1887

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

MyBook is a cheap paperback edition of the original book and will be sold at uniform, low price.

Preview this chapter:
Zoom in
Zoomout

Mechanisms of RNA-Modifying and -Editing Enzymes, Page 1 of 2

| /docserver/preview/fulltext/10.1128/9781555818296/9781555811334_Chap08-1.gif /docserver/preview/fulltext/10.1128/9781555818296/9781555811334_Chap08-2.gif

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

Key Concept Ranking

Brome mosaic virus
0.45263836
Tobacco mosaic virus
0.45263836
Brome mosaic virus
0.45263836
Tobacco mosaic virus
0.45263836
Brome mosaic virus
0.45263836
Tobacco mosaic virus
0.45263836
Hepatitis delta virus
0.4513775
Small Nucleolar RNA
0.4406824
0.45263836
Highlighted Text: Show | Hide
Loading full text...

Full text loading...

Figures

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
Permissions and Reprints Request Permissions
Download as Powerpoint
Image of Figure 2
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
Permissions and Reprints Request Permissions
Download as Powerpoint
Image of Figure 3
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
Permissions and Reprints Request Permissions
Download as Powerpoint
Image of Figure 4
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
Permissions and Reprints Request Permissions
Download as Powerpoint
Image of Figure 5
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
Permissions and Reprints Request Permissions
Download as Powerpoint
Image of Figure 6
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
Permissions and Reprints Request Permissions
Download as Powerpoint
Image of Figure 7
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
Permissions and Reprints Request Permissions
Download as Powerpoint
Image of Figure 8
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
Permissions and Reprints Request Permissions
Download as Powerpoint
Image of Figure 9
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
Permissions and Reprints Request Permissions
Download as Powerpoint
Image of Figure 10
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
Permissions and Reprints Request Permissions
Download as Powerpoint
Image of Figure 11
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
Permissions and Reprints Request Permissions
Download as Powerpoint
Image of Figure 12
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
Permissions and Reprints Request Permissions
Download as Powerpoint
Image of Figure 13
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
Permissions and Reprints Request Permissions
Download as Powerpoint
Image of Figure 14
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
Permissions and Reprints Request Permissions
Download as Powerpoint
Image of Figure 15
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
Permissions and Reprints Request Permissions
Download as Powerpoint
Image of Figure 16
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
Permissions and Reprints Request Permissions
Download as Powerpoint
Image of Figure 17
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
Permissions and Reprints Request Permissions
Download as Powerpoint
Image of Figure 18
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
Permissions and Reprints Request Permissions
Download as Powerpoint
Image of Figure 19
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
Permissions and Reprints Request Permissions
Download as Powerpoint
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
Permissions and Reprints Request Permissions
Download as Powerpoint

