Novel Methyltransferase for Modified Uridine Residues at the Wobble Position of tRNA

Molecular and Cellular Biology

Volumn 23, Issue 24, 2003, Pages 9283-9292

  Kalhor, Hamid R ^a   Clarke, Steven ^a  

^a UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

5 METHYLCARBONYLMETHYL 2 THIOURIDINE; 5 METHYLCARBONYLMETHYLURIDINE; FUNGAL ENZYME; METHYLTRANSFERASE; PAROMOMYCIN; PROTEIN TRM9; TRANSFER RNA; UNCLASSIFIED DRUG; URIDINE DERIVATIVE;

ARTICLE; COMPLEX FORMATION; CONTROLLED STUDY; ENZYME ACTIVE SITE; ENZYME ACTIVITY; ENZYME ASSAY; ESTERIFICATION; GENE DISRUPTION; IN VIVO STUDY; NONHUMAN; PRIORITY JOURNAL; REACTION ANALYSIS; SACCHAROMYCES CEREVISIAE; YEAST CELL;

AMINO ACID SEQUENCE; BASE SEQUENCE; DNA, FUNGAL; GENE DELETION; GENES, FUNGAL; METHYLATION; MOLECULAR SEQUENCE DATA; MUTATION; PROTEIN BIOSYNTHESIS; RNA, FUNGAL; RNA, TRANSFER; RNA, TRANSFER, ARG; RNA, TRANSFER, GLU; SACCHAROMYCES CEREVISIAE; SACCHAROMYCES CEREVISIAE PROTEINS; SEQUENCE HOMOLOGY, AMINO ACID; SUBSTRATE SPECIFICITY; TEMPERATURE; TRNA METHYLTRANSFERASES; URIDINE;

SACCHAROMYCES; SACCHAROMYCES CEREVISIAE;

EID: 0345060040     PISSN: 02707306     EISSN: None     Source Type: Journal    
DOI: 10.1128/MCB.23.24.9283-9292.2003     Document Type: Article

References (59)

