Nematode-specific tRNAs that decode an alternative genetic code for leucine

Nucleic Acids Research

Volumn 40, Issue 8, 2012, Pages 3653-3662

  Hamashima, Kiyofumi ^a,b   Fujishima, Kosuke ^a   Masuda, Takeshi ^a   Sugahara, Junichi ^a   Tomita, Masaru ^a,b   Kanai, Akio ^a,b  

^a KEIO UNIVERSITY   (Japan)

^b Graduate School of Media and Governance   (Japan)

Author keywords

[No Author keywords available]

Indexed keywords

GLYCINE; GUANINE; ISOLEUCINE; LEUCINE; SERINE; TRANSFER RNA;

AMINOACYLATION; ANTICODON; ARTICLE; CAENORHABDITIS ELEGANS; CONTROLLED STUDY; ENZYME ACTIVITY; GENE DELETION; GENE EXPRESSION; GENE MUTATION; GENETIC CODE; GENETIC CONSERVATION; IN VITRO STUDY; MOLECULAR PHYLOGENY; NEMATODE; NONHUMAN; NUCLEOTIDE SEQUENCE; PRIORITY JOURNAL; PROTEIN DEPLETION; PROTEIN SYNTHESIS; RIBOSOME; RNA TRANSLATION; SEQUENCE ANALYSIS;

ANIMALS; ANTICODON; BASE SEQUENCE; CAENORHABDITIS ELEGANS; CODON; EVOLUTION, MOLECULAR; GENETIC CODE; LEUCINE; MOLECULAR SEQUENCE DATA; NEMATODA; PROTEIN BIOSYNTHESIS; RIBOSOMES; RNA, TRANSFER; RNA, TRANSFER, GLY; RNA, TRANSFER, ILE; TRANSFER RNA AMINOACYLATION;

CAENORHABDITIS ELEGANS; EUKARYOTA; NEMATODA;

EID: 84860364684     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gkr1226     Document Type: Article

References (39)

