Unique features of animal mitochondrial translation systems: The non-universal genetic code, unusual features of the translational apparatus and their relevance to human mitochondrial diseases

Proceedings of the Japan Academy Series B: Physical and Biological Sciences

Volumn 86, Issue 1, 2010, Pages 11-39

  Watanabe, Kimitsuna ^a  

^a NATIONAL INSTITUTE OF ADVANCED INDUSTRIAL SCIENCE AND TECHNOLOGY AIST   (Japan)

Author keywords

Animal mitochondria; Genetic code; Mitochondrial diseases; Modified nucleotides; Translation system; tRNA

Indexed keywords

TRANSFER RNA;

AMINO ACID SEQUENCE; ANIMAL; DISORDERS OF MITOCHONDRIAL FUNCTIONS; GENETIC CODE; GENETICS; HUMAN; METABOLISM; MITOCHONDRION; MOLECULAR EVOLUTION; MOLECULAR GENETICS; NUCLEOTIDE SEQUENCE; PROTEIN SYNTHESIS; REVIEW;

AMINO ACID SEQUENCE; ANIMALS; BASE SEQUENCE; EVOLUTION, MOLECULAR; GENETIC CODE; HUMANS; MITOCHONDRIA; MITOCHONDRIAL DISEASES; MOLECULAR SEQUENCE DATA; PROTEIN BIOSYNTHESIS; RNA, TRANSFER;

ANIMALIA; EUKARYOTA;

EID: 77952560288     PISSN: 03862208     EISSN: 13492896     Source Type: Journal    
DOI: 10.2183/pjab.86.11     Document Type: Review

References (152)

1. Barrell, B. G., Bankier, A. T. and Drouin, J. (1979) A different genetic code in human mitochondria. Nature 282, 189-194.
2. Anderson, S., Bankier, A. T., Barrell, B. G., de Bruijn, M. H. L., Coulson, A. R., Drouin, J. et al. (1981) Sequence and organization of the human mitochondrial genome. Nature 290, 457-465.
3. de Bruijn, M. H. L., Schreier, P. H., Eepron, I. C., Barrrell, B. G., Chen, E. Y., Armstrong, P. W. et al. (1980) A mammalian mitochondrial serine transfer RNA lacking the "dihydrouridine" loop and stem. Nucleic Acids Res. 8, 5213-5222.
4. Arcari, P. and Brownlee, G. G. (1980) The nucleotide sequence of a small (3S) seryl-tRNA (anticodon GCU) from beef heart mitochondria. Nucleic Acids Res. 8, 5207-5212.
5. Gesteland, R. F., Ceck, T. R. and Atkins, J. F. (eds.) (1999) The RNA World Second Edition-The nature of modern RNA suggests a prebiotic RNA world. Cold Spring Harbor Laboratory Press., New York, pp. 1-709.
6. Crick, F. H. C. (1966) Codon-anticodon pairings: The wobble hypothesis. J. Mol. Biol. 19, 548-555.
7. Osawa, S. and Jukes, T. H. (1989) Codon reassignment (codon capture) in evolution. J. Mol. Evol. 28, 271-278.
8. Anderson, S., de Bruijn, M. H. L., Coulson, A. R., Eperon, I. C., Sanger, F. and Young, I. G. (1982) Complete sequence of bovine mitochondrial DNA. Conserved features of the mammalian mitochondrial genome. J. Mol. Biol. 156, 683-717.
9. Gadaleta, G., Pepe, G., de Candia, G., Quagliariello, C., Sbisá, E. and Saccone, C. (1989) The complete nucleotide sequence of the Rattus norvegicus mitochondrial genome. Cryptic signals revealed by comparative analysis between vertebrates. J. Mol. Biol. 28, 497-516.
10. Bibb, M. J., Van Etten, R. A., Wright, C. T., Walberg, M. W. and Clayton, D. A. (1981) Sequence and gene organization of mouse mitochondrial DNA. Cell 26, 167-180.
11. Desjardins, P. and Morais, R. (1990) Sequence and gene organization of the chicken mitochondrial genonme. A novel gene order in higher vertebrates. J. Mol. Biol. 212, 599-634.
12. Roe, B. A., Ma, D-P., Wilson, R. K. and Wong, J. F. H. (1985) The complete nucleotide sequence of the Xenopus laevis mitochondrial genome. J. Biol. Chem. 260, 9759-9774.
