg. 1995b. Posttranscriptionally modified nucleosides in transfer RNA: their locations and frequencies. Biochimie 77:139141.
68. Gu, X.,, and D. V. Santi. 1991. The T-arm of tRNA is a substrate for the tRNA (m5U54)-methyltransferase. Biochemistry 30: 29993002.
69. Gu, X.,, and D. V. Santi. 1992. Covalent adducts between tRNA (m5U54)-methyltransferase and RNA substrates. Biochemistry 31:1029510302.
70. Gu, X. G.,, J. Ofengand,, and D. V. Santi. 1994. In vitro methylation of Escherichia coli 16S rRNA by tRNA (m5U54)-methyltransferase. Biochemistry 33:22552261.
71. Gu, X. R.,, K. M. Ivanetich,, and D. V. Santi. 1996. Recognition of the T-arm of tRNA by tRNA (m(5)U54)-methyltransferase is not sequence specific. Biochemistry 35:1165211659.
72. Guenther, R. H.,, R. S. Bakal,, B. Forrest,, Y. Chen,, R. Sengupta,, B. Nawrot,, E. Sochacka,, J. Jankowska,, A. Kraszewski,, A. Mal-kiewicz,, and P. F. Agris. 1994. Aminoacyl-tRNA synthetase and U-54 methyltransferase recognize conformations of the yeast tRNA(Phe) anticodon and T stem/loop domain. Biochimie 76: 11431151.
73. Gustafsson, C.,, and G. R. Björk. 1993. The tRNA-(m5U54)-methyltransferase of Escherichia coli is present in two forms in vivo, one of which is present as bound to tRNA and to a 3'-end fragment of 16S rRNA.J. Biol. Chem. 268:13261331.
74. Hagervall, T. G.,, C. G. Edmonds,, J. A. McCloskey,, and G. R. Björk. 1987. Transfer RNA (5-methylaminomethyl-2-thiouridine)-methyltransferase from Escherichia coli K-12 has two enzymatic activities.J. Biol. Chem. 262:84888495.
75. Haumont, E.,, L. Droogmans,, and H. Grosjean. 1987. Enzymatic formation of queuosine and of glycosyl queuosine in yeast tRNAs microinjected into Xenopus laevis oocytes. Eur. J. Biochem. 168:219.
76. Hayward, R. S.,, and S. B. Weiss. 1966. RNA thiolase: the enzymatic transfer of sulfur from cysteine to sRNA in Escherichia coli extracts. Biochemistry 55:11611168.
77. Hjalmarsson, K. J.,, A. S. Bystrom,, and G. R. Björk. 1983. Purification and characterization of transfer RNA (guanine-l)methyltransferase from Escherichia coli. J. Biol. Chem. 258: 13431351.
78. Hodel, A. E.,, P. D. Gershon,, X. Shi,, and F. A. Quiocho. 1996. The 1.85 Å structure of vaccinia protein VP39: a bifunctional enzyme that participates in the modification of both mRNA ends. Cell 85:247256.
79. Holmes, M. W.,, C. Adraos-Selim,, and M. Redlak. 1995. tRNA-m1G methyltransferase interactions: touching bases with structure. Biochimie 77:6265.
80. Holmes, M. W.,, C. Adraos-Selim,, I. Roberts,, and S. Z. Wahab. 1992. Structural requirements for tRNA methylation. J. Biol. Chem. 267:1344013445.
81. Holtz, J.,, and D. Klambt. 1975. tRNA isopentenyltransferase from Lactobacillus acidophilus ATCC 4963. Hoppe Seylers Z. Physiol. Chem. 356:14591464.
82. Holtz, J.,, and D. Klambt. 1978. tRNA isopentenyltransferase from Zea mays L. Characterization of the isopentenylation reaction of tRNA, oligo (A) and other nucleic acids. Hoppe Seylers Z. Physiol. Chem. 359:89101.
83. Hoops, G. C.,, J. Park,, G. A. Garcia,, and L. B. Townsend. 1996. The synthesis and determination of acidic ionization constants of certain 5-substituted 2-aminopyrrolo[2,3-d]pyrimidin-4-ones and methylated analogs.J. Heterocycl. Chem. 33:767781.
84. Hoops, G. C.,, L. B. Townsend,, and G. A. Garcia. 1995a. Mechanism-based inactivation of tRNA-guanine transglycosylase from Escherichia coli by 2-amino-5-(fluoromethyl)pyrrolo[2,3-d] pyr-imidin-4(3H)-one. Biochemistry 34:1553915544.
