tRNA transfers to the limelight

Genes and Development

Volumn 17, Issue 2, 2003, Pages 162-180

  Hopper, Anita K ^a   Phizicky, Eric M ^b  

^a PENN STATE COLLEGE OF MEDICINE   (United States)

^b UNIVERSITY OF ROCHESTER SCHOOL OF MEDICINE AND DENTISTRY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

AMINO ACID TRANSFER RNA LIGASE; GUANOSINE TRIPHOSPHATASE; MESSENGER RNA; RIBONUCLEASE P; TRANSFER RNA;

GENOMICS; MITOCHONDRION; NONHUMAN; PHENOTYPE; PRIORITY JOURNAL; REVIEW; RNA PROCESSING; RNA SPLICING; RNA TRANSLATION; SACCHAROMYCES CEREVISIAE; YEAST;

ACTIVE TRANSPORT, CELL NUCLEUS; ENDORIBONUCLEASES; GENES, FUNGAL; MITOCHONDRIA; MODELS, BIOLOGICAL; NUCLEIC ACID CONFORMATION; PROTEIN BIOSYNTHESIS; RIBONUCLEASE P; RNA EDITING; RNA PROCESSING, POST-TRANSCRIPTIONAL; RNA SPLICING; RNA, CATALYTIC; RNA, FUNGAL; RNA, TRANSFER; SACCHAROMYCES CEREVISIAE;

SACCHAROMYCES CEREVISIAE;

EID: 0037439213     PISSN: 08909369     EISSN: None     Source Type: Journal    
DOI: 10.1101/gad.1049103     Document Type: Review

References (174)

1. Alexandrov, A.V., Martzen, M.R., and Phizicky, E.M. 2002. Two proteins that form a complex are required for 7-methylguanosine modification of yeast tRNA. RNA 8: 1253-1266.
2. Trp allows decoding of the UGA stop codon in Leishmania tarentolae. EMBO J. 18: 7056-7062.
3. Anderson, J., Phan, L., Cuesta, R., Carlson, B.A., Pak, M., Asano, K., Björk, G.R., Tamame, M., and Hinnebusch, A.G. 1998. The essential Gcd10p-Gcd14p nuclear complex is required for 1-methyladenosine modification and maturation of initiator methionyl-tRNA. Genes & Dev. 12: 3650-3662.
4. Anderson, J., Phan, L., and Hinnebusch, A.G. 2000. The Gcd10p/Gcd14p complex is the essential two-subunit tRNA(1-methyladenosine) methyltransferase of Saccharomyces cerevisiae. Proc. Natl. Acad. Sci. 97: 5173-5178.
5. Ansmant, I., Motorin, Y., Massenet, S., Grosjean, H., and Branlant, C. 2001. Identification and characterization of the tRNA:Ψ 31-synthase (Pus6p) of Saccharomyces cerevisiae. J. Biol. Chem. 276: 34934-34940.
6. Antes, T., Costandy, H., Mahendran, R., Spottswood, M., and Miller, D. 1998. Insertional editing of mitochondrial tRNAs of Physarum polycephalum and Didymium nigripes. Mol. Cell. Biol. 18: 7521-7527.
7. Arts, G.J., Fomerod, M., and Mattaj, I.W. 1998a. Identification of a nuclear export receptor for tRNA. Curr. Biol. 8: 305-314.
8. Arts, G.J., Kuersten, S., Romby, P., Ehresmann, B., and Mattaj, I.W. 1998b. The role of exportin-t in selective nuclear export of mature tRNAs. EMBO J. 17: 7430-7441.
9. Åström, S.U. and Byström, A.S. 1994. Ritl, a tRNA backbone-modifying enzyme that mediates initiator and elongator tRNA discrimination. Cell 79: 535-546.
10. Åström, S.U., Nordlund, M.E., Erickson, F.L., Hannig, E.M., and Byström, A.S. 1999. Genetic interactions between a null allele of the RIT1 gene encoding an initiator tRNA-specific modification enzyme and genes encoding translation factors in Saccharomyces cerevisiae. Mol. Gen. Genet. 261: 967-976.
11. Azad, A.K., Stanford, D.R., Sarkar, S., and Hopper, A.K. 2001. Role of nuclear pools of aminoacyl-tRNA synthetases in tRNA nuclear export. Mol. Biol. Cell 12: 1381-1392.
12. Becker, H.F., Motorin, Y., Planta, R.J., and Grosjean, H, 1997. The yeast gene YNL292w encodes a pseudouridine synthase (Pus4) catalyzing the formation of psi55 in both mitochondrial and cytoplasmic tRNAs. Nucleic Acids Res. 25: 4493-4499.
13. Benko, A.L., Vaduva, G., Martin, N,C., and Hopper, A.K. 2000. Competition between a sterol biosynthetic enzyme and tRNA modification in addition to changes in the protein synthesis machinery causes altered nonsense suppression. Proc. Natl. Acad. Sci. 97: 61-66.