13. Yokobori, S., Ueda, T., Feldmaier-Fucks, G., Pääbo, S., Ueshima, R., Kondow, A. et al. (1999) Complete DNA sequence of the mitochondrial genome of the ascidian Halocynthia roretzi (Chordata, Urochordata). Genetics 153, 1851-1862.
14. Jacobs, H. T., Elliot, D. J., Math, V. B. and Farquharson, A. (1988) Nucleotide sequence and gene organization of sea urchin mitochondrial DNA. J. Mol. Biol. 202, 185-217.
15. Cantatore, P., Roerti, M., Rainaldi, G., Gadaleta, M. N. and Saccone, C. (1989) The complete nucleotide sequence, gene organization and the genetic code of the mitochondrial genome of Peracentrotus lividus. J. Biol. Chem. 264, 10965-10975.
16. Asakawa, S., Himeno, H., Miura, K. and Watanabe, K. (1995) Nucleotide sequence and gene organization of the starfish Asterina pectinifera mitochondrial genome. Genetics 140, 1047-1060.
17. Clary, D. O. and Wolstenholme, D. R. (1985) The mitochondrial DNA molecule of Drosophila yakuba: nucleotide sequence, gene organization and the genetic code. Proc. Natl. Acad. Sci. USA 71, 2777-2781.
18. Okimoto, R., Macfarlane, J. L., Clary, D. O. and Wolstenholme, D. R. (1992) The mitochondrial genomes of two nematodes, Caenorhabditis elegans and Ascaris suum. Genetics 130, 471-498.
19. Attimonelli, M., Altamura, N., Benne, R., Boyen, C., Brennicke, A., Carone, A. et al. (1999) MitBASE: a comprehensive and integrated mitochondrial DNA database. Nucleic Acids Res. 27, 128-133.
20. Hensgens, L. A. M., Brakenho, J., De Vries, B. F., Sloop, P., Tromp, M. C., Van Boon, J. H. et al. (1984) The sequence of the gene for cytochrome c oxydase subunit I, a frameshift containing gene for cytochrome c oxidase subunit II and seven unassigned reading frames in Trypanosoma brucei mitochondrial maxi-circle DNA. Nucleic Acids Res. 12, 7327-7344.
21. Pritchard, A. E., Sable, C. L., Venuti, S. E. and Cummings, D. J. (1990) Analysis of NADH dehydrogenase proteins, ATPase subunit 9, cytochrome b and ribosomal protein 14 encoded in the mitochondrial DNA of Paramecium. Nucleic Acids Res. 18, 163-171.
22. Pritchard, A. E., Seilhamer, J. J., Mahalingam, R., Sable, C. L., Venuti, S. E. and Cummings, D. J. (1990) Nucleotide sequence of the mitochondrial genome of Paramecium. Nucleic Acids Res. 18, 173-180.
23. SerAGY in starfish mitochondrial DNA. Gene 56, 219-230.
24. Yokobori, S., Hasegawa, M., Ueda, T., Okada, N., Nishikawa, K. and Watanabe, K. (1994) Relationship among coelacanths, lungfishes and tetrapods: a phylogenetic analysis based on mitochondrial cytochrome oxidase gene sequences. J. Mol. Evol. 38, 602-609.
25. Yokobori, S., Ueda, T. and Watanabe, K. (1993) Codons AGA and AGG are read as Glycine in ascidian mitochondria. J. Mol. Evol. 36, 1-8.
26. Yamazaki, N., Ueshima, R., Terrett, J. A., Yokobori, S., Kaifu, M., Segawa, R. et al. (1997) Evolution of pulmonate gastropod mitochondrial genomes: comparisons of gene organization of euhadra, cepaea and albinaria and implications of unusual tRNA secondary structures. Genetics 145, 749-758.
27. Sasuga, J., Yokobori, S., Kaifu, M., Ueda, T., Nishikawa, K. and Watanabe, K. (1999) Gene contents and organization of a mitochondrial DNA segment of the squid Loligo bleekeri. J. Mol. Evol. 48, 692-702.
28. Seilhamer, J. J. and Cummings, D. J. (1982) Altered genetic code in Paramecium mitochondria. Possible evolutionary trends. Mol. Gen. Genet. 187, 236-239.
29. Watanabe, K. and Osawa, S. (1995) tRNA sequences and variations in the genetic code. In tRNA: Structure, Biosynthesis and Function (eds. Söll, D. and RajBhandary, U. L.). ASM Press, Washington, D.C. USA, pp. 215-250.
