1887

Chapter 13 : tRNA Sequences and Variations in the Genetic Code

MyBook is a cheap paperback edition of the original book and will be sold at uniform, low price.

Ebook: Choose a downloadable PDF or ePub file. Chapter is a downloadable PDF file. File must be downloaded within 48 hours of purchase

Buy this Chapter
Digital (?) $15.00

Preview this chapter:
Zoom in
Zoomout

tRNA Sequences and Variations in the Genetic Code, Page 1 of 2

| /docserver/preview/fulltext/10.1128/9781555818333/9781555810733_Chap13-1.gif /docserver/preview/fulltext/10.1128/9781555818333/9781555810733_Chap13-2.gif

Abstract:

This chapter reviews the recent status of variations in the genetic code in various mitochondrial and nuclear systems. It explains relationship between the reading patterns of the changed codons and the anticodons of the tRNAs involved. It also considers mRNA editing in plant and protozoan organelles and a revision of codon assignments on the basis of protein gene sequences in the universal code, which is based on mRNA sequences for the proteins.

Citation: Watanabe K, Osawa S. 1995. tRNA Sequences and Variations in the Genetic Code, p 225-250. In tRNA. ASM Press, Washington, DC. doi: 10.1128/9781555818333.ch13

Key Concept Ranking

Saccharomyces cerevisiae
0.5555556
Genetic Code
0.53783643
Neurospora crassa
0.537037
RNA
0.52151597
0.5555556
Highlighted Text: Show | Hide
Loading full text...

Full text loading...

Figures

Image of Figure 1a
Figure 1a

Nucleotide sequences of tRNA or its gene from mitochondria of various organisms shown in cloverleaf form ( ). Almost all sequences are derived from the tRNA gene sequences; those of bovine animals ( ), rats ( ), ( ), ( ), and ( ) are derived from the tRNA sequences. The secondary structures are constructed according to the common rule for the cloverleaf form of usual tRNAs. References are shown by numbers in parentheses.

Citation: Watanabe K, Osawa S. 1995. tRNA Sequences and Variations in the Genetic Code, p 225-250. In tRNA. ASM Press, Washington, DC. doi: 10.1128/9781555818333.ch13
Permissions and Reprints Request Permissions
Download as Powerpoint
Image of Figure 1b
Figure 1b

Nucleotide sequences of tRNA or its gene from mitochondria of various organisms shown in cloverleaf form ( ). Almost all sequences are derived from the tRNA gene sequences; those of bovine animals ( ), rats ( ), ( ), ( ), and ( ) are derived from the tRNA sequences. The secondary structures are constructed according to the common rule for the cloverleaf form of usual tRNAs. References are shown by numbers in parentheses.

Citation: Watanabe K, Osawa S. 1995. tRNA Sequences and Variations in the Genetic Code, p 225-250. In tRNA. ASM Press, Washington, DC. doi: 10.1128/9781555818333.ch13
Permissions and Reprints Request Permissions
Download as Powerpoint
Image of Figure 1c
Figure 1c

Nucleotide sequences of tRNA or its gene from mitochondria of various organisms shown in cloverleaf form ( ). Almost all sequences are derived from the tRNA gene sequences; those of bovine animals ( ), rats ( ), ( ), ( ), and ( ) are derived from the tRNA sequences. The secondary structures are constructed according to the common rule for the cloverleaf form of usual tRNAs. References are shown by numbers in parentheses.

Citation: Watanabe K, Osawa S. 1995. tRNA Sequences and Variations in the Genetic Code, p 225-250. In tRNA. ASM Press, Washington, DC. doi: 10.1128/9781555818333.ch13
Permissions and Reprints Request Permissions
Download as Powerpoint
Image of Figure 2
Figure 2

Nucleotide sequences of selected mitochondrial tRNA genes shown in cloverleaf form ( ). Only the sequence of was determined at RNA level. References are shown by numbers in parentheses.

Citation: Watanabe K, Osawa S. 1995. tRNA Sequences and Variations in the Genetic Code, p 225-250. In tRNA. ASM Press, Washington, DC. doi: 10.1128/9781555818333.ch13
Permissions and Reprints Request Permissions
Download as Powerpoint
Image of Figure 3
Figure 3

Nucleotide sequences of selected mitochondrial tRNA genes shown in cloverleaf form ( ). Only the sequence of yeast ( ) was determined at the RNA level. References are shown by numbers in parentheses.

Citation: Watanabe K, Osawa S. 1995. tRNA Sequences and Variations in the Genetic Code, p 225-250. In tRNA. ASM Press, Washington, DC. doi: 10.1128/9781555818333.ch13
Permissions and Reprints Request Permissions
Download as Powerpoint
Image of Figure 4
Figure 4

Nucleotide sequences of selected mitochondrial tRNA genes shown in cloverleaf form ( ). References are shown by numbers in parentheses.

