Alternative tertiary structure of tRNA for recognition by a posttranscriptional modification enzyme

Cell

Volumn 113, Issue 3, 2003, Pages 383-394

  Ishitani, Ryuichiro ^a,c   Nureki, Osamu ^a,b,c,d   Nameki, Nobukazu ^c   Okada, Norihiro ^e   Nishimura, Susumu ^f   Yokoyama, Shigeyuki ^a,b,c  

^a UNIVERSITY OF TOKYO   (Japan)

^b RIKEN HARIMA INSTITUTE   (Japan)

^c RIKEN YOKOHAMA INSTITUTE   (Japan)

^d JAPAN SCIENCE AND TECHNOLOGY AGENCY   (Japan)

^e TOKYO INSTITUTE OF TECHNOLOGY   (Japan)

^f TAIHO PHARMACEUTICAL CO LTD   (Japan)

Author keywords

[No Author keywords available]

Indexed keywords

GLYCOSYLTRANSFERASE; GUANINE TRANSGLYCOSYLASE; NUCLEOTIDE; TRANSFER RNA; UNCLASSIFIED DRUG;

ACCURACY; ANALYTICAL PARAMETERS; ARTICLE; CRYSTAL STRUCTURE; ENZYME ACTIVE SITE; ENZYME ANALYSIS; ENZYME MODIFICATION; MOLECULAR INTERACTION; NUCLEIC ACID ANALYSIS; PRIORITY JOURNAL; RNA ANALYSIS; RNA BINDING; RNA CONFORMATION; RNA STRUCTURE; RNA TRANSCRIPTION; STRUCTURE ANALYSIS;

TRIFOLIUM;

EID: 0038613099     PISSN: 00928674     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0092-8674(03)00280-0     Document Type: Article

References (50)