85. Hoops, G. C.,, L. B. Townsend,, and G. A. Garcia. 1995b. tRNA-guanine transglycosylase from Escherichia coli:structure-activity studies investigating the role of the aminomethyl substituent of the heterocyclic substrate preQ(l). Biochemistry 34:1538115387.
86. James, T. L.,, A. L. Pogolotti,, K. M. Ivanetich,, Y. Wataya,, S. M. Lam,, and D. V. Santi. 1976. Thymidylate synthase: fluorine-19 NMR characterization of the active site peptide covalently bound to 5-fluoro-2'-deoxyuridylate and 5,10-methylenetetra-hydrofolate. Biochem. Biophys. Res. Commun. 72:404410.
87. Jiang, H.-Q.,, Y. Motorin,, Y.-X. Jin,, and H. Grosjean. 1997. Pleiotropic effects of intron removal on base modification pattern of yeast tRNAph,:: an in vitro study. Nucleic Acids Res. 25: 26942701.
88. Kammen, H. O.,, C. C. Marvel,, L. Hardy, and E. E. Penhoet. 1988. Purification, structure, and properties of Escherichia coli tRNA pseudouridine synthase 1.J. Biol. Chem. 263:22552263.
89. Kasai, H.,, M. Goto,, S. Takemura,, T. Goto,, and S. Matsurra. 1971. Structure and synthesis of a fluorescent Y-like base from Torulopsis utilis tRNA. Tetrahedron Lett. 29:27252728.
90. Kasai, H.,, K. Nakanishi,, R. D. Macfarlane,, D. F. Torgerson,, Z. Ohashi,, J. A. McCloskey,, H. J. Gross,, and S. Nishimura. 1976. The structure of Q nucleoside isolated from rabbit liver transfer ribonucleic acid.J. Am. Chem. Soc. 98:5044.
91. Katze, J. R.,, M. H. Simonian,, and R. B. Mosteller. 1977. Role of methionine in the synthesis of nucleoside Q in Escherichia coli transfer ribonucleic acid.J. Bacteriol. 132:174179.
92. Kealey, J. T.,, X. Gu,, and D. V. Santi. 1994. Enzymatic mechanism of tRNA (m5U54)methyltransferase. Biochimie 76:11331142.
93. Kealey, J. T.,, S. Lee,, H. G. Floss,, and D. V. Santi. 1991. Stereochemistry of methyl transfer catalyzed by tRNA (m5U54)-methyltransferase-evidence for a single displacement mechanism. Nucleic Acids Res. 19:64656468.
94. Kealey, J. T.,, and D. V. Santi. 1991. Identification of the catalytic nucleophile of tRNA (m5U54)methyltransferase. Biochemistry 30:97249728.
95. Keith, J. M.,, E. M. Winters,, and B. Moss. 1980. Purification and characterization of a HeLa cell transfer RNA (cytosine-5-)-methytransferase. J. Biol. Chem. 255:46364644.
96. Kersten, H.,, and W. Kersten,. 1990. Biosynthesis and function of queuine and queuosine tRNAs, p. B69B108. In C. Gehrke, and K. Kuo (ed.), Chromatography and Modification of Nucleosides, part B. Biological Roles and Function of Modification. Elsevier, Amsterdam, The Netherlands.
97. Kirtland, G. M.,, T. D. Morris,, P. H. Moore,, J. J. O'Brian,, C. G. Edmonds,, J. A. McCloskey,, and J. R. Katze. 1988. Novel salvage of queuine from queuosine and absence of queuine synthesis in Chlorella pyrenoidosa and Chlamydomonas reinhardtii. J. Bacteriol. 170:56335641.
98. Klimasauskas, S.,, S. Kumar,, R. J. Roberts,, and X. D. Cheng. 1994. Hha I methyltransferase flips its target base out of the DNA helix. Cell 76:357369.
99. Kline, L. K.,, F. Fittler,, and R. H. Hall. 1969. N6-(A2-IsopentenyI) adenosine. Biosynthesis in transfer ribonucleic acid in vitro. Biochemistry 8:43614371.
100. Koonin, E. V. 1996. Pseudouridine synthases: four families of enzymes containing a putative uridine-binding motif also conserved in dUTPases and dCTP deaminases. Nucleic Acids Res. 24:24112415.
101. Korner, A.,, and D. Söl. 1974. N-(Purin-6-ylcarbamoyl)threonine: biosynthesis in vitro in transfer RNA by an enzyme purified from Escherichia coli. FEBS Lett. 39:301306.