14. Bertrand, E., Houser-Scott, F., Kendall, A., Singer, R.H., and Engelke, D.R. 1998. Nucleolar localization of early tRNA processing. Genes & Dev. 12: 2463-2468.
15. Bhattacharyya, S.N., Chatterjee, S., and Adhya, S. 2002. Mitochondrial RNA import in Leishmania tropica: Aptamers homologous to multiple tRNA domains that interact cooperatively or antagonistically at the inner membrane. Mol. Cell. Biol. 22: 4372-4382.
16. Cys in mitochondria of Oenothera berteriana is initiated in precursor molecules. Mol. Gen. Genet. 244: 67-74.
17. Bishop, A.C., Xu, J., Johnson, R.C., Schimmel, P., and de Crecy-Lagard, V. 2002. Identification of the tRNA-dihydrouridine synthase family. J. Biol. Chem. 277: 25090-25095.
18. Björk, G.R. 1995. Biosynthesis and function of modified nucleosides. In tRNA: Structure, biosynthesis and function (eds. D. Söll and U.L. RajBhandary), pp. 165-205. ASM Press, Washington, D.C.
19. Björk, G.R., Jacobsson, K., Nilsson, K., Johansson, M.J., Byström, A.S., and Persson, O.P. 2001. A primordial tRNA modification required for the evolution of life? EMBO J. 20: 231-239.
20. Boguta, M., Hunter, L.A., Shen, W.C., Gillman, E.C., Martin, N.C., and Hopper, A.K. 1994. Subcellular locations of MOD5 proteins: Mapping of sequences sufficient for targeting to mitochondria and demonstration that mitochondrial and nuclear isoforms commingle in the cytosol. Mol. Cell. Biol. 14: 2298-2306.
21. Bohnsack, M.T., Regener, K., Schwappach, B., Saffrich, R., Paraskeva, E., Hartmann, E., and Görlich, D. 2002. Exp5 exports eEF1A via tRNA from nuclei and synergizes with other transport pathways to confine translation to the cytoplasm. EMBO J. 21: 6205-6215.
22. Brusca, E.M., True, H.L., and Celander, D.W. 2001. Novel RNA-binding properties of Pop3p support a role for eukaryotic RNase P protein subunits in substrate recognition. J. Biol. Chem. 276: 42543-42548.
23. Burger, G., Plante, I., Lonergan, K.M., and Gray, M.W. 1995. The mitochondrial DNA of the amoeboid protozoon, Acanthamoeba castellanii: Complete sequence, gene content and genome organization. J. Mol. Biol. 245: 522-537.
24. Cai, T., Aulds, J., Gill, T., Cerio, M., and Schmitt, M.E. 2002. The Saccharomyces cerevisiae RNase mitochondrial RNA processing is critical for cell cycle progression at the end of mitosis. Genetics 161: 1029-1042.
25. Calado, A., Treichel, N., Muller, E.C., Otto, A., and Kutay, U. 2002. Exportin-5-mediated nuclear export of eukaryotic elongation factor 1A and tRNA. EMBO J. 21: 6216-6224.
26. Calfon, M., Zeng, H., Urano, F., Till, J.H., Hubbard, S.R., Harding, H.P., Clark, S.G., and Ron, D. 2002. IRE1 couples endoplasmic reticulum load to secretory capacity by processing the XBP-1 mRNA. Nature 415: 92-96.
27. Calvo, O., Cuesta, R., Anderson, J., Gutierrez, N., Garcia-Barrio, M.T., Hinnebusch, A.G., and Tamame, M. 1999. GCD14p, a repressor of GCN4 translation, cooperates with Gcd10p and Lhp1p in the maturation of initiator methionyl-tRNA in Saccharomyces cerevisiae. Mol. Cell. Biol. 19: 4167-4181.
28. Carpousis, A.J., Vanzo, N.F., and Raynal, L.C. 1999. mRNA degradation. A tale of poly(A) and multiprotein machines. Trends Genet. 15: 24-28.
29. Cavaillé, J., Chetouani, F., and Bachellerie, J. P. 1999. The yeast Saccharomyces cerevisiae YDL112w ORF encodes the putative 2′-O-ribose methyltransferase catalyzing the formation of Gm18 in tRNAs. RNA 5: 66-81.
30. Chamberlain, J.R., Lee, Y., Lane, W.S., and Engelke, D.R. 1998. Purification and characterization of the nuclear RNase P holoenzyme complex reveals extensive subunit overlap with RNase MRP. Genes & Dev. 12: 1678-1690.
31. Clark, M.W. and Abelson, J. 1987. The subnuclear localization of tRNA ligase in yeast. J. Cell Biol. 105: 1515-1526.
32. Culver, G.M., McCraith, S.M., Zillmann, M., Kierzek, R., Michaud, N., LaReau, R.D., Turner, D.H., and Phizicky, E.M. 1993. An NAD derivative produced during transfer RNA splicing: ADP-ribose 1″-2″ cyclic phosphate. Science 261: 206-208.