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: 294 301.
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: 691 698.
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: 721 730.
5. Ajitkumar, P.,, and J. D. Cherayil. 1988. Thionucleosides in transfer ribonucleic acid: diversity, structure, biosynthesis, and function. Microbiol. Rev. 52: 103 113.
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: 205 208.
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: 258 261.
8. Astrom, S. U.,, and A. S. Bystrom. 1994. Ritl, a tRNA backbone-modifying enzyme that mediates initiator and elongator tRNA discrimination. Cell 79: 535 546.
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: 437 458.
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: 1089 1098.
11. Bachellerie, J.-P.,, and J. Cavaille. 1997. Guiding ribose methylation of rRNA. Trends Biochem. Sci. 22: 257 261.
12. Bartz, J. K.,, L. K. Kline,, and D. Soil. 1970. N 6-(A 2-Isopentenyl)adenosine: biosynthesis in vitro in transfer RNA by an enzyme purified from Escherichia coli. Biochem. Biophys. Res. Commun. 40: 1481 1487.
13. Bartz, J. K.,, and D. Soil. 1972. N 6-(A 2-Isopentenyl)adenosine: biosynthesis in vitro in transfer RNA by an enzyme purified from Escherichia coli. Biochimie 54: 31 39.
14. Bass, B. 1995. An I for editing. Curr. Biol. 5: 598 600.
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: 505 518.
16. Benne, R. 1996. The long and short of it. Nature (London) 380: 391 392.
17. Bokar, J. A.,, M. E. Rath-Shambaugh,, R. Ludwiczak,, P. Narayan,, and F. Rottman. 1994. Characterization and partial purification of mRNA N 6-adenosine methyltransferase from HeLa cell nuclei. Internal mRNA methylation requires a multisubunit complex. J. Biol. Chem. 269: 17697 704.
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: 2309 2316.
19. Britton, H. G.,, V. Rubio,, and S. Grisolia. 1979. Mechanism of carbamoyl-phosphate synthetase. Eur.J. Biochem. 102: 521 530.
20. Buck, M.,, and B. Ames. 1984. A modified nucleoside in tRNA as a possible regulator of aerobiosis. Cell 36: 523 531.
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: 440 446.
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: 447 454.
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: 4147 4152.
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: 515 519.
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: 3694 3701.
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: 3233 3246.
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: 1103 1108.
30. Curnow, A. W.,, and G. A. Garcia. 1994. tRNA-guanine transglycosylase from Escherichia coli: recognition of dimeric, unmodified tRNA Tyr. Biochimie 76: 1183 1191.
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: 17264 17267.
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: 5239 5246.
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: 4387 4390.
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: 7649 7656.
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: 865 882.
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: 1 7.
37. Droogmans, L.,, and H. Grosjean. 1987. Enzymatic conversion of guanosine 3' adjacent to the anticodon of tRNA Phe to N 1-methylguanosine and the wye nucleoside: dependence on the anticodon sequence. EMBO J. 6: 477 483.
38. Droogmans, L.,, E. Haumont,, S. deHenau,, and H. Grosjean. 1986. Enzymatic 2'-O-methylation of the wobble nucleoside of eukaryotic tRNA Phe: specificity depends on structural elements outside the anticodon loop. EMBOJ. 5: 1105 1109.
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: 9546 9551.
40. Edqvist, J.,, H. Grosjean,, and K. B. Straby. 1992. Identity elements for N 2-dimethylation of guanosine-26 in yeast tRNAs. Nucleic Acids Res. 20: 6575 6581.
41. Edqvist, J.,, K. B. Straby,, and H. Grosjean. 1995. Enzymatic formation of N 2,N 2-dimethylguanosine in eukaryotic tRNA: importance of the tRNA architecture. Biochimie 77: 54 61.
42. Edqvist, J.,, K. B. Straby,, and H. Grosjean. 1993. Pleiotrophic effects of point mutation in yeast tRNA Asp on the base modification pattern. Nucleic Acids Res. 21: 413 417.
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: 1115 1122.
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: 4622 4628.
45. Elliott, M. S.,, and R. W. Trewyn. 1984. Inosine biosynthesis in transfer RNA by an enzymatic insertion of hypoxanthine. J. Biol. Chem. 259: 2407 2410.
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 N 2,N 2-dimethylguanosine modification of both mitochondrial and cytoplasmic tRNA in Saccharomyces cerevisiae. J. Biol. Chem. 261: 9703 9709.
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: rl05 rl33.
48. Fittler, F.,, L. K. Kline,, and R. H. Hall. 1968. N 6-(δ 2-Isopentenyl)adenosine: biosynthesis in vitro by an enzyme extract from yeast and rat liver. Biochem. Biophys. Res. Commun. 31: 571 576.
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: 31 40.
