Use of nucleotide analogs by class I and class II CCA-adding enzymes (tRNA nucleotidyltransferase): Deciphering the basis for nucleotide selection

RNA

Volumn 9, Issue 8, 2003, Pages 970-981

  Cho, Hyundae D ^a   Oyelere, Adegboyega K ^b   Strobel, Scott A ^b   Weiner, Alan M ^a  

^a UNIVERSITY OF WASHINGTON SCHOOL OF MEDICINE   (United States)

^b YALE UNIVERSITY   (United States)

Author keywords

Chemogenetics; Collaborative templating; Nucleotide analogs; Nucleotidyltransferase; Scrunching; tRNA

Indexed keywords

2 AMINOPURINE; 2' DEOXY 2' FLUOROADENOSINE; 2' O METHYLADENOSINE; 6 AZACYTIDINE; 6 N METHYLADENOSINE; ADENOSINE TRIPHOSPHATE DERIVATIVE; AZAURIDINE; CYTIDINE TRIPHOSPHATE DERIVATIVE; DEOXYADENOSINE; DIAMINOPURINE; GUANOSINE; INOSINE; NUCLEOTIDE DERIVATIVE; NUCLEOTIDYLTRANSFERASE; PSEUDOISOCYTIDINE; PURINE; TRANSFER RIBONUCLEIC ACID NUCLEOTIDYLTRANSFERASE; TRANSFER RNA; TUBERCIDIN; UNCLASSIFIED DRUG; ZEBULARINE;

ARTICLE; ENZYME ACTIVITY; MOLECULAR DYNAMICS; PRIORITY JOURNAL; STEREOCHEMISTRY;

BASE SEQUENCE; DNA PRIMERS; NUCLEOTIDES; RNA NUCLEOTIDYLTRANSFERASES; STEREOISOMERISM;

EID: 0042808424     PISSN: 13558382     EISSN: None     Source Type: Journal    
DOI: 10.1261/rna.2110903     Document Type: Article

References (57)