30. Yokobori, S., Suzuki, T. and Watanabe, K. (2001) Genetic code variations in mitochondria: tRNA as a major determinant of genetic code plasticity. J. Mol. Evol. 53, 314-326.
31. Bessho, Y., Ohama, T. and Osawa, S. (1992) Planarian mitochondria II. The unique genetic code as deduced from cytochrome c oxidase subunit I gene sequences. J. Mol. Evol. 34, 331-335.
32. Telford, M. J., Herniou, E. A., Russel, R. B. and Littlewood, D. T. J. (2000) Changes in mitochondrial genetic codes as phylogenetic characters: Two examples from the flat worms. Proc. Natl. Acad. Sci. USA 97, 11359-11364.
33. Nakamura, Y. and Ito, K. (1998) How protein reads the stop codon and terminates translation. Genes Cells. 3, 263-278.
34. f-Met and small-subunit ribosomal RNA and standard genetic code specificities for AGR and ATA codons. J. Mol. Evol. 39, 387-399.
35. Batuecas, B., Garesse, R., Calleja, M., Valverde, J. R. and Marco, R. (1988) Genome organization of Artemia mitochondrial DNA. Nucleic Acids Res. 16, 6515-6529.
36. de Bruijn, M. H. L. (1983) Drosophila melanogaster mitochondrial DNA, a novel organization and genetic code. Nature 304, 234-241.
37. Ueda, T., Ohta, T. and Watanabe, K. (1985) Large scale isolation and some properties of AGY-specific serine tRNA from bovine heart mitochondria. J. Biochem. 98, 1275-1284.
38. Yokogawa, T., Kumazawa, Y., Miura, K. and Watanabe, K. (1989) Purification and characterization of two serine tRNAs from bovine mitochondria by using a hybridization assay method. Nucleic Acids Res. 17, 2623-2638.
39. Ser(UCN). Nucleic Acids Res. 19, 6101-6105.
40. Phe lacking the 'conserved' GG and TΨCG sequences as inferred by enzymatic and chemical probing. Nucleic Acids Res. 22, 347-353.
41. GCU lacking the entire D arm. J. Biochem. 121, 1115-1122.
42. Tomita, K., Ueda, T. and Watanabe, K. (1999) The presence of pseudouridine in the anticodon alters the genetic code; a possible mechanism for assignment of the AAA lysine codon as asparagines in echinoderm mitochondria. Nucleic Acids Res. 27, 1683-1689.
43. Matuyama, S., Ueda, T., Crain, P. F., McCloskey, J. A. and Watanabe, K. (1998) A novel wobble rule found in starfish mitochondria. Presence of -methylguanosine at the anticodon wobble position expands decoding capability of tRNA. J. Biol. Chem. 273, 3363-3368.
44. Met possessing unique structural characteristics. Nucleosides Nucleotides 17, 531-539.
45. Gly(U*CU) found in ascidian mitochondria responsible for decoding non-universal codons AGA/AGG as glycine. Nucleic Acids Res. 27, 2554-2559.
46. GCU. Molecular basis for assignment of AGA/AGG codons as serine in invertebrate mitochondria. Biochim. Biophys. Acta 1399, 78-82.
47. Tomita, K., Ueda, T., Ishiwa, S., Crain, P. F., McCloskey, J. A. and Watanabe, K. (1999) Codon reading patterns in Drosophila melenogaster mitochondria based on their tRNA sequences: a unique wobble rule in animal mitochondria. Nucleic Acids Res. 27, 4291-4297.
48. Watanabe, Y., Tsurui, H., Ueda, T., Furushima, R., Takamiya, S., Kita, K. et al. (1994) Primary and higher order structures of nematode (Ascaris suum) mitochondrial tRNAs lacking either the T or D stem. J. Biol. Chem. 269, 22902-22906.
49. Met with a TV-replacement loop by ligation of chemically synthesized RNA fragments. Nucleic Acids Res. 24, 662-667.
50. Sakurai, M., Ohtsuki, T., Suzuki, T. and Watanabe, K. (2005) Unusual usage of wobble modification in mitochondrial tRNAs of the nematode Ascarisn suum. FEBS Lett. 579, 2767-2772.
51. Sakurai, M., Ohtsuki, T. and Watanabe, K. (2005) Modification at position 9 with 1-methyladenosine is crucial for structure and function of nematode mitochondrial tRNAs lacking the entire T-arm. Nucleic Acids Res. 33, 1653-1661.