50. Frey, B.,, J. McCloskey,, W. Kersten,, and H. Kersten. 1988. New function of vitamin B l2: cobamide-dependent reduction of epoxyqueuosine to queuosine in tRNAs of Escherichia coli and Salmonella typhimurium. J. Bacteriol. 170: 2078 2082.
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: 1616 1621.
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: 11 17.
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: 3133 3139.
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: 257 265.
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: 11943 11952.
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. Cell 66: 1269 1278.
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: 2203 2210.
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: 3529 3535.
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: 5199 5203.
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: 3045 3052.
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: 10076 10086.
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: 488 501.
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: 4312 4319.
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: 325 332.
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: 267 273.
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: 67 85.
67. Grosjean, H.,, M. Sprinzl,, and S. Steinberg. 1995b. Posttranscriptionally modified nucleosides in transfer RNA: their locations and frequencies. Biochimie 77: 139 141.
68. Gu, X.,, and D. V. Santi. 1991. The T-arm of tRNA is a substrate for the tRNA (m 5U54)-methyltransferase. Biochemistry 30: 2999 3002.
69. Gu, X.,, and D. V. Santi. 1992. Covalent adducts between tRNA (m 5U54)-methyltransferase and RNA substrates. Biochemistry 31: 10295 10302.
70. Gu, X. G.,, J. Ofengand,, and D. V. Santi. 1994. In vitro methylation of Escherichia coli 16S rRNA by tRNA (m 5U54)-methyltransferase. Biochemistry 33: 2255 2261.
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: 11652 11659.
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: 1143 1151.
73. Gustafsson, C.,, and G. R. Björk. 1993. The tRNA-(m 5U54)-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: 1326 1331.
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: 8488 8495.
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: 1161 1168.
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: 1343 1351.
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: 247 256.
79. Holmes, M. W.,, C. Adraos-Selim,, and M. Redlak. 1995. tRNA-m 1G methyltransferase interactions: touching bases with structure. Biochimie 77: 62 65.
80. Holmes, M. W.,, C. Adraos-Selim,, I. Roberts,, and S. Z. Wahab. 1992. Structural requirements for tRNA methylation. J. Biol. Chem. 267: 13440 13445.
81. Holtz, J.,, and D. Klambt. 1975. tRNA isopentenyltransferase from Lactobacillus acidophilus ATCC 4963. Hoppe Seylers Z. Physiol. Chem. 356: 1459 1464.
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: 89 101.
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: 767 781.
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: 15539 15544.
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: 15381 15387.
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: 404 410.
87. Jiang, H.-Q.,, Y. Motorin,, Y.-X. Jin,, and H. Grosjean. 1997. Pleiotropic effects of intron removal on base modification pattern of yeast tRNA ph,:: an in vitro study. Nucleic Acids Res. 25: 2694 2701.
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: 2255 2263.
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: 2725 2728.
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: 174 179.
92. Kealey, J. T.,, X. Gu,, and D. V. Santi. 1994. Enzymatic mechanism of tRNA (m 5U54)methyltransferase. Biochimie 76: 1133 1142.
93. Kealey, J. T.,, S. Lee,, H. G. Floss,, and D. V. Santi. 1991. Stereochemistry of methyl transfer catalyzed by tRNA (m 5U54)-methyltransferase-evidence for a single displacement mechanism. Nucleic Acids Res. 19: 6465 6468.
94. Kealey, J. T.,, and D. V. Santi. 1991. Identification of the catalytic nucleophile of tRNA (m 5U54)methyltransferase. Biochemistry 30: 9724 9728.
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: 4636 4644.
96. Kersten, H.,, and W. Kersten,. 1990. Biosynthesis and function of queuine and queuosine tRNAs, p. B69 B108. 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: 5633 5641.
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: 357 369.
99. Kline, L. K.,, F. Fittler,, and R. H. Hall. 1969. N 6-(A 2-IsopentenyI) adenosine. Biosynthesis in transfer ribonucleic acid in vitro. Biochemistry 8: 4361 4371.
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: 2411 2415.
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: 301 306.
102. Kuchino, Y.,, H. Kasai,, K. Nihei,, and S. Nishimura. 1976. Biosynthesis of the modified nucleoside Q in transfer RNA. Nucleic Acids Res. 3: 393 398.
103. Kun, E., 1967. Pages 375 401. 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: 13073 13083.