1. Abramovitz, D.L., Friedman, R.A., and Pyle, A.M. 1996. Catalytic role of 2′-hydroxyl groups within a group II intron active site. Science 271: 1410-1413.
2. Aebi, M., Kirchner, G., Chen, J.Y., Vijayraghavan, U., Jacobson, A., Martin, N.C., and Abelson, J. 1990. Isolation of a temperature-sensitive mutant with an altered tRNA nucleotidyltransferase and cloning of the gene encoding tRNA nucleotidyltransferase in the yeast Saccharomyces cerevisiae. J. Biol. Chem. 265: 16216-16220.
3. Armstrong, V.W., Dattagupta, J.K., Eckstein, F., and Saenger, W. 1976. The base catalysed anomerisation of β-5-formyluridine; crystal and molecular structure of α-5-formyluridine. Nucleic Acids Res. 3: 1791-1780.
4. Cho, H.D., Tomita, K., Suzuki, T., and Weiner, A.M. 2002. U2 small nuclear RNA is a substrate for the CCA-adding enzyme (tRNA nucleotidyltransferase). J. Biol. Chem. 277: 3447-3455.
5. Cramer, F., Faulhammer, H., von der Haar, F., Sprinzl, M., and Sternbach, H. 1975. Aminoacyl-tRNA synthetases from baker's yeast: Reacting site of enzymatic aminoacylation is not uniform for all tRNAs. FEBS Lett. 56: 212-214.
6. Deutscher, M.P. 1972. Reactions at the 3′ terminus of transfer ribonucleic aid. IV. Extents of normal and anomalous nucleotide incorporation catalyzed by transfer ribonucleic acid nucleotidyltransferase. J. Biol. Chem. 247: 469-480.
7. -. 1982. tRNA nucleotidyltransferase. The Enzymes 15: 183-215.
8. Doublie, S., Tabor, S., Long, A.M., Richardson, C.C., and Ellenberger, T. 1998. Crystal structure of a bacteriophage T7 DNA replication complex at 2.2 Å resolution. Nature 391: 251-258.
9. Eckstein, F. 1985. Nucleoside phosphorothioates. Annu. Rev. Biochem. 54: 367-402.
10. Eckstein, F. and Gish, G. 1989. Phosphorothioates in molecular biology. Trends Biochem. Sci. 14: 97-100.
11. Eckstein, F. and Thomson, J.B. 1995. Phosphate analogs for study of DNA polymerases. Methods Enzymol. 262: 189-202.
12. Eckstein, F., Romaniuk, P.J., and Connolly, B.A. 1982. Stereochemistry of enzymic phosphoryl and nucleotidyl transfer. Methods Enzymol. 87: 197-212.
13. Eom, S.H., Wang, J., and Steitz, T.A. 1996. Structure of Taq polymerase with DNA at the polymerase active site. Nature 382: 278-281.
14. Fraser, T.H. and Rich, A. 1973. Synthesis and aminoacylation of 3′-amino-3′-deoxy transfer RNA and its activity in ribosomal protein synthesis. Proc. Natl. Acad. Sci. 70: 2671-2675.
15. -. 1975. Amino acids are not all initially attached to the same position on transfer RNA molecules. Proc. Natl. Acad. Sci. 72: 3044-3048.
16. Gaur, R.K. and Krupp, G. 1993. Enzymatic RNA synthesis with deoxynucleoside 5′-O-(1-thiotriphosphates). FEBS Lett. 315: 56-60.
17. Guo, M.J., Hildbrand, S., Leumann, C.J., McLaughlin, L.W., and Waring, M.J. 1998. Inhibition of DNA polymerase reactions by pyrimidine nucleotide analogues lacking the 2-keto group. Nucleic Acids Res. 26: 1863-1869.
18. Hardt, W.D., Erdmann, V.A., and Hartmann, R.K. 1996. Rp-deoxyphosphorothioate modification interference experiments identify 2′-OH groups in RNase P RNA that are crucial to tRNA binding. RNA 2: 1189-1198.
19. Hopper, A.K. 1998. Nuclear functions charge ahead. Science 282: 2003-2004.
20. Hou, Y.M. 2000. Unusual synthesis by the Escherichia coli CCA-adding enzyme. RNA 6: 1031-1043.
21. Knowles, J.R. 1980. Enzyme-catalyzed phosphoryl transfer reactions. Annu. Rev. Biochem. 49: 877-919.
22. Li, F., Wang, J., and Steitz, T.A. 2000. Sulfolobus shibatae CCA-adding enzyme forms a tetramer upon binding two tRNA molecules: A scrunching-shuttling model of CCA specificity. J. Mol. Biol. 304: 483-492.
23. Li, F., Xiong, Y., Wang, J., Cho, H.D., Tomita, K., Weiner, A.M., and Steitz, T.A. 2002. Crystal structures of the Bacillus stearothermophilus CCA-adding enzyme and its complexes with ATP or CTP. Cell 111: 815-824.
24. Li, Z. and Deutscher, M.P. 1994. The role of individual exoribonucleases in processing at the 3′ end of Escherichia coli tRNA precursors. J. Biol. Chem. 269: 6064-6071.
25. Li, Z., Pandit, S., and Deutscher, M.P. 1998. 3′ exoribonucleolytic trimming is a common feature of the maturation of small, stable RNAs in Escherichia coli. Proc. Natl. Acad. Sci. 95: 2856-2861.
26. Lund, E. and Dahlberg, J.E. 1998. Proofreading and aminoacylation of tRNAs before export from the nucleus. Science 282: 2082-2085.
27. Martin, G. and Keller, W. 1996. Mutational analysis of mammalian poly(A) polymerase identifies a region for primer binding and catalytic domain, homologous to the family X polymerases, and to other nucleotidyltransferases. EMBO J. 15: 2593-2603.
28. Martin, G., Jeno, P., and Keller, W. 1999. Mapping of ATP binding regions in poly(A) polymerases by photoaffinity labeling and by mutational analysis identifies a domain conserved in many nucleotidyltransferases. Protein Sci. 8: 2380-2391.
29. Martin, G., Keller, W., and Doublie, S. 2000. Crystal structure of mammalian poly(A) polymerase in complex with an analog of ATP. EMBO J. 19: 4193-4203.
