tRNA Integrity Is a Prerequisite for Rapid CCA Addition: Implication for Quality Control

Journal of Molecular Biology

Volumn 379, Issue 3, 2008, Pages 579-588

  Dupasquier, Marcel ^a   Kim, Sangbumn ^a   Halkidis, Konstantine ^a   Gamper, Howard ^a   Hou, Ya Ming ^a  

^a THOMAS JEFFERSON UNIVERSITY   (United States)

Author keywords

kinetic quality control; single turnover kinetics; tRNA surveillance

Indexed keywords

BACTERIAL ENZYME; TRANSFER RIBONUCLEIC ACID NUCLEOTIDYLTRANSFERASE; TRANSFER RNA;

ADDITION REACTION; ARTICLE; CONTROLLED STUDY; CRYSTAL STRUCTURE; ESCHERICHIA COLI; KINETICS; NONHUMAN; PRIORITY JOURNAL; PROTEIN DOMAIN;

ESCHERICHIA COLI;

EID: 43449087645     PISSN: 00222836     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.jmb.2008.04.005     Document Type: Article

References (51)

1. Deutscher M.P. tRNA nucleotidyltransferase Enzymes 15 1982 183 215
2. Aebi M. Kirchner G. Chen J.Y. Vijayraghavan U. Jacobson A. Martin N.C. Abelson J. 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 1990 16216 16220
3. Yue D. Maizels N. Weiner A.M. 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 1996 895 908
4. Yue D. Weiner A.M. Maizels N. The CCA-adding enzyme has a single active site J. Biol. Chem. 273 1998 29693 29700
5. Li F. Xiong Y. Wang J. Cho H.D. Tomita K. Weiner A.M. Steitz T.A. Crystal structures of the Bacillus stearothermophilus CCA-adding enzyme and its complexes with ATP or CTP Cell 111 2002 815 824
6. Xiong Y. Li F. Wang J. Weiner A.M. Steitz T.A. Crystal structures of an archaeal class I CCA-adding enzyme and its nucleotide complexes Mol. Cell 12 2003 1165 1172
7. Okabe M. Tomita K. Ishitani R. Ishii R. Takeuchi N. Arisaka F. Divergent evolutions of trinucleotide polymerization revealed by an archaeal CCA-adding enzyme structure EMBO J. 22 2003 5918 5927
8. Augustin M.A. Reichert A.S. Betat H. Huber R. Morl M. Steegborn C. Crystal structure of the human CCA-adding enzyme: insights into template-independent polymerization J. Mol. Biol. 328 2003 985 994
9. Xiong Y. Steitz T.A. Mechanism of transfer RNA maturation by CCA-adding enzyme without using an oligonucleotide template Nature 430 2004 640 645
10. Tomita K. Fukai S. Ishitani R. Ueda T. Takeuchi N. Vassylyev D.G. Nureki O. Structural basis for template-independent RNA polymerization Nature 430 2004 700 704
11. Tomita K. Ishitani R. Fukai S. Nureki O. Complete crystallographic analysis of the dynamics of CCA sequence addition Nature 443 2006 956 960
12. Shi P.Y. Maizels N. Weiner A.M. CCA addition by tRNA nucleotidyltransferase: polymerization without translocation? EMBO J. 17 1998 3197 3206
13. Cho H.D. Chen Y. Varani G. Weiner A.M. A model for C74 addition by CCA-adding enzymes: C74 addition, like C75 and A76 addition, does not involve tRNA translocation J. Biol. Chem. 281 2006 9801 9811
14. Cho H.D. Verlinde C.L. Weiner A.M. Archaeal CCA-adding enzymes: central role of a highly conserved beta-turn motif in RNA polymerization without translocation J. Biol. Chem. 280 2005 9555 9566
15. Shi P.Y. Weiner A.M. Maizels N. A top-half tDNA minihelix is a good substrate for the eubacterial CCA-adding enzyme RNA 4 1998 276 284
16. Seth M. Thurlow D.L. Hou Y.M. Poly(C) synthesis by class I and class II CCA-adding enzymes Biochemistry 41 2002 4521 4532
17. Hou Y.M. Gu S.Q. Zhou H. Ingerman L. Metal-ion-dependent catalysis and specificity of CCA-adding enzymes: a comparison of two classes Biochemistry 44 2005 12849 12859
18. Hou Y.M. Unusual synthesis by the Escherichia coli CCA-adding enzyme RNA 6 2000 1031 1043 [In Process Citation]
19. Anand V.S. Patel S.S. Transient state kinetics of transcription elongation by T7 RNA polymerase J. Biol. Chem. 281 2006 35677 35685
20. Yakunin A.F. Proudfoot M. Kuznetsova E. Savchenko A. Brown G. Arrowsmith C.H. Edwards A.M. The HD domain of the Escherichia coli tRNA nucleotidyltransferase has 2′,3′-cyclic phosphodiesterase, 2′-nucleotidase, and phosphatase activities J. Biol. Chem. 279 2004 36819 36827
21. Yap L.P. Stehlin C. Musier-Forsyth K. Use of semi-synthetic transfer RNAs to probe molecular recognition by Escherichia coli proline-tRNA synthetase Chem. Biol. 2 1995 661 666