Citation: Watanabe K, Osawa S. 1995. tRNA Sequences and Variations in the Genetic Code, p 225-250. In tRNA. ASM Press, Washington, DC. doi: 10.1128/9781555818333.ch13
Permissions and Reprints Request Permissions
Download as Powerpoint
Image of Figure 5
Figure 5

Nucleotide sequences of selected mitochondrial tRNA genes shown in cloverleaf form ( ). References are shown by numbers in parentheses.

Citation: Watanabe K, Osawa S. 1995. tRNA Sequences and Variations in the Genetic Code, p 225-250. In tRNA. ASM Press, Washington, DC. doi: 10.1128/9781555818333.ch13
Permissions and Reprints Request Permissions
Download as Powerpoint
Image of Figure 6
Figure 6

Nucleotide sequences of selected mitochondrial tRNA genes shown in cloverleaf form ( ). The sequence of yeast tRNA ( ) was determined at RNA level. References are shown by numbers in parentheses.

Citation: Watanabe K, Osawa S. 1995. tRNA Sequences and Variations in the Genetic Code, p 225-250. In tRNA. ASM Press, Washington, DC. doi: 10.1128/9781555818333.ch13
Permissions and Reprints Request Permissions
Download as Powerpoint
Image of Figure 7
Figure 7

Nucleotide sequences of selected mitochondrial tRNA genes shown in cloverleaf form ( ). The sequences of hamster ( ) and yeast ( ) tRNAs were determined at RNA level. References are shown by numbers in parentheses.

Citation: Watanabe K, Osawa S. 1995. tRNA Sequences and Variations in the Genetic Code, p 225-250. In tRNA. ASM Press, Washington, DC. doi: 10.1128/9781555818333.ch13
Permissions and Reprints Request Permissions
Download as Powerpoint
Image of Figure 8
Figure 8

Incorporation of [3H]amino acids into hot trichloroacetic acid-insoluble material in cell-free translation systems from (a) and (b and c). The mRNAs used are shown above the figures. In (c), two UGAs are replaced by UGGs. (From reference with permission.)

Citation: Watanabe K, Osawa S. 1995. tRNA Sequences and Variations in the Genetic Code, p 225-250. In tRNA. ASM Press, Washington, DC. doi: 10.1128/9781555818333.ch13
Permissions and Reprints Request Permissions
Download as Powerpoint
Image of Figure 9
Figure 9

Secondary structure of tRNA and tRNA . (From reference .)

Citation: Watanabe K, Osawa S. 1995. tRNA Sequences and Variations in the Genetic Code, p 225-250. In tRNA. ASM Press, Washington, DC. doi: 10.1128/9781555818333.ch13
Permissions and Reprints Request Permissions
Download as Powerpoint
Image of Figure 10
Figure 10

Tryptophan tRNA genes from three spp. of (a) (from reference ); (b) (from reference and with permission); and (c) M. (from reference ).

Citation: Watanabe K, Osawa S. 1995. tRNA Sequences and Variations in the Genetic Code, p 225-250. In tRNA. ASM Press, Washington, DC. doi: 10.1128/9781555818333.ch13
Permissions and Reprints Request Permissions
Download as Powerpoint
Image of Figure 11
Figure 11

Secondary structure of three species of glutamine tRNAs. (From reference with permission of Oxford University Press.)

Citation: Watanabe K, Osawa S. 1995. tRNA Sequences and Variations in the Genetic Code, p 225-250. In tRNA. ASM Press, Washington, DC. doi: 10.1128/9781555818333.ch13
Permissions and Reprints Request Permissions
Download as Powerpoint
Image of Figure 12
Figure 12

Incorporation of [H]amino acids into hot trichloroacetic acid-insoluble material in cell-free translation systems from and The mRNA used is shown above the figure. (Reprinted with permission from [ ]. Copyright 1989 Macmillan Magazines Limited.)

Citation: Watanabe K, Osawa S. 1995. tRNA Sequences and Variations in the Genetic Code, p 225-250. In tRNA. ASM Press, Washington, DC. doi: 10.1128/9781555818333.ch13
Permissions and Reprints Request Permissions
Download as Powerpoint
Image of Figure 13
Figure 13

Secondary structure of tRNA (a) and its gene (b) in In b, the anticodon CAG is highlighted. Splicing sites for the tRNA gene are shown by solid arrows and possible splicing sites for the putative ancestral tRNA gene are shown by dotted arrows. (Adapted from reference .)

Citation: Watanabe K, Osawa S. 1995. tRNA Sequences and Variations in the Genetic Code, p 225-250. In tRNA. ASM Press, Washington, DC. doi: 10.1128/9781555818333.ch13
Permissions and Reprints Request Permissions
Download as Powerpoint
Image of Figure 14
Figure 14

Model for translation blockage by unassigned codon CGG (A to B). Compare B with C and D, in which release factor recognizes a stop codon UAA, followed by release of peptidyl-tRNA (D). (Adapted from reference .)