102. Kuchino, Y.,, H. Kasai,, K. Nihei,, and S. Nishimura. 1976. Biosynthesis of the modified nucleoside Q in transfer RNA. Nucleic Acids Res. 3:393398.
103. Kun, E., 1967. Pages 375401. In D. M. Greenberg (ed.), Metabolic Pathways. Academic Press, New York, N.Y..
104. Leung, H.-C. E.,, Y. Chen,, and M. E. Winkler. 1997. Regulation of substrate recognition by the MiaA tRNA prenyl transferase modification enzyme of Escherichia coli K-12. J. Biol. Chem. 272:1307313083.
105. Li, H. J.,, K. Nakanishi,, D. Grunberger,, and I. B. Weinstein. 1973. Biosynthestic studies of the Y base in yeast phenylalanine tRNA. Incorporation of guanine. Biochem. Biophys. Res. Commun. 55: 818823.
106. Limbach, P. A.,, P. F. Crain,, and J. A. McCloskey. 1994. Summary: the modified nucleosides of RNA. Nucleic Acids Res. 22: 21832196.
107. Lipsett, M. N. 1972. Biosynthesis of 4-thiouridylate.J. Biol. Chem. 247:14581461.
108. Lipsett, M. N.,, J. S. Norton,, and A. Peterkofsky. 1967. A requirement for β-mercaptopyruvate in the in vitro thiolation of transfer ribonucleic acid. Biochemistry 6:855860.
109. Lipsett, M. N.,, and A. Peterkofsky. 1966. Enzymatic thiolation of E. coli sRNA. Biochemistry 5:11691174.
110. Lo, R. Y.,, and J. B. Bell. 1981. Characterization of a mutation in Saccharomyces cerevisiae that produces mutant isoaccepting tRNAs for several of its tRNA species. Curr. Genet. 3:7382.
111. Lo, R. Y.,, J. B. Bell,, and K. L. Roy. 1982. Dihydrouridine-deficient tRNAs in Saccharomyces cerevisiae. Nucleic Acids Res. 10: 889902.
112. Matsumoto, T.,, K. Nishikura,, H. Hori,, T. Ohta,, K. Miura,, and K. Watanabe. 1990. Recognition sites of tRNA by a thermostable tRNA (guanosine-2'-)methyltransferase from Thermus thermophilus HB27.J. Biochem. 107:331338.
113. Meister, A. 1989. Mechanism and regulation of the glutamine-dependent carbamyl phosphate synthetase of Escherichia coli. Adv. Enzymol. 62:315374.
114. Merkler, D.,, M. Brenowitz,, and V. Schramm. 1990. The rate constant describing slow-onset inhibition of yeast AMP deaminase by coformycin analogues is independent of inhibitor structure. Biochemistry 29:83588364.
115. Moore, J. A., , and C. D. Poulter. 1997. Escherichia coli dimethylallyl diphosphate:tRNA dimethylallyl transferase: a binding mechanism for recombinant enzyme. Biochemistry 36:604614.
116. Morin, A.,, S. Auxilien,, B. Senger,, R. Tewari,, and H. Grosjean. 1998. Structural requirements for enzymatic formation of threonylcarbamoyl adenosine (t6A) in tRNA: an in vivo study with Xenopus laevis oocytes. RNA 4:2437.
117. Morris, R. C.,, B. J. Brooks,, P. Eriotou,, D. F. Kelly,, S. Sagar,, K. L. Hart,, and M. S. Elliott. 1995. Activation of transfer RNA-guanine ribosyltransferase by protein kinase C. Nucleic Acids Res. 23:24922498.
118. Motorin, Y.,, V. Arluison,, H. Becker,, G. Simos,, E. Hurt,, and H. Grosjean. 1997a. Pseudouridine formation in yeast tRNAs: cloning and characterization of the corresponding enzymes. In Proceedings of 17th International tRNA Workshop, Chiba, Japan.
119. Motorin, Y.,, G. Bee,, R. Tewari,, and H. Grosjean. 1997b. Transfer RNA recognition by the Escherichia coli A2-isopentenyl-pyrophosphate:tRNA A2-isopentenyl transferase: dependence on the anticodon arm structure. RNA 3:721733.
120. Mueller, S. O.,, and R. K. Slany. 1995. Structural analysis of the interaction of the tRNA modifying enzymes Tgt and QueA with a substrate tRNA. FEBS Lett. 361:259264.
121. Mullenbach, G. T.,, H. O. Kammen,, and E. E. Penhoet. 1976. A heterologous system for detecting eukaryotic enzymes which synthesize pseudouridine in transfer ribonucleic acids. J. Biol. Chem. 251:45704578.