52. Roe, B. A., Wong, J. F. H., Chen, E. Y. and Armstrong, P. A. (1981) Sequence analysis of mammalian mitochondrial tRNAs. In Recombinant DNA: Proceedings of the Third Cleveland Symposium on Macromolecules. (ed. Walton, A. G.). Elsevier Scientific Publishing Co., Amsterdam, pp. 167-176.
53. Randerath, K., Agrawal, H. P. and Randerath, E. (1983) tRNA alterations in cancer. Recent Results Cancer Res. 84, 103-120.
54. Andachi, Y., Yamao, F., Muto, A. and Osawa, F. (1989) Codon recognition patterns as deduced from sequences of the complete set of transfer RNA species in Mycoplasma capricolum. Resemblance to mitochondria. J. Mol. Biol. 209, 37-54.
55. Moriya, J., Yokogawa, T., Wakita, K., Ueda, T., Nishikawa, K., Crain, P. F. et al. (1994) A novel modified nucleoside found at the first position of the anticodon of methionine tRNA from bovine liver mitochondria. Biochemistry 33, 2234-2239.
56. 5CAU as revealed with a mitochondrial in vitro translation system. Nucleic Acids Res. 37, 1616-1627.
57. Suzuki, T., Suzuki, T., Wada, T., Saigo, K. and Watanabe, K. (2002) Taurine as a constituent of mitochondrial tRNA: new insights into the functions of taurine and human mitochondrial disease. EMBO J. 21, 6581-6589.
58. Samuelsson, T., Guindy, Y. S., Lustig, F., Borén, T. and Lagerkvist, U. (1987) Apparent lack of discrimination in the reading of certain codons in Mycoplasma mycoides. Proc. Natl. Acad. Sci. USA, 84, 3166-3170.
59. Yokoyama, S. and Nishimura, S. (1995) Modified nucleosides and codon recognition. In tRNA: Structure, Biosynthesis and Function. (eds. Söll, D. and RajBhandary, U. L.) ASM Press, Washington D.C., pp. 207-223.
60. Arg of a nematode Ascaris suum. Occurrence of unmodified adenosine at the first position of the anticodon. Biochim. Biophys. Acta 1350, 119-122.
61. Nishimura, S. (1983) Structure, biosynthesis and function of queosine in transfer RNA. Prog. Nucl. Acid Res. Mol. Biol. 28, 49-73.
62. Borén, T., Elias, P., Samuelsson, T., Claesson, C., Barciszewska, M., Gehrke, C. W. et al. (1993) Undiscriminating codon reading with adenosine in the wobble position. J. Mol. Biol. 230, 739-749.
63. Lagerkvist, U. (1978) "Two out of three": An alternative method for codon reading. Proc. Natl. Acad. Sci. USA 75, 1759-1762.
64. Mitra, S. K., Lustig, F., Åkesson, B., Lagerkvist, U. and Strid, L. (1977) Codon-anticodon recognition in the valine codon family. J. Biol. Chem. 252, 471-478.
65. Osawa, S., Jukes, T. H., Watanabe, K. and Muto, A. (1992) Recent evidence for evolution of the genetic code. Microbiol. Rev. 59, 229-264.
66. Lee, C. C., Timms, K. M., Trotman, C. N. A. and Tate, W. P. (1987) Isolation of a rat mitochondrial release factor. Accomodation of the changed genetic code for termination. J. Biol. Chem. 262, 3548-3552.
67. Soleimanpour-Lichaei, H. R., Kuhl, I., Gaisne, M., Passos, J. F., Wydro, M., Rorbach, J. et al. (2007) mtRF1a is a human mitochondrial translation release factor decoding the major termination codons UAA and UAG. Mol. Cell 27, 745-757.
68. Yamao, F., Iwagami, S., Azumi, Y., Muto, A. and Osawa, S. (1988) Evolutionary dynamics of tryptophan tRNAs in Mycoplasma caplicolum. Mol. Gen. Genet. 212, 364-369.
69. Osawa, S., Ohama, T., Jukes, T. H. and Watanabe, K. (1989) Evolution of the mitochondrial genetic code. I. Origin of AGR serine and stop codons in metazoan mitochondria. J. Mol. Evol. 29, 202-207.
70. Anderson, S., Bankier, A. T., Barrell, B. G., de Bruijn, M. H., Coulson, A. R., Drouin, J. et al. (1982) Comparison of the human and bovine mito-chondrial genomes. In Mitochondrial Genes. Cold Spring Harbor Laboratory, New York, USA, pp. 5-43.