Citation: Watanabe K, Osawa S. 1995. tRNA Sequences and Variations in the Genetic Code, p 225-250. In tRNA. ASM Press, Washington, DC. doi: 10.1128/9781555818333.ch13
Permissions and Reprints Request Permissions
Download as Powerpoint

References

/content/book/10.1128/9781555818333.chap13
1. Ainley, W. M.,, I. G. Macreadie,, and R. A. Butow. 1985. var 1 gene on the mitochondrial genome of Torulopsis glabrata. J. Mol. Biol. 184:565576.
2. Andachi, Y.,, F. Yamao,, M. Iwami,, A. Muto,, and S. Osawa. 1987. Occurrence of unmodified adenine and uracil in the first position of anticodon in threonine tRNAs in Mycoplasma capricolum. Proc. Natl. Acad. Sci. USA 84:73987402.
3. Andachi, Y.,, F. Yamao,, A. Muto,, and S. Osawa. 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. 209:3754.
4. Anderson, S.,, A. T. Bankier,, B. G. Barrell,, M. H. L. de-Bruijn,, A. R. Coulson,, J. Drouin,, I. C. Eperon,, D. P. Nierlich,, B. A. Roe,, F. Sanger,, P. H. Schreier,, A. J. H. Smith,, R. Staden,, and I. G. Young. 1981. Sequence and organization of the human mitochondrial genome. Nature (London) 290:457465.
5. Anderson, S.,, M. H. L. de Bruijn,, A. R. Coulson,, I. C. Eperon,, F. Sanger,, and I. G. Young. 1982. Complete sequence of bovine mitochondrial DNA: conserved features of the mammalian mitochondrial genome, J. Mol. Biol. 156:683717.
6. Araki, T.,, S. Asakawa,, Y. Kumazawa,, K. Miura,, and K. Watanabe. 1988. Gene organization of tRNAs and their secondary structures found in starfish mitochondrial genome. Nucleic Acids Res. Symp. Ser. 20:9394.
6a. Araki, T.,, S. Asakawa,, Y. Kumazawa,, K. Miura,, and K. Watanabe. Unpublished data.
7. Arnason, U.,, A. Gullberg,, and B. Widegren. 1991. The complete nucleotide sequence of the mitochondrial DNA of the fin whale, Balaenoptera physalus. J. Mol. Evol. 33:556568.
8. Arnason, U.,, and E. Johnsson. 1992. The complete mitochondrial DNA sequence of the harbor seal, Phoca vitulina. J. Mol. Evol. 34:493505.
9. Asakawa, S.,, H. Himeno,, K. Miura,, and K. Watanabe. Unpublished data.
10. Baer, R. J.,, and D. T. Dubin. 1980. The sequence of a possible 5S RNA-equivalent in hamster mitochondria. Nucleic Acids Res. 8:36033610.
11. Barahona, I.,, H. Soares,, L. Cyrne,, D. Penque,, P. Denoulet,, and C. Rodrigues-Pousada. 1988. Sequence of one α - and two β -tubulin genes of Tetrahymena pyriformis. Structural and functional relationships with other eukaryotic tubulin genes. J. Mol. Biol. 202:365382.
12. Barrell, B. G.,, S. Anderson,, A. T. Bankier,, M. H. L. de Bruijn,, E. Chen,, A. R. Coulson,, J. Drouin,, I. C. Eperon,, D. P. Nierlich,, R. A. Roe,, F. Sanger,, P. H. Schreier,, A. J. H. Smith,, R. Staden,, and I. G. Yang. 1980. Different pattern of codon recognition by mammalian mitochondrial tRNAs. Proc. Natl. Acad. Sci. USA, 77:31643166.
13. Barrell, B. G.,, A. T. Bankier,, and J. Drouin. 1979. A different genetic code in human mitochondria. Nature (London) 282:189194.
14. Bass, B. L., 1993. RNA editing: new uses for old players in the RNA world, p. 383418. In R. F. Gesteland, and J. F. Atkins (ed.), The RNA World. Cold Spring Harbor Laboratory Press, Cold Spring Habor, N.Y.
15. Begu, D.,, P. V. Graves,, C. Domec,, G. Arselin,, S. Litvak,, and A. Araya. 1990. RNA editing of wheat mitochondrial ATP synthase subunit 9: direct protein and cDNA sequencing. The Plant Cell 2:12831290.
16. Benne, R.,, J. Van den Burg,, J. P. J. Brakenhoff,, P. Sloop,, J. H. Van Boom,, and M. C. Tromp. 1986. Major transcript of the frameshifted coxll gene from trypanosome mitochondria contains four nucleotides that are not encoded in the DNA. Cell 46:819826.
17. Bessho, Y.,, T. Ohama,, and S. Osawa. 1992. Planarian mitochondria. II. The unique genetic code as deduced from cytochrome c oxidase subunit I gene sequences. J. Mol. Evol. 34:331335.
18. Bhat, G. J.,, D. J. Koslowsky,, J. E. Feagin,, B. L. Smiley,, and K. Stuart. 1990. An extensively edited mitochondrial transcript in kinetoplastids encodes a protein homologous to ATPase subunit 6. Cell 61:885894.