122. Munch, H.-J.,, and R. Thiebe. 1975. Biosynthesis of the nucleoside Y in yeast tRNAPh,;: incorporation of the 3-amino-3-carboxy-propyl-group from methionine. FEBS Lett. 51:257258.
123. Nakanishi, S.,, T. Ueda,, H. Hori,, N. Yamazaki,, N. Okada,, and K. Watanabe. 1994. A UGU sequence in the anticodon loop is a minimum requirement for recognition by Escherichia coli tRNA-guanine transglycosylase.J. Biol. Chem. 269:3222132225.
124. Nishikura, K.,, and E. M. De Robertis. 1981. RNA processing in microinjected Xenopus oocytes: sequential addition of base modifications in a spliced transfer RNA.J. Mol. Biol. 145:405420.
125. Noguchi, S.,, Y. Nishimura,, Y. Hirota,, and S. Nishimura. 1982. Isolation and characterization of an Escherichia coli mutant lacking tRNA-guanine transglycosylase. J. Biol. Chem. 257: 65446550.
126. Noguchi, S.,, Z. Yamaizumi,, T. Ohgi,, T. Goto,, Y. Nishimura,, Y. Hirota,, and S. Nishimura. 1978. Isolation of Q nucleoside precursor present in tRNA of an E. coli mutant and its characterization as 7-(cyano)-7-deazaguanine. Nucleic Acids Res. 5: 42154223.
127. Nurse, K.,, J. Wrzesinski,, A. Bakin,, B. G. Lane,, and J. Ofengand. 1995. Purification, cloning, and properties of the tRNA ?55 synthase from Escherichia coli. RNA 1:102112.
128. Okada, N.,, and S. Nishimura. 1977. Enzymatic synthesis of Q* nucleoside containing mannose in the anticodon of tRNA: isolation of a novel mannosyltransferase from a cell-free extract of rat liver. Nucleic Acids Res. 4:29312937.
129. Okada, N.,, and S. Nishimura. 1979. Isolation and characterization of a guanine insertion enzyme, a specific tRNA transglycosylase, from Escherichia coli. J. Biol. Chem. 254:30613066.
130. Pais de Barros, J. P.,, G. Keith,, C. El Adlouni,, A. L. Glasser,, G. Mack,, G. Dirheimer,, and J. Desgres. 1996. 2'-O-methyl-5-formylcytidine (f Cm), a new modified nucleotide at the "wobble" position of two cytoplasmic tRNAsLeu (NAA) from bovine liver. Nucleic Acids Res. 24:14891496.
131. Pergolizzi, R. G.,, D. L. Engelhardt,, and D. Grunberger. 1978. Formation of phenylalanine transfer RNA lacking the wye base in vero cells during methionine starvation. J. Biol. Chem. 253: 63416343.
132. Pergolizzi, R. G.,, D. L. Engelhardt,, and D. Grunberger. 1979. Incorporation of lysine into Y base of phenylalanine tRNA in vero cells. Nucleic Acids Res. 6:22092216.
133. Persson, B.,, C. Gustafsson,, D. Berg,, and G. Björk. 1992. The gene for a tRNA modifying enzyme, msU54-methyltransferase, is essential for viability in Escherichia coli. Proc. Natl. Acad. Sci. USA 89:39953998.
134. Peterkofsky, A.,, and M. N. Lipsett. 1965. The origin of the sulfur in s-RNA. Biochem. Biophys. Res. Commun. 20:780786.
135. Pfleiderer, W. 1961. Uber die Methylierung des 9-Methylguanins und die Struktur des Herbipolins. Liebigs Ann. Chem. 647: 167173.
136. Pogolotti, A. L.,, K. M. Ivanetich,, H. Sommer,, and D. V. Santi. 1986. Thymidylate synthase: studies on the peptide containing covalently bound 5-fluoro-2'-deoxyuridylate and 5,10-methyl-enetetrahydrofolate. Biochem. Biophys. Res. Commun. 70: 972978.
137. Polson, A.,, B. Bass,, and J. Casey. 1996. RNA editing of hepatitis delta virus antigenome by dsRNA-adenosine deaminase. Nature (London) 380:454456.
138. Polson, A.,, P. Crain,, S. Pomerantz,, J. McCloskey,, and B. Bass. 1991. The mechanism of adenosine to inosine conversion by the double-stranded RNA unwinding/modifying activity: a high-performance liquid chromatography-mass spectrometry analysis. Biochemistry 30:1150711514.