33. Culver, G.M., McCraith, S.M., Consaul, S.A., Stanford, D.R., and Phizicky, E.M. 1997. A 2′-phosphotransferase implicated in tRNA splicing is essential in Saccharomyces cerevisiae. J. Biol. Chem. 272: 13203-13210.
34. Dahlberg, J.E., Lund, E., and Goodwin, E. 2003. Translation in the nucleus: What's the evidence? RNA (in press).
35. Del Campo, M., Kaya, Y., and Ofengand, J. 2001. Identification and site of action of the remaining four putative pseudouridine synthases in Escherichia coli. RNA 7: 1603-1615.
36. Deutscher, M.P. 1972. Reactions at the 3′ terminus of transfer ribonucleic acid. 3. Catalytic properties of two purified rabbit liver transfer ribonucleic acid nucleotidyl transferases. J. Biol. Chem. 247: 459-468.
37. Dihanich, M.E., Najarian, D., Clark, R., Gillman, E.C., Martin, N.C., and Hopper, A.K. 1987. Isolation and characterization of MOD5, a gene required for isopentenylation of cytoplasmic and mitochondrial tRNAs of Saccharomyces cerevisiae. Mol. Cell. Biol. 7: 177-184; Erratum 7: 2035.
38. Trp. Nucleic Acids Res. 29: 4518-4529.
39. 2-dimethylguanosine, N- dimethylguanosine modification of both mitochondrial and cytoplasmic tRNA in Saccharomyces cerevisiae. J. Biol. Chem. 261: 9703-9709.
40. Lys for its import into yeast mitochondria. Proc. Natl. Acad. Sci. 95: 2838-2843.
41. Entelis, N.S., Kolesnikova, O.A., Martin, R.P., and Tarassov, I.A. 2001. RNA delivery into mitochondria. Adv. Drug Deliv. Rev. 49: 199-215.
42. Ser contains an intervening sequence. Cell 18: 11-26.
43. Fabbri, S., Fruscoloni, P., Bufardeci, E., Di Nicola Negri, E., Baldi, M.I., Attardi, D.G., Mattoccia, E., and Tocchini-Valentini, G.P. 1998. Conservation of substrate recognition mechanisms by tRNA splicing endonucleases. Science 280: 284-286.
44. Feng, W. and Hopper, A.K. 2002. A Los1p-independent pathway for nuclear export of intronless tRNAs in Saccharomyces cerevisiae. Proc. Natl. Acad. Sci. 99: 5412-5417.
45. Filipowicz, W. and Shatkin, A.J. 1983. Origin of splice junction phosphate in tRNAs processed by HeLa cell extract. Cell 32: 547-557.
46. Galani, K., Grosshans, H., Deinert, K., Hurt, E.C., and Simos, G. 2001. The intracellular location of two aminoacyl-tRNA synthetases depends on complex formation with Arc1p. EMBO J. 20: 6889-6898.
47. Garcia-Barrio, M.T., Naranda, T., Vazquez de Aldana, C.R., Cuesta, R., Hinnebusch, A.G., Hershey, J.W., and Tamame, M. 1995. GCD10, a translational repressor of GCN4, is the RNA-binding subunit of eukaryotic translation initiation factor-3. Genes & Dev. 9: 1781-1796.
48. Gerber, A.P. and Keller, W. 1999. An adenosine deaminase that generates inosine at the wobble position of tRNAs. Science 286: 1146-1149.
49. Gerber, A., Grosjean, H., Melcher, T., and Keller, W. 1998. Tad1p, a yeast tRNA-specific adenosine deaminase, is related to the mammalian pre-mRNA editing enzymes ADAR1 and ADAR2. EMBO J. 17: 4780-4789.
50. Gomes, I. and Gupta, R. 1997. RNA splicing ligase activity in the archaeon Haloferax volcanii. Biochem. Biophys. Res. Comm. 237: 588-594.
51. Gonzalez, T.N., Sidrauski, C., Dorfler, S., and Walter, P. 1999. Mechanism of non-spliceosomal mRNA splicing in the unfolded protein response pathway. EMBO J. 18: 3119-3132.
52. Görlich, D. and Kutay, U. 1999. Transport between the cell nucleus and the cytoplasm. Annu. Rev. Cell Dev. Biol. 15: 607-660.
53. Grayhack, E.J. and Phizicky, E.M. 2001. Genomic analysis of biochemical function. Curr. Opin. Chem. Biol. 5: 34-39.
54. Grosjean, H., Szweykowska-Kulinska, Z., Motorin, Y., Fasiolo, F., and Simos, G. 1997. Intron-dependent enzymatic formation of modified nucleosides in eukaryotic tRNAs: A review. Biochimie 79: 293-302.
55. Grosshans, H., Hurt, E., and Simos, G. 2000. An aminoacylation-dependent nuclear tRNA export pathway in yeast. Genes & Dev. 14: 830-840.
56. Grosshans, H., Lecointe, F., Grosjean, H., Hurt, E., and Simos, G. 2001. Pus1p-dependent tRNA pseudouridinylation becomes essential when tRNA biogenesis is compromised in yeast. J. Biol. Chem. 276: 46333-46339.