19. Bibb, M. J.,, R. A. Van Elten,, C. T. Wright,, M. W. Walberg,, and D. A. Clayton. 1981. Sequence and gene organization of mouse mitochondrial DNA. Cell 26:167180.
20. Binder, S.,, A. Marchfelder,, A. Brennicke,, and B. Wissinger. 1992. RNA editing in trans-splicing intron sequences of nad 2 mRNAs in Oenothera mitochondria. J. Biol. Chem. 267:76157623.
21. Blum, B.,, N. Bakalara,, and L. Simpson. 1990. A model for RNA editing in kinetoplastid mitochondria: "guide" RNA molecules transcribed from maxicircle DNA provide the edited information. Cell 60:189198.
22. Bonitz, S. G.,, and A. Tzagoloff. 1980. Assembly of the mitochondrial membrane system. Sequences of yeast mitochondrial tRNA genes. J. Biol. Chem. 255:90759081.
23. Borsuk, P.,, A. Sirko,, and E. Bartnik. 1986. A methionine tRNA gene from lupine mitochondria. Nucleic Acids Res. 14:7508.
24. Browning, K. S.,, and U. L. RajBhandary. 1982. Cytochrome oxidase subunit III gene in Neurospora crassa mitochondria: location and sequence. J. Biol. Chem. 257:52535256.
25. Burger, G.,, M. H. Citterich,, M. A. Nelson,, S. Werner,, and G. Macino. 1985. RNA processing in Neurospora crassa mitochondria: transfer RNAs punctuate a large precursor transcript. EMBO J. 4:197204.
26. Cantatore, P.,, M. Roberti,, G. Rainaldi,, M. N. Gadaleta,, and C. Saccone. 1989. The complete nucleotide sequence, gene organization, and genetic code of the mitochondrial genome of Paracentrotus lividus. J. Biol. Chem. 264:1096510975.
27. Cattaneo, R. 1991. Different types of messenger RNA editing. Annu. Rev. Genet. 25:7188.
28. Chang, Y. S.,, and F. L. Huang. Unpublished data. EMBL accession no. X61010.
29. Chen, S. H.,, G. Habib,, C.-Y. Yang,, Z.-W. Gu,, B. R. Lee,, S.-A. Weng,, S. R. Silberman,, S.-J. Cai,, J. P. Deslypere,, M. Rosseneu, et al. 1987. Apolipoprotein B-48 is the product of a messenger RNA with an organ-specific in-frame stop codon. Science 238:363366.
30. Chevalier, C.,, C. Saillard,, and J. M. Bove. 1990. Organization and nucleotide sequence of the Spiroplasma citri genes for ribosomal protein S2, elongation factor Ts, Spiralin, phosphofructokinase, pyruvate kinase, and an unidentified protein. J. Bacteriol. 172:26932703.
31. Clark-Walker, G. D.,, C. R. McArthur,, and K. S. Spriprakash. 1985. Location of transcriptional control signals and transfer RNA sequence in Torulopsis glabrata mitochondrial DNA. EMBO J. 4:465473.
32. Clary, D. O.,, and D. R. Wolstenholme. 1985. The mitochondrial DNA molecule of Drosophila yakuba: nucleotide sequence, gene organization, and genetic code. J. Mol. Evol. 22:252271.
33. Conklin, P. L.,, R. K. Wilson,, and M. R. Hanson. 1991. Multiple trans-splicing events are required to produce a mature nad1 transcript in a plant mitochondrion. Gene Dev. 5: 14071415.
34. Coruzzi, G.,, S. G. Bonitz,, B. E. Thalenfeld,, and A. Tzagoloff. 1981. Assembly of the mitochondrial membrane system. Analysis of the nucleotide sequence and transcripts in the oxil region of yeast mitochondrial DNA. J. Biol. Chem. 256:1278012787.
35. Covello, P. S.,, and M. W. Gray. 1989. RNA editing in plant mitochondria. Nature (London) 341:662666.
36. Covello, P. S.,, and M. W. Gray. 1990. Differences in editing at homologous sites in messenger RNAs from angiosperm mitochondria. Nucleic Acids Res. 18:51895196.
37. Crick, E. H. C. 1966. Codon-anticodon pairing: the wobble hypothesis. J. Mol. Biol. 19:548555.
37a. Crozier, R. H.,, and Y. C. Crozier. 1993. The mitochondrial genome of the honeybee Apis mellifera: complete sequence and genome organization. Genetics 133:97117.
38. Cununings, D. J.,, I. A. Macneil,, J. Domenico,, and E. T. Matsuura. 1985. Excision-amplification of mitochondrial DNA during senescence in Podospore anserina. DNA sequence analysis of three unique "plasmids". J. Mol. Biol. 185:659680.
39. de Bruijn, M. H. L. 1983. Drosophila melanogaster mitochondrial DNA, a novel organization and genetic code. Nature (London) 304:234241.