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: 818 823.
106. Limbach, P. A.,, P. F. Crain,, and J. A. McCloskey. 1994. Summary: the modified nucleosides of RNA. Nucleic Acids Res. 22: 2183 2196.
107. Lipsett, M. N. 1972. Biosynthesis of 4-thiouridylate. J. Biol. Chem. 247: 1458 1461.
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: 855 860.
109. Lipsett, M. N.,, and A. Peterkofsky. 1966. Enzymatic thiolation of E. coli sRNA. Biochemistry 5: 1169 1174.
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: 73 82.
111. Lo, R. Y.,, J. B. Bell,, and K. L. Roy. 1982. Dihydrouridine-deficient tRNAs in Saccharomyces cerevisiae. Nucleic Acids Res. 10: 889 902.
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: 331 338.
113. Meister, A. 1989. Mechanism and regulation of the glutamine-dependent carbamyl phosphate synthetase of Escherichia coli. Adv. Enzymol. 62: 315 374.
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: 8358 8364.
115. Moore, J. A., , and C. D. Poulter. 1997. Escherichia coli dimethylallyl diphosphate:tRNA dimethylallyl transferase: a binding mechanism for recombinant enzyme. Biochemistry 36: 604 614.
116. Morin, A.,, S. Auxilien,, B. Senger,, R. Tewari,, and H. Grosjean. 1998. Structural requirements for enzymatic formation of threonylcarbamoyl adenosine (t 6A) in tRNA: an in vivo study with Xenopus laevis oocytes. RNA 4: 24 37.
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: 2492 2498.
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 A 2-isopentenyl-pyrophosphate:tRNA A 2-isopentenyl transferase: dependence on the anticodon arm structure. RNA 3: 721 733.
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: 259 264.
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: 4570 4578.
122. Munch, H.-J.,, and R. Thiebe. 1975. Biosynthesis of the nucleoside Y in yeast tRNA Ph,;: incorporation of the 3-amino-3-carboxy-propyl-group from methionine. FEBS Lett. 51: 257 258.
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: 32221 32225.
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: 405 420.
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: 6544 6550.
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: 4215 4223.
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: 102 112.
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: 2931 2937.
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: 3061 3066.
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 tRNAs Leu (NAA) from bovine liver. Nucleic Acids Res. 24: 1489 1496.
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: 6341 6343.
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: 2209 2216.
133. Persson, B.,, C. Gustafsson,, D. Berg,, and G. Björk. 1992. The gene for a tRNA modifying enzyme, m sU54-methyltransferase, is essential for viability in Escherichia coli. Proc. Natl. Acad. Sci. USA 89: 3995 3998.
134. Peterkofsky, A.,, and M. N. Lipsett. 1965. The origin of the sulfur in s-RNA. Biochem. Biophys. Res. Commun. 20: 780 786.
135. Pfleiderer, W. 1961. Uber die Methylierung des 9-Methylguanins und die Struktur des Herbipolins. Liebigs Ann. Chem. 647: 167 173.
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: 972 978.
137. Polson, A.,, B. Bass,, and J. Casey. 1996. RNA editing of hepatitis delta virus antigenome by dsRNA-adenosine deaminase. Nature (London) 380: 454 456.
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: 11507 11514.
139. Polson, A. G.,, and B. L. Bass. 1994. Preferential selection of adenosines for modification by double-stranded RNA adenosine deaminase. EMBO J. 13: 5701 5711.
140. Poulter, C. D.,, and H. C. Rilling. 1976. Prenyltransferase: the mechanism of the reaction. Biochemistry 15: 1079 1083.
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: 5470 5478.
142. Poulter, C. D.,, D. M. Satterwhite,, and H. C. Rilling. 1976. Prenyltransferase. The mechanism of the reaction. J. Am. Chem. Soc. 98: 3376 3377, (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: 831 838.
144. Powers, S. G.,, and A. Meister. 1978. Mechanism of the reaction catalyzed by carbamyl phosphate synthetase. J. Biol. Chem. 253: 800 803.
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: 2429 2434.
146. Raushel, F. M.,, P. M. Anderson,, and J. J. Villafranca. 1978. Kinetic mechanism of Escherichia coli carbamoyl-phosphate synthetase. Biochemistry 17: 5587 5591.
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: 1131 1148.
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: 7041 7046.
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: 5284 5288.
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: 2256 2264.
151. Roberts, R. J. 1995. On base flipping. Cell 82: 9 12.
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: 1256 1261.
154. Romier, C.,, K. Reuter,, D. Suck,, and R. Ficner. 1996a. Crystal structure of tRNA-guanine transglycosylase: RNA modification by base exchange. EMBOJ. 15: 2850 2857.