1. Agris, P. F., D. Setzer, and C. W. Gehrke. 1977. Characterization of a unique enzyme complex composed of S-adenosyl-L-methionine-tRNA-methyltransferase and aminoacyl-tRNA synthetase activities. Nucleic Acids Res. 4:38-43.
2. Agris, P. F., D. Soll, and T. Seno. 1973. Biological function of 2-thiouridine in Escherichia coli glutamic acid transfer ribonucleic acid. Biochemistry 12: 4331-4337.
3. Alexandrov, A., M. R. Martzen, and E. M. Phizicky. 2002. Two proteins that form a complex are required for 7-methylguanosine modification of yeast tRNA. RNA 8:1253-1266.
4. Anderson, J., L. Phan, and A. G. Hinnebusch. 2000. The Gcd10p/Gcd14p complex is the essential two-subunit tRNA(1-methyladenosine) methyltransferase of Saccharomyces cerevisiae. Proc. Natl. Acad. Sci. USA 97:5173-5178.
5. Avital, S., and D. Elson. 1969. A convenient procedure for preparing transfer ribonucleic acid from Escherichia coli. Biochim. Biophys. Acta. 179:297-307.
6. Baudin, A., O. Ozier-Kalogeropoulos, A. Denouel, F. Lacroute, and C. Cullin. 1993. A simple and efficient method for direct gene deletion in Saccharomyces cerevisiae. Nucleic Acids Res. 21:3329-3330.
7. Bennett, C. B., L. K. Lewis, G. Karthikeyan, K. S. Lobachev, Y. H. Jin, J. F. Sterling, J. R. Snipe, and M. A. Resnick. 2001. Genes required for ionizing radiation resistance in yeast. Nat. Genet. 29:426-434.
8. Björk, G. R., K. Jacobsson, K. Nilsson, M. J. Johansson, A. S. Bystrom, and O. P. Persson. 2001. A primordial tRNA modification required for the evolution of life? EMBO J. 20:231-239.
9. Cai, H., D. Dumlao, J. E. Katz, and S. Clarke. 2001. Identification of the gene and characterization of the activity of the trans-aconitate methyltransferase from Saccharomyces cerevisiae. Biochemistry 40:13699-13709.
10. Carter, A. P., W. M. Clemons, D. E. Brodersen, R. J. Morgan-Warren, B. T. Wimberly, and V. Ramakrishnan. 2000. Functional insights from the structure of the 30S ribosomal subunit and its interactions with antibiotics. Nature 407:340-348.
11. Cavaille, J., F. Chetouani, and J. P. Bachellerie. 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.
12. Chakraburtty, K. 1975. Primary structure of tRNA Arg II of E. coli. Nucleic Acids Res. 2:1787-1792.
13. Crick, F. H. 1966. Codon-anticodon pairing: the wobble hypothesis. J. Mol. Biol. 19:548-555.
14. 2-dimethylguanosine modification of both mitochondrial and cytoplasmic tRNA in Saccharomyces cerevisiae. J. Biol. Chem. 261:9703-9709.
15. Fujioka, M. 1992. Mammalian small molecule methyltransferases: their structural and functional features. Int. J. Biochem. 24:1917-1924.
16. Garcia, G. A., and D. M. Goodenough-Lashua. 1998. Appendix III: general properties of RNA-modifying and -editing enzymes, p. 555-565. In H. Grosjean and R. Benne (ed.), Modification and editing of RNA. ASM Press, Washington, D.C.
17. Gavin, A. C., M. Bosche, R. Krause, P. Grandi, M. Marzioch, A. Bauer, J. Schultz, J. M. Rick, A. M. Michon, C. M. Cruciat, M. Remor, C. Hofert, M. Schelder, M. Brajenovic, H. Ruffner, A. Merino, K. Klein, M. Hudak, D. Dickson, T. Rudi, V. Gnau, A. Bauch, S. Bastuck, B. Huhse, C. Leutwein, M. A. Heurtier, R. R. Copley, A. Edelmann, E. Querfurth, V. Rybin, G. Drewes, M. Raida, T. Bouwmeester, P. Bork, B. Seraphin, B. Kuster, G. Neubauer, and G. Superti-Furga. 2002. Functional organization of the yeast proteome by systematic analysis of protein complexes. Nature 415:141-147.
18. Gehrke, C. W., and K. C. Kuo. 1989. Ribonucleoside analysis by reversed-phase high-performance liquid chromatography. J. Chromatogr. 471:3-36.
19. Grosjean, H., J. Edqvist, K. B. Straby, and R. Giege. 1996. Enzymatic formation of modified nucleosides in tRNA: dependence on tRNA architecture. J. Mol. Biol. 255:67-85.