40. Desjardins, P.,, and R. Morais. 1990. Sequence and gene organization of the chicken mitochondrial genome. A novel gene order in higher vertebrates. J. Mol. Biol. 212:599634.
41. Dubin, D. T.,, C.-C. HsuChen,, G. R. Cleaves,, and K. D. Timko. 1984. Sequence and structure of a serine tRNA with GCU anticodon from mosquito mitochondria, J. Mol. Biol. 176:251260.
42. Dudler, R.,, C. Schmidhausen R,, W. Parish,, R. E. H. Wettenhall,, and T. Schmidt. 1988. A mycoplasma high-affinity transport system and the in vitro invasiveness of mouse sarcoma cells. EMBO J. 7:39633970.
42a. Durrheim, G. A.,, V. A. Corfield,, E. H. Harley,, and M. H. Ricketts. 1993. Nucleotide sequence of cytochrome oxidase (subunit III) from the mitochondrion of the tunicate Pyura stolonifera: evidence that AGR encodes glycine. Nucleic Acids Res. 21:35873588.
43. Feagin, J. E.,, J. M. Abraham,, and K. Stuart. 1988. Extensive editing of the cytochrome c oxidase III transcript in Trypanosoma brucei. Cell 53:413422.
44. Fox, T. D. 1987. Natural variation in the genetic code. Annu. Rev. Genet. 21:6791.
45. Fox, T. D.,, and C. J. Leaver. 1981. The zea mays mitochondrial gene coding cytochrome oxidase subunit II has an intervening sequence and does not contain TGA codons. Cell 26:315323.
46. Fujii, H.,, T. Shimada,, Y. Goto,, and T. Okazaki. 1988. Cloning of the mitochondrial genome of Rana catesbeiana and the nucleotide sequences of the ND2 and five tRNA genes. J. Biochem. 103:474481.
47. Gadaleta, G.,, G. Pepe,, G. De Candia,, C. Quagliariello,, E. Sbisa,, and C. Saccone. 1989. The complete nucleotide sequence of the Rattus norvegicus mitochondrial genome: cryptic signals revealed by comparative analysis between vertebrates. J. Mol. Evol. 28:497516.
48. Garesse, R. 1988. Drosophila melanogaster mitochondrial DNA: gene organization and evolutionary considerations. Genetics 118:649683.
49. Garey, J. R.,, and D. R. Wolstenholme. 1989. Platyhelminth mitochondrial DNA: evidence for early evolutionary origin of a tRNASerAGN that contains a dihydrouridine arm replacement loop, and of serine-specifying AGA and AGG codons. J. Mol. Evol. 28:374387.
50. Grisi, E.,, T. A. Brown,, R. B. Waring,, C. Scazzocchio,, and R. W. Davies. 1982. Nucleotide sequence of a region of the mitochondrial genome of Aspergillus nidulans including the gene for ATPase subunit 6. Nucleic Acids Res. 10:35313539.
51. Gualberto, J. M.,, G. Bonnard,, L. Lamattina,, and J. M. Grienenberger. 1991. Expression of the wheat mitochondrial nad3-rps12 transcription unit: correlation between editing and mRNA maturation. The Plant Cell 3:11091120.
52. Gualberto, J. M.,, L. Lamattina,, G. Bonnard,, J.-H. Weil,, and J.-M. Grienenberger. 1989. RNA editing in wheat mitochondria results in the conservation of protein sequences. Nature (London) 341:660662.
53. Gualberto, J. M.,, J.-H. Weil,, and J.-M. Grienenberger. 1990. Editing of the wheat coxIII transcript: evidence for twelve C to U and one U to C conversions and for sequence similarities around editing sites. Nucleic Acids Res. 18:37713776.
54. Guthrie, C.,, and J. Abelson. 1982. Organization and expression of tRNA genes in Saccharomyces cerevisiae, p. 487528. In The Molecular Biology of the Yeast Saccharomyces, Metabolism and Gene Expression. Cold Spring Harbor Laboratory, Cold Spring Harbor, N.Y.
55. Hanyu, N.,, Y. Kuchino,, and S. Nishimura. 1986. Dramatic events in ciliate evolution: alteration of UAA and UAG termination codons to glutamine codons due to anticodon mutations in two Tetrahymena tRNAsGln. EMBO J. 5:13071311.
56. Harper, D. S.,, and C. L. Jahn. 1989. Differential use of termination codons in ciliated protozoa. Proc. Natl. Acad. Sci. USA 86:32523256.
57. Heckman, J. E.,, L. I. Hecker,, S. D. Schwartzbach,, W. E. Barnett,, B. Baumstark,, and U. L. RajBhandary. 1978. Structure and function of initiator methionine tRNA from the mitochondria of Neurospora crassa. Cell 13:8395.