1. 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.
2. Aravind L., Koonin E.V. Novel predicted RNA-binding domains associated with the translation machinery. J. Mol. Evol. 48:1999;291-302.
3. Bai Y., Fox D.T., Lacy J.A., Van Lanen S.G., Iwata-Reuyl D. Hypermodification of tRNA in Thermophilic archaea. Cloning, overexpression, and characterization of tRNA-guanine transglycosylase from Methanococcus jannaschii. J. Biol. Chem. 275:2000;28731-28738.
4. Björk, G.R. (1995). Biosynthesis and function of modified nucleosides. In tRNA: Structure, Biosynthesis, and Function, D. Söll, and U. RajBhandary, eds., pp. 165-205.
5. Björk G.R., Durand J.M., Hagervall T.G., Leipuviene R., Lundgren H.K., Nilsson K., Chen P., Qian Q., Urbonavicius J. Transfer RNA modification. influence on translational frameshifting and metabolism FEBS Lett. 452:1999;47-51.
6. Brünger A.T., Adams P.D., Clore G.M., DeLano W.L., Gros P., Grosse-Kunstleve R.W., Jiang J.S., Kuszewski J., Nilges M., Pannu N.S.et al. Crystallography & NMR system. A new software suite for macromolecular structure determination Acta Crystallogr. D54:1998;905-921.
7. Charette M., Gray M.W. Pseudouridine in RNA. what, where, how, and why IUBMB Life. 49:2000;341-351.
8. Davis, D.R. (1998). Biophysical and conformational properties of modified nucleosides in RNA (nuclear magnetic resonance studies). In Modification and Editing of RNA, H. Grosjean, and R. Benne, eds. (ASM Press), pp. 85-102.
9. Edmonds C.G., Crain P.F., Gupta R., Hashizume T., Hocart C.H., Kowalak J.A., Pomerantz S.C., Stetter K.O., McCloskey J.A. Posttranscriptional modification of tRNA in thermophilic archaea (Archaebacteria). J. Bacteriol. 173:1991;3138-3148.
10. Ferré-D'Amaré A.R. RNA-modifying enzymes. Curr. Opin. Struct. Biol. 13:2003;49-55.
11. Giegé R., Sissler M., Florentz C. Universal rules and idiosyncratic features in tRNA identity. Nucleic Acids Res. 26:1998;5017-5035.
12. Green R., Noller H.F. Reconstitution of functional 50S ribosomes from in vitro transcripts of Bacillus stearothermophilus 23S rRNA. Biochemistry. 38:1999;1772-1779.
13. Gregson J.M., Crain P.F., Edmonds C.G., Gupta R., Hashizume T., Phillipson D.W., McCloskey J.A. Structure of the archaeal transfer RNA nucleoside G*-15 (2-amino-4,7-dihydro-4-oxo-7-β-D-ribofuranosyl-1H-pyrrolo[2,3-d] pyrimidine-5-carbox-imidamide (archaeosine)). J. Biol. Chem. 268:1993;10076-10086.
14. Gupta R. Halobacterium volcanii tRNAs. Identification of 41 tRNAs covering all amino acids, and the sequences of 33 class I tRNAs. J. Biol. Chem. 259:1984;9461-9471.
15. Gutgsell N., Englund N., Niu L., Kaya Y., Lane B.G., Ofengand J. 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. 6:2000;1870-1881.
16. Gutgsell N.S., Del Campo M.D., Raychaudhuri S., Ofengand J. A second function for pseudouridine synthases. A point mutant of RluD unable to form pseudouridines 1911, 1915, and 1917 in Escherichia coli 23S ribosomal RNA restores normal growth to an RluD-minus strain RNA. 7:2001;990-998.
17. Heiss N.S., Knight S.W., Vulliamy T.J., Klauck S.M., Wiemann S., Mason P.J., Poustka A., Dokal I. X-linked dyskeratosis congenita is caused by mutations in a highly conserved gene with putative nucleolar functions. Nat. Genet. 19:1998;32-38.
18. (UUR). Nucleic Acids Res. 27:1999;756-763.
19. Hoang C., Ferré-D'Amaré A.R. Cocrystal structure of a tRNA Ψ55 pseudouridine synthase. nucleotide flipping by an RNA-modifying enzyme Cell. 107:2001;929-939.
20. Ile1 species from an extreme thermophile, Thermus thermophilus HB8. effect of 2-thiolation of ribothymidine on the thermostability of tRNA Biochemistry. 24:1985;5711-5715.
21. Ishitani R., Nureki O., Kijimoto T., Watanabe M., Kondo H., Nameki N., Okada N., Nishimura S., Yokoyama S. Crystallization and preliminary X-ray analysis of the archaeosine tRNA- guanine transglycosylase from Pyrococcus horikoshii. Acta Crystallogr. D57:2001;1659-1662.
22. Ishitani R., Nureki O., Fukai S., Kijimoto T., Nameki N., Watanabe M., Kondo H., Sekine M., Okada N., Nishimura S., Yokoyama S. Crystal structure of archaeosine tRNA-guanine transglycosylase. J. Mol. Biol. 318:2002;665-677.
23. Jones T.A., Zou J.-Y., Cowan S.W., Kjeldgaard M. Improved methods for binding protein models in electron density maps and the location of errors in these models. Acta Crystallogr. A47:1991;110-119.
24. Kawai G., Yamamoto Y., Kamimura T., Masegi T., Sekine M., Hata T., Iimori T., Watanabe T., Miyazawa T., Yokoyama S. Conformational rigidity of specific pyrimidine residues in tRNA arises from posttranscriptional modifications that enhance steric interaction between the base and the 2′-hydroxyl group. Biochemistry. 31:1992;1040-1046.