57. Guerrier-Takada, C. and Altman, S. 1984. Catalytic activity of an RNA molecule prepared by transcription in vitro. Science 223: 285-286.
58. Gustafsson, C., Reid, R., Greene, P.J., and Santi, D.V. 1996. Identification of new RNA modifying enzymes by iterative genome search using known modifying enzymes as probes. Nucleic Acids Res. 24: 3756-3762.
59. Gutgsell, N., Englund, N., Niu, L., Kaya, Y., Lane, B.G., and Ofengand, J. 2000. Deletion of the Escherichia coli pseudouridine synthase gene truB blocks formation of pseudouridine 55 in tRNA in vivo, does not affect exponential growth, but confers a strong selective disadvantage in competition with wild-type cells. RNA 6: 1870-1881.
60. Gwizdek, C., Bertrand, E., Dargemont, C., Lefebvre, J.C., Blanchard, J.M., Singer, R.H., and Doglio, A. 2001. Terminal minihelix, a novel RNA motif that directs polymerase III transcripts to the cell cytoplasm. Terminal minihelix and RNA export. J. Biol. Chem. 276: 25910-25918.
61. Hellmuth, K., Lau, D.M., Bischoff, F.R., Kunzler, M., Hurt, E., and Simos, G. 1998. Yeast Los1p has properties of an exportin-like nucleocytoplasmic transport factor for tRNA. Mol. Cell. Biol. 18: 6374-6386.
62. Hellmuth, K., Grosjean, H., Motorin, Y., Deinert, K., Hurt, E., and Simos, G. 2000. Cloning and characterization of the Schizosaccharomyces pombe tRNA:pseudouridine synthase Puslp. Nucleic Acids Res. 28: 4604-4610.
63. Ho, C.K., Rauhut, R., Vijayraghavan, U., and Abelson, J. 1990. Accumulation of pre-tRNA splicing ′2/3′ intermediates in a Saccharomyces cerevisiae mutant. EMBO J. 9: 1245-1252.
64. Hopper, A.K., Banks, F., and Evangelides, V. 1978. A yeast mutant which accumulates precursor tRNAs. Cell 14: 211-219.
65. Hopper, A.K., Schultz, L.D., and Shapiro, R.A. 1980. Processing of intervening sequences: A new yeast mutant which fails to excise intervening sequences from precursor tRNAs. Cell 19: 741-751.
66. Hopper, A.K., Furukawa, A.H., Pham, H.D., and Martin, N.C. 1982. Defects in modification of cytoplasmic and mitochondrial transfer RNAs are caused by single nuclear mutations. Cell 28: 543-550.
67. Hou, Y.M. 2000. Unusual synthesis by the Escherichia coli CCA-adding enzyme. RNA 6: 1031-1043.
68. Houser-Scott, F., Xiao, S., Millikin, C.E., Zengel, J.M., Lindahl, L., and Engelke, D.R. 2002. Interactions among the protein and RNA subunits of Saccharomyces cerevisiae nuclear RNase P. Proc. Natl. Acad. Sci. 99: 2684-2689.
69. Hurt, D.J., Wang, S.S., Lin, Y.H., and Hopper, A.K. 1987. Cloning and characterization of LOS1, a Saccharomyces cerevisiae gene that affects tRNA splicing. Mol. Cell. Biol. 7: 1208-1216.
70. Intine, R.V., Dundr, M., Misteli, T., and Maraia, R.J. 2002. Aberrant nuclear trafficking of La protein leads to disordered processing of associated precursor tRNAs. Mol. Cell 9: 1113-1123.
71. Ishigaki, Y., Li, X., Serin, G., and Maquat, L.E. 2001. Evidence for a pioneer round of mRNA translation: mRNAs subject to nonsense-mediated decay in mammalian cells are bound by CBP80 and CBP20. Cell 106: 607-617.
72. Janke, A. and Paabo, S. 1993. Editing of a tRNA anticodon in marsupial mitochondria changes its codon recognition. Nucleic Acids Res. 21: 1523-1525.
73. Jarrous, N. 2002. Human ribonuclease P: Subunits, function, and intranuclear localization. RNA 8: 1-7.
74. 5U54)methyltransferase in tRNA maturation. RNA 8: 324-335.
75. Tyr gene intron is essential for correct modification of its tRNA product. Nature 302: 681-687.
76. Kleman-Leyer, K., Armbruster, D.W., and Daniels, C.J. 1997. Properties of H. volcanii tRNA intron endonuclease reveal a relationship between the archaeal and eucaryal tRNA intron processing systems. Cell 89: 839-847.
77. Ko, Y.G., Kang, Y.S., Kim, E.K., Park, S.G., and Kim, S. 2000. Nucleolar localization of human methionyl-tRNA synthetase and its role in ribosomal RNA synthesis. J. Cell Biol. 149: 567-574.
78. Kolesnikova, O.A., Entelis, N.S., Mireau, H., Fox, T.D., Martin, R.P., and Tarassov, I.A. 2000. Suppression of mutations in mitochondrial DNA by tRNAs imported from the cytoplasm. Science 289: 1931-1933.