58. Heckman, J. E.,, J. Sarnoff,, B. Alzner-DeWeerd,, S. Yin,, and U. L. RajBhandary. 1980. Novel features in the genetic code and codon reading patterns in Neurospora crassa mitochondria based on sequences of six mitochondrial tRNAs. Proc. Natl. Acad. Sci. USA 77:31593163.
59. Heinonen, T. Y. K.,, M. N. Schnare,, P. G. Young,, and M. W. Gray. 1987. Rearranged coding segments, separated by a transfer RNA gene, specify the two parts of a discontinuous large subunit ribosomal RNA in Tetrahymena pyriformis mitochondria. J. Biol. Chem. 262:28792887.
60. Helftenbein, E. 1985. Nucleotide sequence of a macro-nuclear DNA molecule coding for a-tubulin from the ciliate Stylonychia lemnae. Special codon usage: TAA is not a translation termination codon. Nucleic Acids Res. 13:415433.
61. Helftenbein, E.,, and E. Muller. 1988. Both a-tubulin genes are transcriptionally active in Stylonychia lemnae. Curr. Genet. 13:425432.
61a. Hensgens, L. A. M.,, J. Brakenhoff,, B. F. De Vries,, P. Sloof,, M. C. Tromp,, J. H. Van Boom,, and R. Benne. 1984. The sequence of the gene for cytochrome c oxidase 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. 12:73277344.
62. Hensgens, L. A. M.,, L. A. Grivell,, P. Borst,, and J. L. Bos. 1979. Nucleotide sequence of the mitochondrial structural gene for subunit 9 of yeast ATPase complex. Proc. Natl. Acad. Sci. USA 76:16631667.
63. Herrick, G.,, D. Hunter,, K. Williams,, and K. Kotten 1987. Alternate processing during development of a macronuclear chromosome family in Oxytricha fallax. Genes Dev. 1:10471058.
64. Hiesel, R.,, B. Wissinger,, W. Schuster,, and A. Brennicke. 1989. RNA editing in plant mitochondria. Science 246:16321634.
65. Himeno, H.,, H. Masaki,, T. Kawai,, T. Ohta,, I. Kumagai,, K. Miura,, and K. Watanabe. 1987. Unusual genetic codes and a novel genome structure for tRNASerAGY in starfish mitochondrial DNA. Gene 56:219230.
66. Hoch, B.,, R. M. Maier,, K. Appel,, G. L. Igloi,, and H. Kossel. 1991. Editing of a chloroplast mRNA by creation of an initiation codon. Nature (London) 353:178180.
67. Hoffmann, R. J.,, J. L. Boore,, and W. M. Brown. 1992. A novel mitochondrial genome organization for the blue mussel, Mytilus edulis. Genetics 131:397412.
68. Horowitz, S.,, and M. A. Gorovsky. 1985. An unusual genetic code in nuclear genes of Tetrahymena. Proc. Natl. Acad. Sci. USA 82:24522455.
69. HsuChen, C.-C.,, G. R. Cleaves,, and D. T. Dubin. 1983. A major lysine tRNA with a CUU anticodon in insect mitochondria. Nucleic Acids Res. 11:86598662.
70. HsuChen, C.-C.,, and D. T. Dubin. 1984. A cluster of four transfer RNA genes in mosquito mitochondrial DNA. Biochem. Intern. 8:385391.
71. HsuChen, C.-C.,, R. M. Kotin,, and D. T. Dubin. 1984. Sequences of the coding and flanking regions of the large ribosomal subunit RNA gene of mosquito mitochondria. Nucleic Acids Res. 12:77717785.
72. Hudspeth, M. E. S.,, W. M. Ainley,, D. S. Shumard,, R. A. Butow,, and L. I. Grossman. 1982. Location and structure of the varl gene on yeast mitochondrial DNA: nucleotide sequence of the 40.0 allele. Cell 30:617626.
73. Inagaki, Y.,, Y. Bessho,, and S. Osawa. 1992. Unpublished data.
74. Inamine, J. M.,, T. P. Denny,, S. Loechel,, U. Schaper,, C.-H. Huang,, K. F. Bott, and P-C. Hu. 1988. Nucleotide sequence of the P1 attachment-protein gene of Mycoplasma pneumoniae. Gene 64:217229.
75. Inamine, J. M.,, K.-C. Ho,, S. Loechel,, and P.-C. Hu. 1990. Evidence that UGA is read as a tryptophan rather than as a stop codon by Mycoplasma pneumoniae, Mycoplasma genitalium and Mycoplasma gallisepticum. J. Bacteriol. 172:504506.
76. Jacobs, H. T.,, S. Asakawa,, T. Araki,, K. Miura,, M. Smith,, and K. Watanabe. 1989. Conserved tRNA gene cluster in starfish mitochondrial DNA. Curr. Genet. 15:193206.
77. Jacobs, H. T.,, D. J. Elliott,, V. B. Math,, and A. Farquharson. 1988. Nucleotide sequence and gene organization of sea-urchin mitochondrial DNA. J. Mol. Biol. 202:185217.