30. Masiakowski, P., and Deutscher, M.P. 1980. Dissection of the active site of rabbit liver tRNA nucleotidyltransferase. Specificity and properties of the tRNA and acceptor subsites determined with model acceptor substrates. J. Biol. Chem. 255: 11233-11239.
31. Nagaike, T., Suzuki, T., Tomari, Y., Takemoto-Hori, C., Negayama, F., Watanabe, K., and Ueda, T. 2001. Identification and characterization of mammalian mitochondrial tRNA nucleotidyltransferases. J. Biol. Chem. 276: 40041-40049.
32. Oh, B.K. and Pace, N.R. 1994. Interaction of the 3′-end of tRNA with ribonuclease P RNA. Nucleic Acids Res. 22: 4087-4094.
33. Ortoleva-Donnelly, L., Szewczak, A.A., Gutell, R.R., and Strobel, S.A. 1998. The chemical basis of adenosine conservation throughout the Tetrahymena ribozyme. RNA 4: 498-519.
34. Romaniuk, P.J. and Eckstein, F. 1982. A study of the mechanism of T4 DNA polymerase with diastereomeric phosphorothioate analogues of deoxyadenosine triphosphate. J. Biol. Chem. 257: 7684-7688.
35. Ryder, S.P. and Strobel, S.A. 1999. Nucleotide analog interference mapping. Methods 18: 38-50.
36. Sawaya, M.R., Pelletier, H., Kumar, A., Wilson, S.H., and Kraut, J. 1994. Crystal structure of rat DNA polymerase β: Evidence for a common polymerase mechanism. Science 264: 1930-1935.
37. Secrist, J.A., 3rd, Barrio, J.R., and Leonard, N.J. 1972. A fluorescent modification of adenosine triphosphate with activity in enzyme systems: 1,N 6-ethenoadenosine triphosphate. Science 175: 646-647.
38. Seth, M., Thurlow, D.L., and Hou, Y.M. 2002. Poly(C) synthesis by class I and class II CCA-adding enzymes. Biochemistry 41: 4521-4532.
39. Shi, P.Y., Maizels, N., and Weiner, A.M. 1998a. CCA addition by tRNA nucleotidyltransferase: Polymerization without translocation? EMBO J. 17: 3197-3206.
40. Shi, P.Y., Weiner, A.M., and Maizels, N. 1998b. A top-half tDNA minihelix is a good substrate for the eubacterial CCA-adding enzyme. RNA 4: 276-284.
41. Sprinzl, M., and Cramer, F. 1979. The -C-C-A end of tRNA and its role in protein biosynthesis. Prog. Nucleic Acid Res. Mol. Biol. 22: 1-69.
42. phe with tRNA nucleotidyl transferase in vitro. Eur. J. Biochem. 25: 262-266.
43. Sprinzl, M., Scheit, K.H., and Cramer, F. 1973a. Preparation in vitro of a 2-thiocytidine-containing yeast tRNA Phe-A73-C74-S2C75-A76 and its interaction with p-hydroxymercuribenzoate. Eur. J. Biochem. 34: 306-310.
44. Sprinzl, M., Scheit, K.H., Sternbach, H., von der Haar, F., and Cramer, F. 1973b. In vitro in corporation of 2′-deoxyadenosine and 3′-deoxyadenosine into yeast tRNA Phe using t-RNA nucleotidyl transferase, and properties of tRNA Phe -C-C-2′dA and tRNA Phe-C-C-3′dA. Biochem. Biophys. Res. Commun. 51: 881-887.
45. Sprinzl, M., Sternbach, H., von der Haar, F., and Cramer, F. 1977. Enzymatic incorporation of ATP and CTP analogues into the 3′ end of tRNA. Eur. J. Biochem. 81: 579-589.
46. Steitz, T.A. 1998. A mechanism for all polymerases. Nature 391: 231-232.
47. Strobel, S.A. and Shetty, K. 1997. Defining the chemical groups essential for Tetrahymena group I intron function by nucleotide analog interference mapping. Proc. Natl. Acad. Sci. 94: 2903-2908.
48. Thurlow, D.L., Pulido, G.M., and Millar, K.J. 1997. Unidentified open reading frames in the genome of Methanococcus jannaschii are similar in sequence to an archaebacterial gene for tRNA nucleotidyltransferase. J. Mol. Evol. 44: 686-689.
49. Tomari, Y., Suzuki, T., Watanabe, K., and Ueda, T. 2000. The role of tightly bound ATP in Escherichia coli tRNA nucleotidyltransferase. Genes Cells 5: 689-698.
50. Tomita, K. and Weiner, A.M. 2001. Collaboration between CC- and A-adding enzymes to build and repair the 3′-terminal CCA of tRNA in Aquifex aeolicus. Science 294: 1334-1336.
51. Uretsky, S.C., Acs, G., Reich, E., Mori, M., and Altwerger, L. 1968. Pyrrolopyrimidine nucleotides and protein synthesis. J. Biol. Chem. 243: 306-312.
52. Ward, D.C., Cerami, A., Reich, E., Acs, G., and Altwerger, L. 1969. Biochemical studies of the nucleoside analogue, formycin. J. Biol. Chem. 244: 3243-3250.
53. Wolfe, C.L., Hopper, A.K., and Martin, N.C. 1996. Mechanisms leading to and the consequences of altering the normal distribution of ATP(CTP):tRNA nucleotidyltransferase in yeast. J. Biol. Chem. 271: 4679-4686.
54. Yue, D., Maizels, N., and Weiner, A.M. 1996. CCA-adding enzymes and poly(A) polymerases are all members of the same nucleotidyltransferase superfamily: Characterization of the CCA-adding enzyme from the archaeal hyperthermophile Sulfolobus shibatae. RNA 2: 895-908.
55. Yue, D., Weiner, A.M., and Maizels, N. 1998. The CCA-adding enzyme has a single active site. J. Biol. Chem. 273: 29693-29700.
56. Zachau, H.G. and Hertz, H.S. 1974. Lack of incorporation of 1:N6-ethenoadenosine triphosphate into yeast tRNAPhe and tRNASer under standard conditions. Eur. J. Biochem. 44: 289-291.
57. Zhu, L. and Deutscher, M.P. 1987. tRNA nucleotidyltransferase is not essential for Escherichia coli viability. EMBO J. 6: 2473-2477.