79. Konarska, M., Filipowicz, W., and Gross, H.J. 1982. RNA ligation via 2′-phosphomonoester, 3′5′-phosphodiester linkage: Requirement of 2′,3′-cyclic phosphate termini and involvement of a 5′-hydroxyl polynucleotide kinase Proc. Natl. Acad. Sci. 79: 1474-1478.
80. 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.
81. Kuersten, S., Arts, G.J., Walther, T.C., Englmeier, L., and Matraj, I.W. 2002. Steady-state nuclear localization of exportin-t involves RanGTP binding and two distinct nuclear pore complex interaction domains. Mol. Cell. Biol. 22: 5708-5720.
82. Trp precedes 5′-processing. RNA (in press).
83. Kutay, U., Lipowsky, G., Izaurralde, E., Bischoff, F.R., Schwarzmaier, P., Hartmann, E., and Görlich, D. 1998. Identification of a tRNA-specific nuclear export receptor. Mol. Cell 1: 359-369.
84. Kuwabara, T., Warashina, M., Sano, M., Tang, H., Wong-Staal, F., Munekata, E., and Taira, K. 2001. Recognition of engineered tRNAs with an extended 3′ end by exportin-t (Xpo-t) and transport of tRNA-attached ribozymes to the cytoplasm in somatic cells. Biomacromolecules 2: 1229-1242.
85. Laski, F.A., Fire, A.Z., RajBhandary, U.L., and Sharp, P.A. 1983. Characterization of tRNA precursor splicing in mammalian extracts. J. Biol. Chem. 258: 11974-11980.
86. Laten, H., Gorman, J., and Bock, R.M. 1978. Isopentenyladenosine deficient tRNA from an antisuppressor mutant of Saccharomyces cerevisiae. Nucleic Acids Res. 5: 4329-4342.
87. Lavrov, D.V., Brown, W.M., and Boore, J.L. 2000. A novel type of RNA editing occurs in the mitochondrial tRNAs of the centipede Lithobius forficatus. Proc. Natl. Acad. Sci. 97: 13738-13742.
88. Lecointe, F., Simos, G., Sauer, A., Hurt, E.C., Motorin, Y., and Grosjean, H. 1998. Characterization of yeast protein Deg1 as pseudouridine synthase (Pus3) catalyzing the formation of Ψ 38 and Ψ 39 in tRNA anticodon loop. J. Biol. Chem. 273: 1316-1323.
89. Lemieux, J., Lakowski, B., Webb, A., Meng, Y., Ubach, A., Bussiere, F., Barnes, T., and Hekimi, S. 2001. Regulation of physiological rates in Caenorhabditis elegans by a tRNA-modifying enzyme in the mitochondria. Genetics 159: 147-157.
90. 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.
91. Li, H., Trotta, C.R., and Abelson, J. 1998a. Crystal structure and evolution of a transfer RNA splicing enzyme. Science 280: 279-284.
92. 2-dimethyl-guanosine-specific tRNA methyltransferase contains both nuclear and mitochondrial targeting signals in Saccharomyces cerevisiae. J. Cell Biol. 109: 1411-1419.
93. 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.
94. 1996. Maturation pathways for E. coli tRNA precursors: A random multienzyme process in vivo. Cell 86: 503-512.
95. 2002. RNase E plays an essential role in the maturation of Escherichia coli tRNA precursors. RNA 8: 97-109.
96. Li, Z., Pandit, S., and Deutscher, M.P. 1998b. Polyadenylation of stable RNA precursors in vivo. Proc. Natl. Acad. Sci. 95: 12158-12162.
97. Li, Z., Reimers, S., Pandit, S., and Deutscher, M.P. 2002. RNA quality control: Degradation of defective transfer RNA. EMBO J. 21: 1132-1138.
98. Lipowsky, G., Bischoff, F.R., Izaurralde, E., Kutay, U., Schafer, S., Gross, H.J., Beier, H., and Görlich, D. 1999. Coordination of tRNA nuclear export with processing of tRNA. RNA 5: 539-549.
99. Lonergan, K.M. and Gray, M.W. 1993. Editing of transfer RNAs in Acanthamoeba castellanii mitochondria. Science 259: 812-816.
100. Lund, E. and Dahlberg, J.E. 1998. Proofreading and aminoacylation of tRNAs before export from the nucleus. Science 282: 2082-2085.
101. Lykke-Andersen, J. and Garrett, R.A. 1997. RNA-protein interactions of an archaeal homotetrameric splicing endoribo-nuclease with an exceptional evolutionary history. EMBO J. 16: 6290-6300.
102. Maniatis, T. and Reed, R. 2002. An extensive network of coupling among gene expression machines. Nature 416: 499-506.
103. Maraia, R.J. and Intine, R.V. 2002. La protein and its associated small nuclear and nucleolar precursor RNAs. Gene Expr. 10: 41-57.