20. Grosjean, H. J., S. de Henau, and D. M. Crothers. 1978. On the physical basis for ambiguity in genetic coding interactions. Proc. Natl. Acad. Sci. USA 75:610-614.
21. Hagervall, T. G., Y. H. Jönsson, C. G. Edmonds, J. M. McCloskey, and G. R. Björk. 1990. Chorismic acid, a key metabolite in modification of tRNA. J. Bacteriol. 172:252-259.
22. Hagervall, T. G., S. C. Pomerantz, and J. A. McCloskey. 1998. Reduced misreading of asparagine codons by Escherichia coli tRNALys with hypomodified derivatives of 5-methylaminomethyl-2-thiouridine in the wobble position. J. Mol. Biol. 284:33-42.
23. Hrycyna, C. A., M. C. Yang, and S. Clarke. 1994. Protein carboxyl methylation in Saccharomyces cerevisiae: evidence for STE14-dependent and STE14-independent pathways. Biochemistry 33:9806-9812.
24. Isel, C., J. M. Lanchy, S. F. Le Grice, C. Ehresmann, B. Ehresmann, and R. Marquet. 1996. Specific initiation and switch to elongation of human immunodeficiency virus type 1 reverse transcription require the post-transcriptional modifications of primer tRNA3Lys. EMBO J. 15:917-924.
25. Isel, C., R. Marquet, G. Keith, C. Ehresmann, and B. Ehresmann. 1993. Modified nucleotides of tRNA(3Lys) modulate primer/template loop-loop interaction in the initiation complex of HIV-1 reverse transcription. J. Biol. Chem. 268:25269-25272.
26. Kalhor, H. R., K. Luk, A. Ramos, P. Zobel-Thropp, and S. Clarke. 2001. Protein phosphatase methyltransferase 1 (Ppm1p) is the sole activity responsible for modification of the major forms of protein phosphatase 2A in yeast. Arch. Biochem. Biophys. 395:239-245.
27. Kalhor, H. R., A. Niewmierzycka, K. F. Faull, X. Yao, S. Grade, S. Clarke, and P. A. Rubenstein. 1999. A highly conserved 3-methylhistidine modification is absent in yeast actin. Arch. Biochem. Biophys. 370:105-111.
28. Keith, G., and G. Dirheimer. 1980. Reinvestigation of the primary structure of brewer's yeast tRNA 3 Arg. Biochem. Biophys. Res. Commun. 92:116-119.
29. Kennedy, T. D., and B. G. Lane. 1975. Selective labelling of the methyl carboxylate substituents found in the anticodon sequences of some species of yeast transfer RNA. Can. J. Biochem. 53:1-10.
30. Kobayashi, T., T. Irie, M. Yoshida, K. Takeishi, and T. Ukita. 1974. The primary structure of yeast glutamic acid tRNA specific to the GAA codon. Biochim. Biophys. Acta. 366:168-181.
31. Kuntzel, B., J. Weissenbach, R. E. Wolff, T. D. Tumaitis-Kennedy, B. G. Lane, and G. Dirheimer. 1975. Presence of the methylester of 5-carboxymethyl uridine in the wobble position of the anticodon of tRNAIII Arg from brewer's yeast. Biochimie 57:61-70.
32. Laemmli, U. K. 1970. Cleavage of structural proteins during the assembly of the head of bacteriophage T4. Nature 227:680-685.
33. Lim, V. I., and J. F. Curran. 2001. Analysis of codon:anticodon interactions within the ribosome provides new insights into codon reading and the genetic code structure. RNA 7:942-957.
34. Lustig, F., P. Elias, T. Axberg, T. Samuelsson, I. Tittawella, and U. Lagerkvist. 1981. Codon reading and translational error. Reading of the glutamine and lysine codons during protein synthesis in vitro. J. Biol. Chem. 256:2635-2643.
35. McBride, A. E., and P. A. Silver. 2001. State of the arg: protein methylation at arginine comes of age. Cell 106:5-8.
36. Meehan, R. R., and I. Stancheva. 2001. DNA methylation and control of gene expression in vertebrate development. Essays Biochem. 37:59-70.
37. Motorin, Y., and H. Grosjean. 1999. Multisite-specific tRNA:m5C-methyltransferase (Trm4) in yeast Saccharomyces cerevisiae: identification of the gene and substrate specificity of the enzyme. RNA 5:1105-1118.
38. Nau, F. 1976. The methylation of tRNA. Biochimie 58:629-645.
39. Niewmierzycka, A. 1998. Ph.D. thesis. University of California-Los Angeles, Los Angeles.