71. Roe, B. A., Wong, J. F. H., Chen, E. Y., Armstrong, P. W., Stankierwicz, A., Ma, D. P. et al. (1982) Mammalian mitochondrial tRNAs: A modified nucleotide 3' to the anticodon may modulate their codon response. In Mitochondrial Genes. Cold Spring Harbor Laboratory, New York, USA, pp. 45-49.
72. Ser to common three-dimensional constraints. J. Mol. Biol. 236, 982-989.
73. UGA: chemical modification and computer modeling. Nucleic Acids Res. 22, 5378-5384.
74. de Bruijn, M. H. and Klug, A. (1983) A model for the tertiary structure of mammalian mitochondrial transfer RNAs lacking the entire 'dihydrouridine' loop and stem. EMBO J. 2, 1309-1321.
75. Wolstenholme, D. R. (1992) Animal mitochondrial DNA: structure and evolution. Int. Rev. Cytol. 141, 173-216.
76. Ser(AGY) is a main recognition site for homologous seryl-tRNA synthetase. Nucleic Acids Res. 20, 2217-2222.
77. UGA investigated by proton NMR spectroscopy. J. Mol. Biol. 284, 57-69.
78. Pyl structure reveals the molecular basis of orthogonality. Nature 457, 1163-1167.
79. Met having a TV-replacement loop. J. Biochem. 124, 28-34.
80. Gray, M. W. (1992) The endosymbiont hypothesis revisited. Int. Rev. Cytol. 141, 233-357.
81. Kumazawa, Y., Schwartzbach, C. J., Liao, H-X., Mizumoto, K., Kaziro, Y., Miura, K. et al. (1991) Interactions of bovine mitochondrial phenylalanyl-tRNA with ribosomes and elongation factors from mitochondria and bacteria. Biochim. Biophys. Acta 1090, 167-172.
82. Met to decode AUG and AUA codons. Biochimie 77, 104-108.
83. Ser with unusual secondary structures in an in vitro translation system of bovine mitochondria. Genes Cells 6, 1019-1030.
84. Hou, Y. M. and Schimmel, P. (1988) A simple structural feature is a major determinant of the identity of a transfer RNA. Nature 333, 140-145.
85. Kumazawa, Y., Himeno, H., Miura, K. and Watanabe, K. (1991) Unilateral aminoacylation specificity between bovine mitochondria and eubacteria. J. Biochem. 109, 421-427.
86. Gebhardt-Singh, E. and Sprinzl, M. (1986) SertRNAs from bovine mitochondrion form ternary complexes with bacterial elongation factor Tu and GTP. Nucleic Acids Res. 14, 7175-7188.
87. Denslow, N. D. and O'Brien, T. W. (1979) Elongation factors EF-G from E. coli and mammalian mitochondria are not functionally interchangeable. Biochem. Biophys. Res. Commun. 90, 1257-1265.
88. Eberly, S. L., Locklear, V. and Spremulli, L. L. (1985) Bovine mitochondrial ribosomes. Elongation factor specificity. J. Biol. Chem. 260, 8721-8725.
89. Terasaki, M., Suzuki, T., Hanada, T. and Watanabe, K. (2004) Functional compatibility of elongation factors between mammalian mitochondrial and bacterial ribosomes: characterization of GTPase activity and translation elongation by hybrid ribosomes bearing heterologous L7/L12 proteins. J. Mol. Evol. 336, 331-342.
90. Ser. Nucleic Acids Res. 18, 6815-6819.
91. Ser domains to aminoacylation by E. coli seryl-tRNA synthetase. A kinetic analysis using model RNA substrates. Nucleic Acids Res. 21, 4467-4475.
92. Fujinaga, M., Berthet-Colomonas, C., Yaremchuk, A. D., Tukalo, M. A. and Cusack, S. (1993) Refined crystal structure of the seryl-tRNA synthetase from Thermus thermophilus at 2.5 Å resolution. J. Mol. Biol. 234, 222-233.
93. Ser by seryl-tRNA synthetase in mammalian mitochondria. EMBO J. 24, 3369-3379.
94. Phe, EF-Tu, and a GTP analog. Science 270, 1464-1472.
95. CysEF-Tu-GDPNP reveals general and specific features in the ternary complex and in tRNA. Structure 7, 143-156.
96. Ohtsuki, T., Watanabe, Y., Takemoto, C., Kawai, G., Ueda, T., Kita, K. et al. (2001) An "elongated" translation elongation factor Tu for truncated tRNAs in nematode mitochondria. J. Biol. Chem. 276, 21571-21577.