104. Phe from precursors in plant mitochondria. J. Biol, Chem. 271: 1898-1903.
105. Marechal-Drouard, L., Ramamonjisoa, D., Cosset, A., Weil, J.H., and Dietrich, A. 1993. Editing corrects mispairing in the acceptor stem of bean and potato mitochondrial phenylalanine transfer RNAs. Nucleic Acids Res. 21: 4909-4914.
106. Marechal-Drouard, L., Cosset, A., Remacle, C., Ramamonjisoa, D., and Dietrich, A. 1996a. A single editing event is a prerequisite for efficient processing of potato mitochondrial phenylalanine tRNA. Mol. Cell. Biol. 16: 3504-3510.
107. His precursors is a prerequisite for processing. Nucleic Acids Res. 24: 3229-3234.
108. Martzen, M.R., McCraith, S.M., Spinelli, S.L., Torres, F.M., Fields, S., Grayhack, E.J., and Phizicky, E.M. 1999. A biochemical genomics approach for identifying genes by the activity of their products. Science 286: 1153-1155.
109. Massenet, S., Motorin, Y., Lafontaine, D.L., Hurt, E.C., Grosjean, H., and Branlant, C. 1999. Pseudouridine mapping in the Saccharomyces cerevisiae spliceosomal U small nuclear RNAs (snRNAs reveals that pseudouridine synthase pus1p exhibits a dual substrate specificity for U2 sn-RNA and tRNA. Mol, Cell. Biol. 19: 2142-2154.
110. Melton, D.A., De Robertis, E.M., and Cortese, R. 1980. Order and intracellular location of the events involved in the maturation of a spliced tRNA. Nature 284: 143-148.
111. 5C-methyltransferase (Trm4) in yeast Saccharomyces cerevisiae: Identification of the gene and substrate specificity of the enzyme. RNA 5: 1105-1118.
112. Motorin, Y., Bec, G., Tewari, R., and Grosjean, H. 1997. Transfer RNA recognition by the Escherichia coli Δ2-isopentenyl-pyrophosphate:tRNA Δ2-isopentenyl transferase: Dependence on the anticodon arm structure. RNA 3: 721-733.
113. Motorin, Y., Keith, G., Simon, C., Foiret, D., Simos, G., Hurt, E., and Grosjean, H. 1998. The yeast tRNA:pseudouridine synthase Pus1p displays a multisite substrate specificity. RNA 4: 856-869.
114. Nathanson, L. and Deutscher, M.P. 2000. Active aminoacyl-tRNA synthetases are present in nuclei as a high molecular weight multienzyme complex. J. Biol. Chem. 275: 31559-31562.
115. Nishikura, K. and De Robertis, E.M. 1981. RNA processing in microinjected Xenopus oocytes. Sequential addition of base modifications in the spliced transfer RNA. J. Mol. Biol. 145: 405-420.
116. Niwa, M., Sidrauski, C., Kaufman, R.J., and Walter, P. 1999. A role for presenilin-1 in nuclear accumulation of Ire1 fragments and induction of the mammalian unfolded protein response. Cell 99: 691-702.
117. 5U54)methyltransferase of Saccharomyces cerevisiae. RNA 6: 844-860.
118. O'Connor, J.P. and Peebles, C.L. 1991. In vivo pre-tRNA processing in Saccharomyces cerevisiae. Mol. Cell. Biol. 11: 425-439.
119. O'Hara, E.B., Chekanova, J.A., Ingle, C.A., Kushner, Z.R., Peters, E., and Kushner, S.R. 1995. Polyadenylylation helps regulate mRNA decay in Escherichia coli. Proc. Natl. Acad. Sci. 92: 1807-1811.
120. Ow, M.C. and Kushner, S.R. 2002. Initiation of tRNA maturation by RNase E is essential for cell viability in E. coli. Genes & Dev. 16: 1102-1115.
121. Papadimitriou, A. and Gross, H.J. 1996. Pre-tRNA 3′-processing in Saccharomyces cerevisiae. Purification and characterization of exo- and endoribonucleases. Eur. J. Biochem. 242: 747-759.
122. Peebles, C.L., Ogden, R.C., Knapp, G., and Abelson, J. 1979. Splicing of yeast tRNA precursors: A two-stage reaction. Cell 18: 27-35.
123. Peebles, C.L., Gegenheimer, P., and Abelson, J. 1983. Precise excision of intervening sequences from precursor tRNAs by a membrane-associated yeast endonuclease. Cell 32: 525-536.
124. Persson, B.C., Gustafsson, C., Berg, D.E., and Bjork, G.R. 1992. The gene for a tRNA modifying enzyme, m5U54-methyl-transferase, is essential for viability in Escherichia coli. Proc. Natl. Acad. Sci. 89: 3995-3998.
125. Phillips, J.H. and Kjellin-Stråby, K. 1967. Studies on microbial ribonucleic acid. IV. Two mutants of Saccharomyces cerevisiae lacking N-2-dimethylguanine in soluble ribonucleic acid. J. Mol. Biol. 26: 509-518.
126. Phizicky, E.M., Consaul, S.A., Nehrke, K.W., and Abelson, J. 1992. Yeast tRNA ligase mutants are nonviable and accumulate tRNA splicing intermediates. J. Biol. Chem. 267: 4577-4582.