40. Niewmierzycka, A., and S. Clarke. 1999. S-Adenosylmethionine-dependent methylation in Saccharomyces cerevisiae. Identification of a novel protein arginine methyltransferase. J. Biol. Chem. 274:814-824.
41. Nordlund, M. E., J. O. Johansson, U. von Pawel-Rammingen, and A. S. Bystrom. 2000. Identification of the TRM2 gene encoding the tRNA(m5U54)methyltransferase of Saccharomyces cerevisiae. RNA 6:844-860.
42. Ortwerth, B. J., and J. V. Carlson. 1977. Lysine transfer RNA from liver: a sulfur-containing species that codes for AAG. Arch. Biochem. Biophys. 178:278-284.
43. Pintard, L., F. Lecointe, J. M. Bujnicki, C. Bonnerot, H. Grosjean, and B. Lapeyre. 2002. Trm7p catalyses the formation of two 2′-O-methylriboses in yeast tRNA anticodon loop. EMBO J. 21:1811-1820.
44. Pomerantz, S. C., and J. A. McCloskey. 1990. Analysis of RNA hydrolyzates by liquid chromatography-mass spectrometry. Methods Enzymol. 193:796-824.
45. Raba, M., K. Limburg, M. Burghagen, J. R. Katze, M. Simsek, J. E. Heckman, U. L. Rajbhandary, and H. J. Gross. 1979. Nucleotide sequence of three isoaccepting lysine tRNAs from rabbit liver and SV40-transformed mouse fibroblasts. Eur. J. Biochem. 97:305-318.
46. Rozenski, J., P. F. Crain, and J. A. McCloskey. 1999. The RNA modification database: 1999 update. Nucleic Acids Res. 27:196-197.
47. Sprinzl, M., C. Horn, M. Brown, A. Ioudovitch, and S. Steinberg. 1998. Compilation of tRNA sequences and sequences of tRNA genes. Nucleic Acids Res. 26:148-153.
48. Sundaram, M., P. C. Durant, and D. R. Davis. 2000. Hypermodified nucleosides in the anticodon of tRNALys stabilize a canonical U-turn structure. Biochemistry. 39:12575-12584.
49. Tsurui, H., Y. Kumazawa, R. Sanokawa, Y. Watanabe, T. Kuroda, A. Wada, K. Watanabe, and T. Shirai. 1994. Batchwise purification of specific tRNAs by a solid-phase DNA probe. Anal. Biochem. 221:166-172.
50. Uziel, M., and A. J. Weinberger. 1975. Sequence of E. coli tRNA-Glu1 by automated sequential degradation. Nucleic Acids Res. 2:469-475.
51. Vicens, Q., and E. Westhof. 2001. Crystal structure of paromomycin docked into the eubacterial ribosomal decoding A site. Structure (Cambridge) 9:647-658.
52. Weissenbach, J., and G. Dirheimer. 1978. Pairing properties of the methylester of 5-carboxymethyl uridine in the wobble position of yeast tRNA3Arg. Biochim. Biophys. Acta. 518:530-534.
53. Williams, R. J., W. Nagel, B. Roe, and B. Dudock. 1974. Primary structure of E. coli alanine transfer RNA: relation to the yeast phenylalanyl tRNA synthetase recognition site. Biochem. Biophys. Res. Commun. 60:1215-1221.
54. Yarian, C., H. Townsend, W. Czestkowski, E. Sochacka, A. J. Malkiewicz, R. Guenther, A. Miskiewicz, and P. F. Agris. 2002. Accurate translation of the genetic code depends on tRNA modified nucleosides. J. Biol. Chem. 277: 16391-16395.
55. Yasukawa, T., T. Suzuki, N. Ishii, S. Ohta, and K. Watanabe. 2001. Wobble modification defect in tRNA disturbs codon-anticodon interaction in a mitochondrial disease. EMBO J. 20:4794-4802.
56. Yokoyama, S., T. Watanabe, K. Murao, H. Ishikura, Z. Yamaizumi, S. Nishimura, and T. Miyazawa. 1985. Molecular mechanism of codon recognition by tRNA species with modified uridine in the first position of the anticodon. Proc. Natl. Acad. Sci. USA 82:4905-4909.
57. Yokoyama, S., and S. Nishimura. 1995. Modified nucleosides and codon recognition, p. 207-223. In D. Soll and U. L. RajBhandary (ed.), tRNA: structure, biosynthesis, and function. ASM Press, Washington, D.C.
58. Zobel-Thropp, P., J. D. Gary, and S. Clarke. 1998. Delta-N-methylarginine is a novel posttranslational modification of arginine residues in yeast proteins. J. Biol. Chem. 273:29283-29286.
59. Zobel-Thropp, P., M. C. Yang, L. Machado, and S. Clarke. 2000. A novel post-translational modification of yeast elongation factor 1A. Methylesterification at the C terminus. J. Biol. Chem. 275:37150-37158.