78. Janke, A.,, and S. Paabo. 1993. Editing of a tRNA anticodon in marsupial mitochondria changes its codon recognition. Nucleic Acids Res. 21:15231525.
79. Johansen, S.,, P. H. Guddal,, and T. Johansen. 1990. Organization of the mitochondrial genome of atlantic cod, Gadus morhua. Nucleic Acids Res. 18:411419.
80. Joyce, P. B. M.,, and M. W. Gray. 1989. Aspartate and asparagine tRNA genes in wheat mitochondrial DNA: a cautionary note on the isolation of tRNA genes from plants. Nucleic Acids Res. 17:78657878.
81. Joyce, P. B. M.,, and M. W. Gray. 1989. Nucleotide sequence of a wheat mitochondrial lysine tRNA gene. Biochim. Biopbys. Acta. 1008:355356.
82. Jukes, T. H.,, Y. Bessho,, T. Ohama,, and S. Osawa. 1991. Release factors and genetic code. Nature (London) 352:575.
83. Kano, A.,, Y. Andachi,, T. Ohama,, and S. Osawa. 1991. Novel anticodon composition of transfer RNAs in Micrococcus luteus, a bacterium with a high genomic G + C content. Correlation with codon usage, J. Mol. Biol. 221:387401.
84. Kano, A.,, T. Ohama,, and S. Osawa. 1992. Unpublished data.
85. Kawaguchi, Y.,, H. Honda,, J. Taniguchi-Morimura., and S. Iwasaki. 1989. The codon CUG is read as serine in an asporogenic yeast Candida cylindracea. Nature (London) 341:164166.
86. Knoop, V.,, W. Schuster,, B. Wissinger,, and A. Brennicke. 1991. Trans splicing integrates an exon of 22 nucleotides into the nad 5 mRNA in higher plant mitochondria. EMBO J. 10: 34833493.
87. Kochel, H. G.,, C. M. Lazarus,, N. Basak,, and H. Kuntzel. 1981. Mitochondrial tRNA gene clusters in Aspergillus nidulans: organization and nucleotide sequence. Cell 23:625633.
88. Kojima, A.,, S. Yokoyama,, Y. Andachi,, Y. Bessho,, T. Ohama,, and S. Osawa. 1992. Unpublished data.
89. Kondo, K.,, H. Sone,, H. Yoshida,, T. Toida,, K. Kanatani,, Y.-M. Hong,, N. Nishino,, and J. Tanaka. 1990. Cloning and sequence analysis of the arginine deiminase gene from Mycoplasma arginini. Mol. Gen. Genet. 221:8186.
90. Koslowsky, D. J.,, G. J. Bhat,, A. L. Perrollaz,, J. E. Feagin,, and K. Stuart. 1990. The MURF3 gene of T. brucei contains multiple domains of extensive editing and is homologous to a subunit of NADH dehydrogenase. Cell 62:901911.
91. Koslowsky, D. J.,, G. J. Bhat,, L. K. Read,, and K. Stuart. 1991. Cycles of progressive realignment of gRNA with mRNA in RNA editing. Cell 67:537546.
92. Kuchino, Y.,, N. Hanyu,, F. Tashiro,, and S. Nishimura. 1985. Tetrabymena thermopbilia glutamine tRNA and its gene that corresponds to UAA termination codon. Proc. Natl. Acad. Sci. USA 82:47584762.
93. Kudla, J.,, G. L. Igloi,, M. Metzlaff,, R. Hagemann,, and H. Kossel. 1992. RNA editing in tobacco chloroplasts leads to the formation of a translatable psbL mRNA by a C to U substitution within the initiation codon. EMBO J. 11:10991103.
94. Kumazawa, Y.,, C. J. Schwartzbach,, H.-X. Liao,, K. Mizumoto,, Y. Kaziro,, K. Miura,, K. Watanabe,, and L. L. Spremulli. 1991. Interactions of bovine mitochondrial phenylalanyl-tRNA with ribosomes and elongation factors from mitochondria and bacteria. Biochim. Biophys. Acta. 1090:167172.
95. Lamattina, L.,, and J. M. Grienenberger. 1991. RNA editing of the transcript coding for subunit 4 of NADH dehydrogenase in wheat mitochondria: uneven distribution of the editing sites among four exons. Nucleic Acids Res. 19:32753282.
96. Lee, C. C.,, K. M. Timms,, C. N. A. Trotman,, and W. P. Tate. 1987. Isolation of a rat mitochondrial release factor. Accommodation of the changed genetic code for termination. J. Biol. Chem. 262:35483552.
97. Leon, P.,, V. Walbot,, and P. Bedingen 1989. Molecular analysis of the linear 2.3 kb plasmid of maize mitochondria: apparent capture of tRNA genes. Nucleic Acids Res. 17:40894099.
98. Li, M.,, and A. Tzagoloff. 1979. Assembly of the mitochondrial membrane system: sequence of yeast mitochondrial valine and an unusual threonine tRNA gene. Cell 18:4753.
99. Liu, H.,, and A. T. Beckenbach. 1992. Evolution of the mitochondrial cytochrome oxidase II gene among 10 orders of insects. Mol. Phylog. Evol. 1:4152.