127. Pick, L. and Hurwitz, J. 1986. Purification of wheat germ RNA ligase. I. Characterization of a ligase-associated 5′-hydroxyl polynucleotide kinase activity. J. Bio]. Chem. 261: 6684-6693.
128. Pintard, L., Lecointe, F., Bujnicki, J.M., Bonnerot, C., Grosjean, H., and Lapeyre, B. 2002. Trm7p catalyses the formation of two 2′-O-methylriboses in yeast tRNA anticodon loop. EMBO J. 21: 1811-1820.
129. Price, D.H. and Gray, M.W. 1999. A novel nucleotide incorporation activity implicated in the editing of mitochondrial transfer RNAs in Acanthamoeba castellanii. RNA 5: 302-317.
130. Qiu, H., Hu, C., Anderson, J., Bjork, G.R., Sarkar, S., Hopper, A.K., and Hinnebusch, A.G. 2000. Defects in tRNA processing and nuclear export induce GCN4 translation independently of phosphorylation of the α subunit of eukaryotic translation initiation factor 2. Mol. Cell. Biol. 20: 2505-2516.
131. Raychaudhuri, S., Niu, L., Conrad, J., Lane, B.G., and Ofengand, J. 1999. Functional effect of deletion and mutation of the Escherichia coli ribosomal RNA and tRNA pseudouridine synthase RluA. J. Biol. Chem. 274: 18880-18886.
132. 2-dimethyl-guanosine-specific tRNA methyltransferase. Biochimie 77: 45-53.
133. Ruegsegger, U., Leber, J.H., and Walter, P. 2001. Block of HAC1 mRNA translation by long-range base pairing is released by cytoplasmic splicing upon induction of the unfolded protein response. Cell 107: 103-114.
134. Sarkar, S. and Hopper, A.K. 1998. tRNA nuclear export in Saccharomyces cerevisiae: In situ hybridization analysis. Mol. Biol. Cell 9: 3041-3055.
135. Sarkar, S., Azad, A.K., and Hopper, A.K. 1999. Nuclear tRNA aminoacylation and its role in nuclear export of endogenous tRNAs in Saccharomyces cerevisiae. Proc. Natl. Acad. Sci. 96: 14366-14371.
136. Schiffer, S., Rosch, S., and Marchfelder, A. 2002. Assigning a function to a conserved group of proteins: The tRNA 3′processing enzymes. EMBO J. 21: 2769-2777.
137. Schneider, A. and Marechal-Drouard, L. 2000. Mitochondrial tRNA import: Are there distinct mechanisms? Trends Cell Biol. 10: 509-513.
138. Sharma, K., Fabre, E., Tekotte, H., Hurt, E.C., and Tollervey, D. 1996. Yeast nucleoporin mutants are defective in pre-tRNA splicing. Mol. Cell. Biol. 16: 294-301.
139. Shen, W.C., Selvakumar, D., Stanford, D.R., and Hopper, A.K. 1993. The Saccharomyces cerevisiae LOS1 gene involved in pre-tRNA splicing encodes a nuclear protein that behaves as a component of the nuclear matrix. J. Biol. Chem. 268: 19436-19444.
140. Shi, P.Y., Maizels, N., and Weiner, A.M. 1998. CCA addition by tRNA nucleotidyltransferase: Polymerization without translocation? EMBO J. 17: 3197-3206.
141. Sidrauski, C. and Walter, P. 1997. The transmembrane kinase Irelp is a site-specific endonuclease that initiates mRNA splicing in the unfolded protein response. Cell 90: 1031-1039.
142. Sidrauski, C., Cox, J.S., and Walter, P. 1996. tRNA ligase is required for regulated mRNA splicing in the unfolded protein response. Cell 87: 405-413.
143. Simos, G., Tekotte, H., Grosjean, H., Segref, A., Sharma, K., Tollervey, D., and Hurt, E.C. 1996. Nuclear pore proteins are involved in the biogenesis of functional tRNA. EMBO J. 15: 2270-2284.
144. Smith, C.M. and Steitz, J.A. 1997. Sno storm in the nucleolus: New roles for myriad small RNPs. Cell 89: 799-809.
145. Spinelli, S.L., Consaul, S.A., and Phizicky, E.M. 1997. A conditional lethal yeast phosphotransferase [tpt1] mutant accumulates tRNAs with a 2′-phosphate and an undermodified base at the splice junction. RNA 3: 1388-1400.
146. Spinelli, S.L., Malik, H.S., Consaul, S.A., and Phizicky, E. M. 1998. A functional homolog of a yeast tRNA splicing enzyme is conserved in higher eukaryotes and in Escherichia coli. Proc. Natl. Acad. Sci. 95: 14136-14141.
147. Sprinzl, M., Horn, C., Brown, M., Ioudovitch, A., and Steinberg, S. 1998. Compilation of tRNA sequences and sequences of tRNA genes. Nucleic Acids Res. 26: 148-153.