139. Polson, A. G.,, and B. L. Bass. 1994. Preferential selection of adenosines for modification by double-stranded RNA adenosine deaminase. EMBO J. 13:57015711.
140. Poulter, C. D.,, and H. C. Rilling. 1976. Prenyltransferase: the mechanism of the reaction. Biochemistry 15:10791083.
141. Poulter, C. D.,, and D. M. Satterwhite. 1977. Mechanism of the prenyl-transfer reaction. Studies with (E)- and (Z)-3-trifluoromethyl-2-buten-l-yl pyrophosphate. Biochemistry 16: 54705478.
142. Poulter, C. D.,, D. M. Satterwhite,, and H. C. Rilling. 1976. Prenyltransferase. The mechanism of the reaction. J. Am. Chem. Soc. 98:33763377, (Letter.)
143. Powers, D. M.,, and A. Peterkofsky. 1972. Biosynthesis and specific labeling of N-(purin-6-ylcarbamoyl)threonine of Escherichia coli transfer RNA. Biochem. Biophys. Res. Commun. 46:831838.
144. Powers, S. G.,, and A. Meister. 1978. Mechanism of the reaction catalyzed by carbamyl phosphate synthetase.J. Biol. Chem. 253: 800803.
145. Prior, J. J.,, and D. V. Santi. 1984. On the mechanism of the acid-catalyzed hydrolysis of uridine to uracil. J. Biol. Chem. 259: 24292434.
146. Raushel, F. M.,, P. M. Anderson,, and J. J. Villafranca. 1978. Kinetic mechanism of Escherichia coli carbamoyl-phosphate synthetase. Biochemistry 17:55875591.
147. Reinhart, M. P.,, J. M. Lewis,, and P. S. Leboy. 1986. A single tRNA (guanine)-methyltransferase for Tetrahymena pyriformis with both mono- and di-methylating activity. Nucleic Acids Res. 14: 11311148.
148. Reuter, K.,, S. Chong,, F. Ullrich,, H. Kersten,, and G. A. Garcia. 1994. Serine-90 is required for enzymic activity by tRNA-guanine transglycosylase from Escherichia coli. Biochemistry 33: 70417046.
149. Reuter, K.,, and R. Ficner. 1995. Sequence analysis and overexpression of the Zymomonas mobilis tgt gene encoding tRNA-guanine transglycosylase: purification and biochemical characterization of the enzyme.J. Bacteriol. 177:52845288.
150. Reuter, K.,, R. Slany,, F. Ullrich,, and H. Kersten. 1991. Structure and organization of Escherichia coli genes involved in biosynthesis of the deazaguanine derivative queuine, a nutrient factor for eukaryotes.J. Bacteriol. 173:22562264.
151. Roberts, R. J. 1995. On base flipping. Cell 82:912.
152. Roe, B. A.,, A. F. Stankiewicz,, H. L. Rizi,, C. Weisz,, M. DiLauro,, D. Pike,, C. Y. Chen,, and E. Y. Chen. 1979. Comparison of rat liver and Walker 256 carcinosarcoma tRNAs. Nucleic Acids Res. 6:673.
153. Romeo, J. M.,, A. S. Delk,, and J. C. Rabinowitz. 1974. The occurrence of a transmethylation reaction not involving S-adenosylmethionine in the formation of ribothymidine in Bacillus subtilis transfer-RNA. Biochem. Biophys. Res. Commun. 61: 12561261.
154. Romier, C.,, K. Reuter,, D. Suck,, and R. Ficner. 1996a. Crystal structure of tRNA-guanine transglycosylase: RNA modification by base exchange. EMBOJ. 15:28502857.
155. Romier, C.,, K. Reuter,, D. Suck,, and R. Ficner. 1996. Mutagenesis and crystallographic studies of Zymomonas mobilis tRNA-guanine transglycosylase reveal aspartate 102 as the active site nucleophile. Biochemistry 35:1573415739.
156. Rosenbaum, N.,, and M. L. Gefter. 1972. δ2-Isopentenylpyrophosphate: transfer ribonucleic acid δ2-isopentenyltransferase from Escherichia coli. Purification and properties of the enzyme.J. Biol. Chem. 247:56755680.
157. Rottman, F. M.,, J. A. Bokar,, P. Narayan, M. E. Shambaugh, and R. Ludwiczak. 1994. N6-adenosine methylation in mRNA: substrate specificity and enzyme complexity. Biochimie 76: 11091114.