97. Ohtsuki, T., Sato, A., Watanabe, Y. and Watanabe, K. (2002) A unique serine-specific elongation factor Tu found in nematode mitochondria. Nature Str. Biol. 9, 669-673.
98. Patel, V. B., Cunningham, C. C. and Hantgan, R. R. (2001) Physiochemical properties of rat liver mitochondrial ribosomes. J. Biol. Chem. 276, 6739-6746.
99. O'Brien, T. W. (1971) The general occurrence of 55 S ribosomes in mammalian liver mitochondria. J. Biol. Chem. 246, 3409-3417.
100. Matthews, D. E., Hessler, R. A., Denslow, N. D., Edwards, J. S. and O'Brien, T. W. (1982) Protein composition of the bovine mitochondrial ribosome. J. Biol. Chem. 257, 8788-8794.
101. Goldschmidt-Reisin, S., Kitakawa, M., Herfurth, E., Wittmann-Liebold, B., Grohmann, L. and Graack, H. R. (1998) Mammalian mitochondrial ribosomal proteins. N-terminal amino acid sequencing, characterization, and identification of corresponding gene sequences. J. Biol. Chem. 273, 34828-34836.
102. Graack, H. R., Bryant, M. L. and O'Brien, T. W. (1999) Identification of mammalian mitochondrial ribosomal proteins (MRPs) by N-terminal sequencing of purified bovine MRPs and comparison to Data Bank sequences: The large ribosomal particle. Biochemistry 38, 16569-16577.
103. O'Brien, T. W., Fiesler, S. E., Denslow, N. D., Thiede, B., Wittmann-Liebold, B., Mougey, E. B. et al. (1999) Mammalian mitochondrial ribosomal proteins (2). Amino acid sequencing, characterization and identification of corresponding gene sequencing. J. Biol. Chem. 274, 36043-36051.
104. O'Brien, T. W., Liu, J., Sylvester, J. E., Mougey, E. B., Fischel-Ghodsian, N., Thiede, B. et al. (2000) Mammalian mitochondrial ribosomal proteins (4). Amino acid sequencing, characterization and identification of corresponding gene sequencing. J. Biol. Chem. 275, 18153-18159.
105. Cavdar Koc, E., Blackburn, K., Burkhart, W. and Spremulli, L. L. (1999) Identification of a mammalian mitochondrial homolog of ribosomal protein S7. Biochem. Biophys. Res. Commun. 266, 141-146.
106. Cavdar Koc, E., Burkhart, W., Blackburn, K., Moseley, A., Koc, H. and Spremulli, L.L. (2000) A proteomics approach to the identification of mammalian mitochondrial small subunit ribosomal proteins. J. Biol. Chem. 275, 32585-32591.
107. Cavdar Koc, E., Burkhart, W., Blackburn, K., Moseley, A. and Spremulli, L. L. (2001) The small subunit of the mammalian mitochondrial ribosome. Identification of the full complement of ribosomal proteins present. J. Biol. Chem. 276, 19363-19374.
108. Suzuki, T., Terasaki, M., Takemoto-Hori, C., Hanada, T., Ueda, T., Wada, A. et al. (2001) Structural compensation for the deficit of rRNA with proteins in the mammalian mitochondrial ribosome. Systematic analysis of protein components of the large ribosomal subunit from mammalian mitochondria. J. Biol. Chem. 276, 21724-21736.
109. Suzuki, T., Terasaki, M., Takemoto-Hori, C., Hanada, T., Ueda, T., Wada, A. et al. (2001) Proteomic analysis of the mammalian mitochondrial ribosome. Identification of protein components in the 28S small subunit. J. Biol. Chem. 276, 33181-33195.
110. Ban, N., Nissen, P., Hansen, J., Moore, P. B. and Steitz, T. A. (2000) The complete atomic structure of the large ribosomal subunit at 2.4 Å resolution. Science 289, 905-920.
111. Gutell, R. R., Schnare, M. N. and Gray, M. W. (1990) The small subunit of the mammalian mitochondrial ribosome. Identification of the full complement of ribosomal proteins present. Nucleic Acids Res. 18, 2319-2330.
112. Zhao, F., Ohtsuki, T., Yamada, K., Yoshinari, S., Kita, K., Watanabe, Y. et al. (2005) Isolation and physicochemical properties of protein-rich nematode mitochondrial ribosomes. Biochemistry 44, 9232-9237.