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: 15734 15739.
156. Rosenbaum, N.,, and M. L. Gefter. 1972. δ 2-Isopentenylpyrophosphate: transfer ribonucleic acid δ 2-isopentenyltransferase from Escherichia coli. Purification and properties of the enzyme. J. Biol. Chem. 247: 5675 5680.
157. Rottman, F. M.,, J. A. Bokar,, P. Narayan, M. E. Shambaugh, and R. Ludwiczak. 1994. N 6-adenosine methylation in mRNA: substrate specificity and enzyme complexity. Biochimie 76: 1109 1114.
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: 291 297.
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: 355 367.
160. Rubio, V.,, H. G. Britton,, and S. Grisolia. 1979. Mechanism of carbamoyl phosphate synthetase. Eur. J. Biochem. 93: 245 256.
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: 1969 1974.
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: 1491 1494.
163. Santi, D. V.,, and L. W. Hardy. 1987. Catalytic mechanism and inhibition of tRNA-(uracil-5-)methyltransferase: evidence for covalent catalysis. Biochemistry 26: 8599 8606.
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: 467 470.
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: 487 493.
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: 695 714.
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: 1043 1051.
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: 2897 2901.
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: 20700 20706.
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: 334 343.
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: 24385 24389.
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: 8096 8100.
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: 88 101.
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: 3909 3920.
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: 2421 2426.
176. Singer, C. E.,, and G. R. Smith. 1972. Histidine regulation in Salmonella typhimurium. J. Biol. Chem. 247: 289 300.
177. Singer, C. E.,, G. R. Smith,, R. Cortese,, and B. N. Ames. 1972. Mutant tRNA Hls ineffective in repression and lacking two pseudouridine modifications. Nat. New Biol. 238: 72 74.
178. Singhal, R. P. 1983. Queuine: an addendum. Prog. Nucleic Acids Res. Mol. Biol. 28: 75 80.
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: 7811 7817.
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: 221 228.
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: 1434 1440.
182. Söll, D.,, and L. Kline,. 1982. RNA methylation, p. 557 566. 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: 11 19.
184. Sprinzl, M.,, C. Steegborn,, F. Hubel,, and S. Steinberg. 1996. Compilation of tRNA sequences and sequences of tRNA genes. Nucleic Acids Res. 24: 68 72.
185. Stadtman, T. C. 1994. Emerging awareness of the critical roles of S-phosphocysteine and selenophosphate in biological systems. Biofactors 4: 181 185.
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: 368 376.
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: 4636 4644.
188. Thiebe, R.,, and K. Poralla. 1973. Origin of the nucleoside Y in yeast tRNA plu'. FEBS Lett. 38: 27 28.
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: 199 207.
190. Ueland, P. M. 1982. Pharmacological and biochemical aspects of S-adenosylhomocysteine and S-adenosylhomocysteine hydrolase. Pharmacol. Rev. 34: 223 246.
191. Veres, Z.,, I. Y. Kim,, T. D. Scholz,, and T. C. Stadtman. 1994. Selenophosphate synthetase. J. Biol. Chem. 269: 10597 10603.
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: 8092 8096.
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: 2975 2979.
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: 869 876.
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: 20146 20151.
197. Wilson, D.,, and F. Quiocho. 1994. Crystallographic observation of a trapped tetrahedral intermediate in a metalloenzyme. Nat. Struct. Biol. 1: 691 694.
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: 1278 1284.
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: 540 550.
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: 2376 2386.
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 tRNA Phe. RNA 1: 437 448.
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: 8904 8913.
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: 4768 4774.
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: 141 142.
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: 1128 1133.
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: 77 81.
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: 18227 18233.
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: 1950 1955.

Tables

Generic image for table
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

This is a required field
Please enter a valid email address
Please check the format of the address you have entered.
Approval was a Success
Invalid data
An Error Occurred
Approval was partially successful, following selected items could not be processed due to error