148. Srisawat, C., Houser-Scott, F., Bertrand, E., Xiao, S., Singer, R.H., and Engelke, D.R. 2002. An active precursor in assembly of yeast nuclear ribonuclease P. RNA 8: 1348-1360.
149. Steiger, M.A., Kierzek, R., Turner, D.H., and Phizicky, E.M. 2001. Substrate recognition by a yeast 2′-phosphotransferase involved in tRNA splicing and by its Escherichia coli homolog. Biochemistry 40: 14098-14105.
150. lle. EMBO J. 13: 4636-4644.
151. Tan, T.H., Pach, R., Crausaz, A., Ivens, A., and Schneider, A. 2002. tRNAs in Trypanosoma brucei: Genomic organization, expression, and mitochondrial import. Mol. Cell. Biol. 22: 3707-3717.
152. Tavernarakis, N., Alexandraki, D., Liodis, P., Tzamarias, D., and Thireos, G. 1996. Gene overexpression reveals alternative mechanisms that induce GCN4 mRNA translation. Gene 179: 271-277.
153. Tolerico, L.H., Benko, A.L., Aris, J.P., Stanford, D.R., Martin, N.C., and Hopper, A.K. 1999. Saccharomyces cerevisiae Mod5p-II contains sequences antagonistic for nuclear and cytosolic locations. Genetics 151: 57-75.
154. 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.
155. Tyr. Nucleic Acids Res. 24: 4987-4991.
156. Trotta, C.R., Miao, F., Arn, E.A., Stevens, S.W., Ho, C.K., Rauhut, R., and Abelson, J.N. 1997. The yeast tRNA splicing endonuclease: A tetrameric enzyme with two active site subunits homologous to the archaeal tRNA endonucleases. Cell 89: 849-858.
157. Urbonavicius, J., Qian, Q., Durand, I.M., Hagervall, T.G., and Björk, G.R. 2001. Improvement of reading frame maintenance is a common function for several tRNA modifications. EMBO 1. 20: 4863-4873.
158. [Ser]Sec lacking isopente-nyladenosine. J. Biol. Chem. 275: 28110-28119.
159. Wolin, S.L. and Cedervall, T. 2002. The La protein. Annu. Rev. Biochem. 71: 375-403.
160. Wolin, S.L. and Matera, A.G. 1999. The trials and travels of tRNA. Genes & Dev. 13: 1-10.
161. Wu, P., Brockenbrough, J.S., Paddy, M.R., and Aris, J.P. 1998. NCL1, a novel gene for a non-essential nuclear protein in Saccharomyces cerevisiae. Gene 220: 109-117.
162. Xiao, S., Scott, F., Fierke, C.A., and Engelke, D.R. 2002. Eukaryotic ribonuclease P: A plurality of ribonucleoprotein enzymes. Annu. Rev. Biochem. 71: 165-189.
163. Xing, F., Martzen, M.R., and Phizicky, E.M. 2002. A conserved family of Saccharomyces cerevisiae synthases affects dihydrouridine modification of tRNA. RNA 8: 370-381.
164. Xu, F., Lin-Chao, S., and Cohen, S.N. 1993. The Escherichia coli pcnB gene promotes adenylylation of antisense RNAI of Co1E1-type plasmids in vivo and degradation of RNA I decay intermediates. Proc. Natl. Acad. Sci. 90: 6756-6760.
165. Yermovsky-Kammerer, A.E. and Hajduk, S.L. 1999. In vitro import of a nuclearly encoded tRNA into the mitochondrion of Trypanosoma brucei. Mol. Cell. Biol. 19: 6253-6259.
166. Yokobori, S. and Paabo, S. 1995a. Transfer RNA editing in land snail mitochondria. Proc. Natl. Acad. Sci. 92: 10432-10435.
167. 1995b. tRNA editing in metazoans. Nature 377: 490.
168. Tyr. J. Mol. Biol. 265: 95-99.
169. Yoo, C.J. and Wolin, S.L. 1997. The yeast La protein is required for the 3′ endonucleolytic cleavage that matures tRNA precursors. Cell 89: 393-402.
170. Yue, D., Weiner, A.M., and Maizels, N. 1998. The CCA-adding enzyme has a single active site. J. Biol. Chem. 273: 29693-29700.
171. Yukawa, Y., Fan, H., Akama, K., Beier, H., Gross, H.L., and Sugiura, M. 2001. A tobacco nuclear extract supporting transcription, processing, splicing and modification of plant introncontaining tRNA precursors. Plant J. 28: 583-594.
172. Zillman, M., Gorovsky, M.A., and Phizicky, E.M. 1991. Conserved mechanism of tRNA splicing in eukaryotes. Mol. Cell. Biol. 11: 5410-5416.
173. 1992. HeLa cells contain a 2′-phosphate-specific phosphotransferase similar to a yeast enzyme implicated in tRNA splicing. J. Biol. Chem. 267: 10289-10294.
174. Zofallova, L., Guo, Y., and Gupta, R. 2000. Junction phosphate is derived from the precursor in the tRNA spliced by the archaeon Haloferax volcanii cell extract. RNA 6: 1019-1030.