1. 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.
2. Freist, W. (1989) Mechanisms of aminoacyl-tRNA synthetases: a critical consideration of recent results. Biochemistry, 28, 6787-6795.
3. McClain, W.H. (1993) Rules that govern tRNA identity in protein synthesis. J. Mol. Biol., 234, 257-280.
4. Breitschopf, K., Achsel, T., Busch, K. and Gross, H.J. (1995) Identity elements of human tRNA(Leu): structural requirements for converting human tRNA(Ser) into a leucine acceptor in vitro. Nucleic Acids Res., 23, 3633-3637.
5. Soma, A., Uchiyama, K., Sakamoto, T., Maeda, M. and Himeno, H. (1999) Unique recognition style of tRNA(Leu) by Haloferax volcanii leucyl-tRNA synthetase. J. Mol. Biol., 293, 1029-1038.
6. Biou, V., Yaremchuk, A., Tukalo, M. and Cusack, S. (1994) The 2.9 A crystal structure of T. thermophilus seryl-tRNA synthetase complexed with tRNA(Ser). Science, 263, 1404-1410.
7. Yaremchuk, A., Kriklivyi, I., Tukalo, M. and Cusack, S. (2002) Class I tyrosyl-tRNA synthetase has a class II mode of cognate tRNA recognition. EMBO J., 21, 3829-3840.
8. Saks, M.E., Sampson, J.R. and Abelson, J.N. (1994) The transfer RNA identity problem: a search for rules. Science, 263, 191-197.
9. Achsel, T. and Gross, H.J. (1993) Identity determinants of human tRNA(Ser): sequence elements necessary for serylation and maturation of a tRNA with a long extra arm. EMBO J., 12, 3333-3338.
10. Sugahara, J., Yachie, N., Sekine, Y., Soma, A., Matsui, M., Tomita, M. and Kanai, A. (2006) SPLITS: a new program for predicting split and intron-containing tRNA genes at the genome level. In Silico Biol., 6, 411-418.
11. Sugahara, J., Yachie, N., Arakawa, K. and Tomita, M. (2007) In silico screening of archaeal tRNA-encoding genes having multiple introns with bulge-helix-bulge splicing motifs. RNA, 13, 671-681.
12. Sugahara, J., Kikuta, K., Fujishima, K., Yachie, N., Tomita, M. and Kanai, A. (2008) Comprehensive analysis of archaeal tRNA genes reveals rapid increase of tRNA introns in the order thermoproteales. Mol. Biol. Evol., 25, 2709-2716.
13. Sugahara, J., Fujishima, K., Morita, K., Tomita, M. and Kanai, A. (2009) Disrupted tRNA gene diversity and possible evolutionary scenarios. J. Mol. Evol., 69, 497-504.
14. Fujishima, K., Sugahara, J., Kikuta, K., Hirano, R., Sato, A., Tomita, M. and Kanai, A. (2009) Tri-split tRNA is a transfer RNA made from 3 transcripts that provides insight into the evolution of fragmented tRNAs in archaea. Proc. Natl Acad. Sci. USA, 106, 2683-2687.
15. Soma, A., Onodera, A., Sugahara, J., Kanai, A., Yachie, N., Tomita, M., Kawamura, F. and Sekine, Y. (2007) Permuted tRNA genes expressed via a circular RNA intermediate in Cyanidioschyzon merolae. Science, 318, 450-453.
16. Maruyama, S., Sugahara, J., Kanai, A. and Nozaki, H. (2009) Permuted tRNA genes in the nuclear and nucleomorph genomes of photosynthetic eukaryotes. Mol. Biol. Evol., 27, 1070-1076.
17. Chan, P.P., Cozen, A.E. and Lowe, T.M. (2011) Discovery of permuted and recently split transfer RNAs in Archaea. Genome Biol., 12, R38.
18. Marck, C. and Grosjean, H. (2002) tRNomics: analysis of tRNA genes from 50 genomes of Eukarya, Archaea, and Bacteria reveals anticodon-sparing strategies and domain-specific features. RNA, 8, 1189-1232.
19. Chan, P.P. and Lowe, T.M. (2009) GtRNAdb: a database of transfer RNA genes detected in genomic sequence. Nucleic Acids Res., 37, D93-D97.
20. Lowe, T.M. and Eddy, S.R. (1997) tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence. Nucleic Acids Res., 25, 955-964.
21. Larkin, M.A., Blackshields, G., Brown, N.P., Chenna, R., McGettigan, P.A., McWilliam, H., Valentin, F., Wallace, I.M., Wilm, A., Lopez, R. et al. (2007) Clustal W and Clustal X version 2.0. Bioinformatics, 23, 2947-2948.
22. Letunic, I. and Bork, P. (2007) Interactive tree of life (iTOL): an online tool for phylogenetic tree display and annotation. Bioinformatics, 23, 127-128.
23. Kohrer, C. and Rajbhandary, U.L. (2008) The many applications of acid urea polyacrylamide gel electrophoresis to studies of tRNAs and aminoacyl-tRNA synthetases. Methods, 44, 129-138.
24. Sato, A., Soga, T., Igarashi, K., Takesue, K., Tomita, M. and Kanai, A. (2011) GTP-dependent RNA 30-terminal phosphate cyclase from the hyperthermophilic archaeon Pyrococcus furiosus. Genes Cells., 16, 1190-1199.
25. Masuda, T., Tomita, M. and Ishihama, Y. (2008) Phase transfer surfactant-aided trypsin digestion for membrane proteome analysis. J Proteome Res., 7, 731-740.
26. Masuda, T., Saito, N., Tomita, M. and Ishihama, Y. (2009) Unbiased quantitation of Escherichia coli membrane proteome using phase transfer surfactants. Mol. Cell Proteomics, 8, 2770-2777.
27. Rappsilber, J., Ishihama, Y. and Mann, M. (2003) Stop and go extraction tips for matrix-assisted laser desorption/ionization, nanoelectrospray, and LC/MS sample pretreatment in proteomics. Anal. Chem., 75, 663-670.
28. Ishihama, Y., Rappsilber, J., Andersen, J.S. and Mann, M. (2002) Microcolumns with self-assembled particle frits for proteomics. J. Chromatogr. A, 979, 233-239.
29. Olsen, J.V., Ong, S.-E. and Mann, M. (2004) Trypsin cleaves exclusively C-terminal to arginine and lysine residues. Mol. Cell Proteomics, 3, 608-614.
30. Fujita, P.A., Rhead, B., Zweig, A.S., Hinrichs, A.S., Karolchik, D., Cline, M.S., Goldman, M., Barber, G.P., Clawson, H., Coelho, A. et al. (2010) The UCSC Genome Browser database: update 2011. Nucleic Acids Res., 39, D876-D882.
31. Galli, G., Hofstetter, H. and Birnstiel, M. (1981) Two conserved sequence blocks within eukaryotic tRNA genes are major promoter elements. Nature, 294, 626-631.
32. Stern, L. and Schulman, L.H. (1978) The role of the minor base N4-acetylcytidine in the function of the Escherichia coli noninitiator methionine transfer RNA. J. Biol. Chem., 253, 6132-6139.
33. Szweykowska-Kulinska, Z., Senger, B., Keith, G., Fasiolo, F. and Grosjean, H. (1994) Intron-dependent formation of pseudouridines in the anticodon of Saccharomyces cerevisiae minor tRNA(Ile). EMBO J., 13, 4636-4644.
34. Fukunaga, R. and Yokoyama, S. (2005) Aminoacylation complex structures of leucyl-tRNA synthetase and tRNALeu reveal two modes of discriminator-base recognition. Nat. Struct. Mol. Biol., 12, 915-922.
35. Asahara, H., Himeno, H., Tamura, K., Hasegawa, T., Watanabe, K. and Shimizu, M. (1993) Recognition nucleotides of Escherichia coli tRNA(Leu) and its elements facilitating discrimination from tRNASer and tRNA(Tyr). J. Mol. Biol., 231, 219-229.
36. Soma, A., Kumagai, R., Nishikawa, K. and Himeno, H. (1996) The anticodon loop is a major identity determinant of Saccharomyces cerevisiae tRNA(Leu). J. Mol. Biol., 263, 707-714.
37. Varani, G. and McClain, W.H. (2000) The G x U wobble base pair. A fundamental building block of RNA structure crucial to RNA function in diverse biological systems. EMBO Rep., 1, 18-23.
38. Wendrich, T.M., Blaha, G., Wilson, D.N., Marahiel, M.A. and Nierhaus, K.H. (2002) Dissection of the mechanism for the stringent factor RelA. Mol. Cell, 10, 779-788.
39. Netzer, N., Goodenbour, J.M., David, A., Dittmar, K.A., Jones, R.B., Schneider, J.R., Boone, D., Eves, E.M., Rosner, M.R., Gibbs, J.S. et al. (2009) Innate immune and chemically triggered oxidative stress modifies translational fidelity. Nature, 462, 522-526.