158. Roy-Burman, P.,, S. Roy-Burman,, and D. W. Visser. 1965. Incorporation of 5,6-dihydrouridine triphosphate into ribonucleic acid by DNA-dependent RNA polymerase. Biochem. Biophys. Res. Commun. 20:291297.
159. Roy-Burman, P.,, S. Roy-Burman,, and D. W. Visser. 1967. Utilization of 5,6-dihydrouridine 5'-triphosphate in the reaction catalyzed by Escherichia coli RNA polymerase. Biochim. Biophys. Acta 142:355367.
160. Rubio, V.,, H. G. Britton,, and S. Grisolia. 1979. Mechanism of carbamoyl phosphate synthetase. Eur. J. Biochem. 93:245256.
161. Rubio, V.,, H. G. Britton,, S. Grisolia,, B. S. Sproat,, and G. Lowe. 1981. Mechanism of activation of bicarbonate ion by mitochondrial carbamoyl-phosphate synthetase: formation of enzyme-bound adenosine diphosphate from the adenosine triphosphate that yields inorganic phosphate. Biochemistry 20:19691974.
162. Rueter, S. M.,, C. M. Burns,, S. A. Coode,, P. Mookherjee,, and R. B. Emeson. 1995. Glutamate receptor RNA editing in vitro by enzymatic conversion of adenosine to inosine. Science (Washington, D.C.) 267:14911494.
163. Santi, D. V.,, and L. W. Hardy. 1987. Catalytic mechanism and inhibition of tRNA-(uracil-5-)methyltransferase: evidence for covalent catalysis. Biochemistry 26:85998606.
164. Santi, D. V.,, C. S. McHenry,, and E. R. Perriard. 1974. A filter assay for thymidylate synthetase using 5-fluoro-2'deoxyuridylate as an active site titrant. Biochemistry 13:467470.
165. Savva, R.,, K. McAuley-Hecht,, T. Brown,, and L. Pearl. 1995. The structural basis of specific base excision repair by uracil-DNA glycosylase. Nature (London) 373:487493.
166. Schibler, U.,, D. E. Kelley,, and R. P. Perry. 1977. Comparison of methylated sequences in messenger RNA and heterogeneous nuclear RNA from mouse L cells.J. Mol. Biol. 115:695714.
167. Schmidt, W.,, H. Arnold,, and H. Kersten. 1975. Biosynthetic pathway of ribothymidine in B. subtilis and M. lysodeikticus involving different coenzymes for transfer RNA and ribosomal RNA. Nucleic Acids Res. 2:10431051.
168. Schnierle, B. S.,, P. D. Gershon,, and B. Moss. 1992. Cap-specific mRNA (nucleoside-02'-)-methyltransferase and poly(A) polymerase stimulatory activities of vaccinia virus are mediated by a single protein. Proc. Natl. Acad. Sci. USA 89:28972901.
169. Schnierle, B. S.,, P. D. Gershon,, and B. Moss. 1994. Mutational analysis of a multifunctional protein, with mRNA 5' cap-specific (nucleoside-2'-0-)-methyltransferase and 3'-adenylyltransferase stimulatory activities, encoded by vaccinia virus. J. Biol. Chem. 269:2070020706.
170. Segal, D. M.,, and D. C. Eichler. 1989. The specificity of interaction between S-adenosyl-L-methionine and a nucleolar 2'-O-methyltransferase. Arch. Biochem. Biophys. 275:334343.
171. Segal, D. M.,, and D. C. Eichler. 1991. A nucleolar 2'-0-methyltransferase: specificity and evidence for its role in the methylation of 28S precursor ribosomal RNA. J. Biol. Chem. 266:2438524389.
172. Sharmeen, L.,, B. Bass,, N. Sonenberg,, H. Weintraub,, and M. Groudine. 1991. Tat-dependent adenosine-to-inosine modification of wild-type transactivation response RNA. Proc. Natl. Acad. Sci. USA 88:80968100.
173. Shi, X.,, P. Yao,, T. Jose,, and P. D. Gershon. 1996. Methyltransferase-specific domains within VP39, a bifunctional protein that participates in the modification of both mRNA ends. RNA 2: 88101.
174. Shibata, H.,, T. S. Ro-Choi,, P. Reddy,, Y. C. Choi,, D. Henning,, and H. Busch. 1975. The primary nucleotide sequence of nuclear U-2 ribonucleic acid. J. Biol. Chem. 250:39093920.
175. Shimba, S.,, J. A. Bokar,, F. Rottman,, and R. Reddy. 1995. Accurate and efficient N-6-adenosine methylation in spliceosomal U6 small nuclear RNA by HeLa cell extract in vitro. Nucleic Acids Res. 23:24212426.