25. Khaitovich P., Tenson T., Kloss P., Mankin A.S. Reconstitution of functionally active Thermus aquaticus large ribosomal subunits with in vitro-transcribed rRNA. Biochemistry. 38:1999;1780-1788.
26. Kim S.H., Quigley G.J., Suddath F.L., McPherson A., Sneden D., Kim J.J., Weinzierl J., Rich A. Three-dimensional structure of yeast phenylalanine transfer RNA. folding of the polynucleotide chain Science. 179:1973;285-288.
27. Kiss T. Small nucleolar RNA-guided post-transcriptional modification of cellular RNAs. EMBO J. 20:2001;3617-3622.
28. Kiss T. Small nucleolar RNAs. an abundant group of noncoding RNAs with diverse cellular functions Cell. 109:2002;145-148.
29. Lafontaine D.L., Bousquet-Antonelli C., Henry Y., Caizergues-Ferrer M., Tollervey D. The box H + ACA snoRNAs carry Cbf5p, the putative rRNA pseudouridine synthase. Genes Dev. 12:1998;527-537.
30. Laskowski R.A., MacArthur M.W., Morris A.L., Thornton J.M. Procheck. a program to check the stereochemical quality of protein structures J. Appl. Crystallogr. 26:1993;283-291.
31. Limbach P.A., Crain P.F., McCloskey J.A. Summary. the modified nucleosides of RNA Nucleic Acids Res. 22:1994;2183-2196.
32. Marck C., Grosjean H. tRNomics. analysis of tRNA genes from 50 genomes of Eukarya, Archaea, and Bacteria reveals anticodon-sparing strategies and domain-specific features RNA. 8:2002;1189-1232.
33. McCloskey J.A., Crain P.F. The RNA modification database - 1998. Nucleic Acids Res. 26:1998;196-197.
34. McCloskey J.A., Graham D.E., Zhou S., Crain P.F., Ibba M., Konisky J., Söll D., Olsen G.J. Post-transcriptional modification in archaeal tRNAs. identities and phylogenetic relations of nucleotides from mesophilic and hyperthermophilic Methanococcales Nucleic Acids Res. 29:2001;4699-4706.
35. Nicholls A., Sharp K.A., Honig B. Protein folding and association. insights from the interfacial and thermodynamic properties of hydrocarbons Proteins. 11:1991;281-296.
36. Ofengand J. Ribosomal RNA pseudouridines and pseudouridine synthases. FEBS Lett. 514:2002;17-25.
37. (UCU) having a short T arm and lacking the entire D arm FEBS Lett. 514:2002;37-43.
38. Okimoto R., Wolstenholme D.R. A set of tRNAs that lack either the T ψ C arm or the dihydrouridine arm. towards a minimal tRNA adaptor EMBO J. 9:1990;3405-3411.
39. Okimoto R., Macfarlane J.L., Clary D.O., Wolstenholme D.R. The mitochondrial genomes of two nematodes, Caenorhabditis elegans and Ascaris suum. Genetics. 130:1992;471-498.
40. Otwinowski, Z., and Minor, W. (1997). Processing of X-ray diffraction data collected in oscillation mode. In Methods in Enzymology, J. Carter, C.W., and R. M. Sweet, eds. (Academic Press), pp. 307-326.
41. Roe B.A., Ma D.P., Wilson R.K., Wong J.F. The complete nucleotide sequence of the Xenopus laevis mitochondrial genome. J. Biol. Chem. 260:1985;9759-9774.
42. Sanner, M.F., Olson, A.J., and Spehner, J.-C. (1995). Fast and robust computation of molecular surfaces. Proc. 11th ACM Symp. Comp. Geom., 104-106.
43. Shi H., Moore P.B. The crystal structure of yeast phenylalanine tRNA at 1.93 Å resolution. a classic structure revisited RNA. 6:2000;1091-1105.
44. Sprinzl M., Horn C., Brown M., Ioudovitch A., Steinberg S. Compilation of tRNA sequences and sequences of tRNA genes. Nucleic Acids Res. 26:1998;148-153.
45. Vagin A., Teplyakov A. Molrep. an automated program for molecular replacement J. Appl. Crystallogr. 30:1997;1022-1025.
46. Watanabe M., Matsuo M., Tanaka S., Akimoto H., Asahi S., Nishimura S., Katze J.R., Hashizume T., Crain P.F., McCloskey J.A., Okada N. 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. 272:1997;20146-20151.
47. Watanabe M., Nameki N., Matsuo-Takasaki M., Nishimura S., Okada N. tRNA recognition of tRNA-guanine transglycosylase from a hyperthermophilic archaeon, Pyrococcus horikoshii. J. Biol. Chem. 276:2000;2387-2394.
48. Watkins N.J., Gottschalk A., Neubauer G., Kastner B., Fabrizio P., Mann M., Luhrmann R. Cbf5p, a potential pseudouridine synthase, and Nhp2p, a putative RNA-binding protein, are present together with Gar1p in all H BOX/ACA-motif snoRNPs and constitute a common bipartite structure. RNA. 4:1998;1549-1568.
49. Wolstenholme D.R., Macfarlane J.L., Okimoto R., Clary D.O., Wahleithner J.A. Bizarre tRNAs inferred from DNA sequences of mitochondrial genomes of nematode worms. Proc. Natl. Acad. Sci. USA. 84:1987;1324-1328.
50. Yokoyama, S., and Nishimura, S. (1995). Modified nucleosides and codon recognition. In tRNA: Structure, Biosynthesis, and Function, D. Söll, and U. RajBhandary, eds. (ASM Press), pp. 207-223.