113. Kaneko, T., Suzuki, T., Kapushoc, S. T., Rubio, M. A., Ghahvini, J., Watanabe, K. et al. (2003) Wobble modification difierences and subcellular localization of tRNAs in Leishmania tarentolae. Implication for tRNA sorting mechanism. EMBO J. 22, 657-667.
114. Suzuki, T. (2005) Biosynthesis and function of tRNA wobble modifications. In Topics in Current Genetics, Springer-Verlag, New York, Vol. 12, pp. 24-69.
115. Tsurui, H., Kumazawa, Y., Sanokawa, R., Watanabe, Y., Kuroda, T., Wada, A. et al. (1994) Batchwise purification of specific tRNAs by a solid-phase DNA probe. Anal. Biochem. 221, 166-172.
116. Huxtable, R. J. (1992) Physiological actions of taurine. Physiol. Rev. 72, 101-163.
117. Schon, E. A., Bonilla, E. and DiMauro, S. (1997) Mitochondrial DNA mutations and pathogenesis. J. Bioenerg. Biomembr. 29, 131-149.
118. Wallace, D. C. and Lott, M. T. (2003) MITOMAP: A human mitochondrial genome Database. http://www.mitomap.org/
119. Kobayashi, Y., Momoi, M. Y., Tominaga, K., Momoi, T., Nihei, K., Yanagisawa, M. et al. (1990) A point mutation in the mitochondrial tRNA-Leu(UUR) gene in MELAS (mitochondrial myopathy, encephalopathy, lactic acidosis and strokelike episodes). Biochem. Biophys. Res. Commun. 173, 816-822.
120. Leu(UUR) gene in mitochondrial myopathy, encephalopathy, lactic acidosis and strokelike episodes (MELAS). Am. J. Hum. Genet. 49, 590-599.
121. Leu(UUR) gene associated with the MELAS subgroup of mitochondrial encephalomyopathies. Nature 348, 651-653.
122. Leu(UUR) gene in a large pedigree with maternally transmitted type II diabetes mellitus and deafness. Nat. Genet. 1, 368-371.
123. Johns, D. R. and Hurko, O. (1991) Mitochondrial leucine tRNA mutation in neurological diseases. Lancet 337, 927-928.
124. Moraes C. T., Ciacci, F., Silvestri, G., Shanske, S., Sciacco, M., Hirano, M. et al. (1993) Atypical clinical presentations associated with the MELAS mutation at position 3243 of human mitochondrial DNA. Neuromuscul. Disord. 3, 43-50.
125. Shoner, J. M., Lott, M. T., Lezza, A. M., Seibel, P., Ballinger, S. W. and Wallace, D. C. (1990) Myoclonic epilepsy and ragged-red fiber disease (MERRF) is associated with a mitochondrial DNA tRNA(Lys) mutation. Cell 61, 931-937.
126. King, M. P. and Attardi, G. (1989) Human cells lacking mtDNA. Repopulation with exogeneous mitochondria by complementation. Science 246, 500-503.
127. Hayashi, J., Ohta, S., Kikuchi, A., Takemitsu, M., Goto, Y. and Nonaka, I. (1991) Introduction of disease-related mitochondrial DNA deletions into HeLa cells lacking mitochondrial DNA results in mitochondrial dysfunction. Proc. Natl. Acad. Sci. USA 88, 10614-10618.
128. Chomyn, A., Meola, G., Bresolin, N., Lai, S. T., Scarlato, G. and Attardi, G. (1991) In vitro genetic transfer of protein synthesis and respiration defects to mitochondrial DNA-less cells with myopathypatient mitochondria. Mol. Cell. Biol. 11, 2236-2244.
129. (Leu)(UUR) gene introduced from a MELAS patient to HeLa cells lacking mtDNA results in progressive inhibition of mitochondrial respiratory function. Biochem. Biophys. Res. Commun. 197, 1049-1055.
130. Dunbar, D. R., Moonie, P. A., Zeviani, M. and Holt, I. J. (1996) Complex I deficiency is associated with 3243G:C mitochondrial DNA in osteosarcoma cell hybrid. Hum. Mol. Genet. 5, 123-129.
131. Jacobs, H. T. (2003) Disorders of mitochondrial protein synthesis. Hum. Mol. Genet. 12, 293-301.
132. (Leu)(UUR) with pathogenic mutation of mitochondrial myopathy, encephalopathy, lactic acidosis and stroke-like episodes. J. Biol. Chem. 275, 4251-4257.