176. Singer, C. E.,, and G. R. Smith. 1972. Histidine regulation in Salmonella typhimurium. J. Biol. Chem. 247:289300.
177. Singer, C. E.,, G. R. Smith,, R. Cortese,, and B. N. Ames. 1972. Mutant tRNAHls ineffective in repression and lacking two pseudouridine modifications. Nat. New Biol. 238:7274.
178. Singhal, R. P. 1983. Queuine: an addendum. Prog. Nucleic Acids Res. Mol. Biol. 28:7580.
179. Slany, R. K.,, M. Bosl,, P. F. Crain,, and H. Kersten. 1993. A new function of S-adenosylmethionine: the ribosyl moiety of AdoMet is the precursor of the cyclopentenediol moiety of the tRNA wobble base queuine. Biochemistry 32:78117817.
180. Slany, R. K.,, and S. O. Muller. 1995. tRNA-guanine transglycosylase from bovine liver-purification of the enzyme to homogeneity and biochemical characterization. Eur. J. Biochem. 230: 221228.
181. Smith, C.,, P. G. Schmidt,, J. Petsch,, and P. F. Agris. 1985. Nuclear magnetic resonance signal assignments of purified [13CJmethyl-enriched yeast phenylalanine transfer ribonucleic acid. Biochemistry 24:14341440.
182. Söll, D.,, and L. Kline,. 1982. RNA methylation, p. 557566. In P. D. Boyer (ed.), The Enzymes. Academic Press, New York, N.Y..
183. Sommer, B.,, M. Kohler,, R. Sprengel,, and P. H. Seeburg. 1991. RNA editing in brain controls a determinant of ion flow in glutamate-gated channels. Cell 67:1119.
184. Sprinzl, M.,, C. Steegborn,, F. Hubel,, and S. Steinberg. 1996. Compilation of tRNA sequences and sequences of tRNA genes. Nucleic Acids Res. 24:6872.
185. Stadtman, T. C. 1994. Emerging awareness of the critical roles of S-phosphocysteine and selenophosphate in biological systems. Biofactors 4:181185.
186. Sullivan, M. A.,, J. F. Cannon,, F. H. Webb,, and R. M. Bock. 1985. Antisuppressor mutation in Escherichia coli defective in biosynthesis of 5-methylaminomethyl-2-thiouridine.J. Bacteriol. 161: 368376.
187. Szweykowska-Kulinska, Z.,, B. Senger,, G. Keith,, F. Fasiolo,, and H. Grosjean. 1994. Intron-dependent formation of pseudouridines in the anticodon of Saccharomyces cerevisiae minor tRNA(Ile). EMBO J. 13:46364644.
188. Thiebe, R.,, and K. Poralla. 1973. Origin of the nucleoside Y in yeast tRNAplu'. FEBS Lett. 38:2728.
189. Tidwell, T.,, and E. Howard. 1972. The thiolation, methylation, and formation of pseudouridine and dihydrouridine in tRNA of regenerating rat liver, human phytohemagglutinin stimulated lymphocytes, and Novikoff ascites cells. Cell Differ. 1:199207.
190. Ueland, P. M. 1982. Pharmacological and biochemical aspects of S-adenosylhomocysteine and S-adenosylhomocysteine hydrolase. Pharmacol. Rev. 34:223246.
191. Veres, Z.,, I. Y. Kim,, T. D. Scholz,, and T. C. Stadtman. 1994. Selenophosphate synthetase.J. Biol. Chem. 269:1059710603.
192. Veres, Z.,, and T. C. Stadtman. 1994. A purified selenophosphate-dependent enzyme from Salmonella typhimurium catalyzes the replacement of sulfur in 2-thiouridine residues in tRNAs with selenium. Proc. Natl. Acad. Sci. USA 91:80928096.
193. Veres, Z.,, L. Tsai,, T. D. Scholz,, M. Politino,, and R. S. Balaban. 1992. Synthesis of 5-methylaminomethyl-2-selenouridine in tRNAs: "P NMR studies show the labile selenium donor synthesized by the selD gene product contains selenium bonded to phosphorus. Proc. Natl. Acad. Sci. USA 89:29752979.
194. VoLd, B. S.,, M. E. Longmire,, and D. E. Keith. 1981. Thiolation and 2-methylthio- modification of Bacillus subtilis transfer ribonucleic acids.J. Bacteriol. 148:869876.