22. Liu H. Peterson R. Kessler J. Musier-Forsyth K. Molecular recognition of tRNA(Pro) by Escherichia coli proline tRNA synthetase in vitro Nucleic Acids Res. 23 1995 165 169
23. Sherlin L.D. Bullock T.L. Nissan T.A. Perona J.J. Lariviere F.J. Uhlenbeck O.C. Scaringe S.A. Chemical and enzymatic synthesis of tRNAs for high-throughput crystallization RNA 7 2001 1671 1678
24. Nandakumar J. Shuman S. Dual mechanisms whereby a broken RNA end assists the catalysis of its repair by T4 RNA ligase 2 J. Biol. Chem. 280 2005 23484 23489
25. Fukai S. Nureki O. Sekine S. Shimada A. Tao J. Vassylyev D.G. Yokoyama S. Structural basis for double-sieve discrimination of l -valine from l -isoleucine and l -threonine by the complex of tRNA(Val) and valyl-tRNA synthetase Cell 103 2000 793 803
26. Phe Biochemistry 27 1988 5771 5777
27. Phe mutants Biochemistry 29 1990 2515 2523
28. Cho H.D. Oyelere A.K. Strobel S.A. Weiner A.M. Use of nucleotide analogs by class I and class II CCA-adding enzymes (tRNA nucleotidyltransferase): deciphering the basis for nucleotide selection RNA 9 2003 970 981
29. Alexandrov A. Chernyakov I. Gu W. Hiley S.L. Hughes T.R. Grayhack E.J. Phizicky E.M. Rapid tRNA decay can result from lack of nonessential modifications Mol. Cell 21 2006 87 96
30. Ogawa T. Tomita K. Ueda T. Watanabe K. Uozumi T. Masaki H. A cytotoxic ribonuclease targeting specific transfer RNA anticodons Science 283 1999 2097 2100
31. Lu J. Huang B. Esberg A. Johansson M.J. Bystrom A.S. The Kluyveromyces lactis gamma-toxin targets tRNA anticodons RNA 11 2005 1648 1654
32. Ho C.K. Rauhut R. Vijayraghavan U. Abelson J. Accumulation of pre-tRNA splicing ‘2/3’ intermediates in a Saccharomyces cerevisiae mutant EMBO J. 9 1990 1245 1252
33. Li Z. Reimers S. Pandit S. Deutscher M.P. RNA quality control: degradation of defective transfer RNA EMBO J. 21 2002 1132 1138
34. Met in S. cerevisiae Genes Dev. 18 2004 1227 1240
35. Deutscher M.P. Degradation of RNA in bacteria: comparison of mRNA and stable RNA Nucleic Acids Res. 34 2006 659 666
36. Wegscheid B. Hartmann R.K. The precursor tRNA 3′-CCA interaction with Escherichia coli RNase P RNA is essential for catalysis by RNase P in vivo RNA 12 2006 2135 2148
37. Wegscheid B. Hartmann R.K. In vivo and in vitro investigation of bacterial type B RNase P interaction with tRNA 3′-CCA Nucleic Acids Res. 35 2007 2060 2073
38. Lund E. Dahlberg J.E. Proofreading and aminoacylation of tRNAs before export from the nucleus [see comments] Science 282 1998 2082 2085
39. Sarkar S. Azad A.K. Hopper A.K. Nuclear tRNA aminoacylation and its role in nuclear export of endogenous tRNAs in Saccharomyces cerevisiae Proc. Natl Acad. Sci. USA 96 1999 14366 14371
40. Grosshans H. Hurt E. Simos G. An aminoacylation-dependent nuclear tRNA export pathway in yeast Genes Dev. 14 2000 830 840
41. de Duve C. Transfer RNAs: the second genetic code Nature 333 1988 117 118
42. Weiner A.M. Maizels N. tRNA-like structures tag the 3′ ends of genomic RNA molecules for replication: implications for the origin of protein synthesis Proc. Natl Acad. Sci. USA 84 1987 7383 7387
43. McClain W.H. Guerrier-Takada C. Altman S. Model substrates for an RNA enzyme Science 238 1987 527 530
44. Phe, EF-Tu, and a GTP analog [see comments] Science 270 1995 1464 1472
45. Cys–EF-Tu–GDPNP reveals general and specific features in the ternary complex and in tRNA Structure 7 1999 143 156
46. Keiler K.C. Waller P.R. Sauer R.T. Role of a peptide tagging system in degradation of proteins synthesized from damaged messenger RNA [see comments] Science 271 1996 990 993
47. Hou Y.M. Schimmel P. A simple structural feature is a major determinant of the identity of a transfer RNA Nature 333 1988 140 145
48. McClain W.H. Foss K. Changing the identity of a tRNA by introducing a G–U wobble pair near the 3′ acceptor end Science 240 1988 793 796
49. Francklyn C. Schimmel P. Aminoacylation of RNA minihelices with alanine Nature 337 1989 478 481
50. Holbrook S.R. Sussman J.L. Warrant R.W. Kim S.H. Crystal structure of yeast phenylalanine transfer RNA: II. Structural features and functional implications J. Mol. Biol. 123 1978 631 660
51. Cochella L. Green R. An active role for tRNA in decoding beyond codon:anticodon pairing Science 308 2005 1178 1180