133. Lys with the MERRF encephalopathy pathogenic mutation. FEBS Lett. 467, 175-178.
134. Björk, G. R. (1995) Biosynthesis and function of modified nucleosides. In tRNA: Structure, Biosynthesis and functions. (eds. Söll, D. and RajBhandary, U. L.). ASM Press, Washington DC, pp. 165-205.
135. Chomyn, A., Martinuzzi, A., Yoneda, M., Daga, A., Hurko, O., Johns, D. et al. (1992) MELAS mutation in mtDNA binding site for transcription termination factor causes defects in protein synthesis and in respiration but no change in levels of upstream and downstream mature transcripts. Proc. Natl. Acad. Sci. USA, 89, 4221-4225.
136. Suzuki, T., Ueda, T. and Watanabe, K. (1997) The 'polysemous' codon-a codon with multiple amino acid assignment caused by dual specificity of tRNA identity. EMBO J. 16, 1122-1134.
137. Kirino, Y., Yasukawa, T., Ohta, S., Akira, S., Ishihara, K., Watanabe, K. et al. (2004) Codonspecific translational defect caused by a wobble modification deficiency in mutant tRNA from a human mitochondrial disease. Proc. Natl. Acad. Sci. USA 101, 15070-15075.
138. Asp. Nature 288, 669-674.
139. Leu(UUR) mutation disrupts a fragile anticodon stem. Nucleic Acids Res. 31, 596-601.
140. Ravn, K., Wibrand, F., Hansen, F. J., Horn, N., Rosenberg, T. and Schwartz, M. (2001) An mtDNA mutation, 14453G → A, in the NADH dehydrogenase subunit 6 associated with severe MELAS syndrome. Eur. J. Hum. Genet. 9, 805-809.
141. Koga, Y., Nonaka, I., Kobayashi, M., Tojyo, M. and Nihei, K. (1988) Finding in muscle in complex I (NADH coenzyme Q reductase) deficiency. Ann. Neurol. 24, 749-756.
142. Goto, Y., Horai, S., Matsuoka, T., Koga, Y., Nihei, K., Kobayashi, M. et al. (1992) Mitochondrial myopathy, encephalopathy, lactic acidosis and stroke-like episodes (MELAS): A correlative study of the clinical features and mitochondrial DNA mutation. Neurology 42, 545-550.
143. Yasukawa, T., Suzuki, T., Ishii, N., Ohta, S. and Watanabe, K. (2001) Wobble modification defect in tRNA disturbs codon-anticodon interaction in a mitochondrial disease. EMBO J. 20, 4794-4802.
144. Ashraf, S. S., Sochacka, E., Cain, R., Guenther, R., Malkiewicz, A. and Agris, P. F. (1999) Single atom modification (O → S) of tRNA confers ribosoma binding. RNA 5, 188-194.
145. Yoneda, M., Miyatake, T. and Attardi, G. (1994) Complementaiton of mutant and wild-type human mitochondrial DNAs coexisting since the mutation event and lack of complementation of DNAs introduced separately into a cell within distinct organelles. Mol. Cell. Biol. 14, 2699-2712.
146. Enriquez, J. A., Chomyn, A. and Attardi, G. (1995) MtDNA mutation in MERRF syndrome causes defective aminoacylation of tRNA(Lys) and premature translation termination. Nat. Genet. 10, 47-55.
147. Margulis, L. (1981) Symbiosis in cell evolution. Life and its environment on the early earth. Freeman and Company, W. H., USA.
148. Lang, B. F., Burger, G., O'Kelly, C. J., Cedergren, R., Golding, G. B., Lemieux, C. et al. (1977) An ancestral mitochondrial DNA resembling a eubacterial genome in miniature. Nature 387, 493-497.
149. Holt, I. J., Lorimer, H. E. and Jacobs, H. T. (2000) Coupled leading- and lagging-strand synthesis of mammalian mitochondrial DNA. Cell 100, 515-524.
150. Clayton, D. A. (1982) Replication of animal mitochondrial DNA. Cell 28, 693-705.
151. Sprinzl, M., Horn, C., Brown, M., Ioudovitch, A. and Steinberg, S. (1988) Compilation of tRNA sequences and sequences of tRNA genes. Nucleic Acids Res. 26, 148-153.
152. Mattaj, I. W. and Englmeier, L. (1998) Nucleoplasmic transport: The soluble phase. Ann. Rev. Biochem. 67, 265-306