195. Walsh, C. T. 1979. Enzymatic Reaction Mechanisms. W. H. Freeman and Co., San Francisco, Calif..
196. Watanabe, M.,, M. Matsuo,, S. Tanaka,, H. Akimoto,, S. Asahi,, S. Nishimura,, J. Katze,, T. Hashizume,, P. F. Crain,, J. A. McCloskey,, and N. Okada. 1997. Biosynthesis of archaeosine, a novel derivative of 7-deazaguanosine specific to archaeal tRNA, proceeds via a pathway involving base replacement on the tRNA polynucleotide chain.J. Biol. Chem. 272:2014620151.
197. Wilson, D.,, and F. Quiocho. 1994. Crystallographic observation of a trapped tetrahedral intermediate in a metalloenzyme. Nat. Struct. Biol. 1:691694.
198. Wilson, D.,, F. Rudolph,, and F. Quiocho. 1991. Atomic structure of adenosine deaminase complexed with a transition-state analog: understanding catalysis and immunodeficiency mutations. Science (Washington, D.C.) 252:12781284.
199. Wittwer, A. J.,, and T. C. Stadtman. 1986. Biosynthesis of 5-methylaminomethyl-2-selenouridine, a naturally occurring nucleoside in Escherichia coli tRNA. Arch. Biochem. Biophys. 248: 540550.
200. Wong, T. W.,, S. B. Weiss,, G. L. Eliceiri,, and J. Bryant. 1970. Ribonucleic acid sulfurtransferase from Bacillus subtilis W168. Sulfuration with β-mercaptopyruvate and properties of the system. Biochemistry 9:23762386.
201. Wrzesinski, J.,, K. Nurse,, A. Bakin,, B. G. Lane,, and J. Ofengand. 1995a. A dual-specificity pseudouridine synthase: an Escherichia coli synthase purified and cloned on the basis of its specificity for ?746 in 23S RNA is also specific for Ψ32 in tRNAPhe. RNA 1:437448.
202. Wrzesinski, J.,, K. Nurse,, A. Bakin,, B. G. Lane,, and J. Ofengand. 1995b. Purification, cloning and properties of the 16S RNA pseudouridine 516 synthase from Escherichia coli. Biochemistry 34:89048913.
203. Xiang, S.,, S. Short,, R. Wolfenden,, and C. Carter. 1997. The structure of cytidine deaminase-product complex provides evidence for efficient proton transfer and ground-state stabilization. Biochemistry 36:47684774.
204. Yamazaki, N.,, H. Hori,, K. Ozawa,, S. Nakanishi,, T. Ueda,, I. Kumagai,, K. Watanabe,, and K. Nishikawa. 1992. Purification and characterization of tRNA (adenosine-l-)-methyltransferase from Thermus thermophilus HB27. Nucleic Acids Symp. Ser. 27: 141142.
205. Yamazaki, N.,, H. Hori,, K. Ozawa,, S. Nakanishi,, T. Ueda,, I. Kumagai,, K. Watanabe,, and K. Nishikawa. 1994. Substrate specificity of tRNA (adenine-l-)-methyltransferase from Thermus thermophilus HB27. Biosci. Biotechnol. Biochem. 58:11281133.
206. Yang, J.,, P. Sklar,, R. Axel,, and T. Maniatis. 1995. Editing of glutamate receptor subunit B pre-mRNA by site-specific deamination of adenosine. Nature (London) 374:7781.
207. Yu, W.,, and W. Schuster. 1995. Evidence for a site-specific cytidine deamination reaction involved in C to U RNA editing of plant mitochondria.J. Biol. Chem. 270:1822718233.
208. Zhao, X. M.,, and D. A. Horne. 1997. The role of cysteine residues in the rearrangement of uridine to pseudouridine catalyzed by pseudouridine synthase I.J. Biol. Chem. 272:19501955.

Tables

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Table 1

Classification of methylation modifications

Citation: Garcia G, Goodenough-Lashua D. 1998. Mechanisms of RNA-Modifying and -Editing Enzymes, p 135-168. In Grosjean H, Benne R (ed), Modification and Editing of RNA. ASM Press, Washington, DC. doi: 10.1128/9781555818296.ch8
Generic image for table
Table 2

Examples of RNA-modifying and -editing reactions

Citation: Garcia G, Goodenough-Lashua D. 1998. Mechanisms of RNA-Modifying and -Editing Enzymes, p 135-168. In Grosjean H, Benne R (ed), Modification and Editing of RNA. ASM Press, Washington, DC. doi: 10.1128/9781555818296.ch8

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