100. Macino, G.,, G. Coruzzi,, F. G. Nobrega,, M. Li,, and A. Tzagoloff. 1979. Use of the UGA terminator as a tryptophan codon in yeast mitochondria. Proc. Natl. Acad. Sci. USA 76:37843785.
101. Macino, G.,, and A. Tzagoloff. 1979. Assembly of the mitochondrial membrane system: partial sequence of a mitochondrial ATPase gene in Saccharomyces cerevisiae. Proc. Natl. Acad. Sci. USA 76:131135.
102. Mahendran, R.,, M. R. Spottswood,, and D. L. Miller. 1991. RNA editing by cytidine insertion in mitochondria of Physarum polycephalum. Nature (London) 349:434438.
103. Marechal, L.,, P. Guillemaut,, J.-M. Grienenberger,, G. Jeannin,, and J.-H. Weil. 1985. Sequence and codon recognition of bean mitochondria and chloroplast tRNAsTrP: evidence for a high degree of homology. Nucleic Acids Res. 13:44114416.
104. Marechal, L.,, P. Runeberg-Roos,, J. M. Grinenberger,, J. Colin,, J. H. Weil,, B. Lejeune,, F. Quetier,, and D. M. Lonsdale. 1987. Homology in the region containing a tRNATrP gene and a (complete or partial) tRNAPro gene in wheat mitochondrial and chloroplast genomes. Curr. Genet. 12:9198.
105. Martin, R. P.,, J.-M. Schneller,, A. J. C. Stahl,, and G. Dirheimer. 1979. Import of nuclear deoxyribonucleic acid coded lysine-accepting transfer ribonucleic acid (anticodon C-U-U) into yeast mitochondria. Biochemistry 18:46004605.
106. Martin, R.,, A.-P. Sibler,, and G. Dirheimer. 1982. The primary structures of three yeast mitochondrial serine tRNA isoacceptors. Biochimie 64:10731079.
107. Maslov, D. A.,, and L. Simpson. 1992. The porality of editing within a multiple gRNA-mediated domain is due to formation of anchors for upstream gRNAs by downstream editing. Cell 70:459467.
108. Meyer, F. M.,, H. J. Schmidt,, E. Plumper,, A. Hasilik,, G. Mersmann,, H. E. Meyer,, A. Engstrom,, and K. Heckmann. 1991. UGA is translated as cysteine in pheromone 3 of Euplotes octocarinatus. Proc. Natl. Acad. Sci. USA 88:37583761.
109. Miller, D. L.,, R. Mahandran,, M. Spottswood,, M. Ling,, S. Wang,, N. Yang,, and H. Costandy,. 1993. RNA editing in mitochondria of Physarum polycephalum, p. 87103. In R. Behne (ed.), RNA Editing: the Alteration of Protein Coding Sequences of RNA. Ellis Horwood Ltd., New York.
110. Moriya, J.,, T. Yokogawa,, K. Wakita,, T. Ueda,, K. Nishikawa,, P. F. Crain,, T. Hashizume,, S. C. Pomerantz,, J. A. McCloskey,, G. Kawai,, N. Hayashi,, S. Yokoyama,, and K. Watanabe. 1994. A novel modified nucleoside found at the first position of the anticodon of methionine tRNA from bovine liver mitochondria. Biochemistry 33:22342239.
111. Muramatsu, T.,, K. Nishikawa,, F. Nemoto,, Y. Kuchino,, S. Nishimura,, T. Miyazawa,, and S. Yokoyama. 1988. Codon and amino acid specificities of a transfer RNA are both converted by a single post-transcriptional modification. Nature (London) 336:179181.
112. Muramatsu, T.,, S. Yokoyama,, N. Horie,, A. Matsuda,, T. Ueda,, Z. Yamaizumi,, Y. Kuchino,, S. Nishimura,, and T. Miyazawa. 1988. A novel lysine-substituted nucleoside in the first position of the anticodon of minor isoleucine tRNA from Escherichia coli. J. Biol. Chem. 263:92619267.
113. Netzker, R.,, H. G. Kochel,, N. Basak,, and H. Kuntzel. 1982. Nucleotide sequence of Aspergillus nidulans mitochondrial genes coding for ATPase subunit 6, cytochrome oxidase sub-unit 3, seven unidentified proteins, four tRNAs and L-rRNA. Nucleic Acids Res. 10:47834794.
114. Nomoto, M.,, N. Imai,, H. Saigo,, T. Matsui,, and T. Mita. 1987. Characterization of two types of histone H2B genes from macronuclei of Tetrahymena thermophila. Nucleic Acids Res. 15:56815698.
115. Nowak, C.,, and U. Kuck. 1990. RNA editing of the mitochondrial atp9 transcript from wheat. Nucleic Acids Res. 18:71647164.
116. Oba, T.,, Y. Andachi,, A. Muto,, and S. Osawa. 1991. CGG: an unassigned or nonsense codon in Mycoplasma capricolum. Proc. Natl. Acad. Sci. USA 88:921925.
117. Oba, T.,, Y. Andachi,, A. Muto,, and S. Osawa. 1991. Translation in vitro of codon UGA as tryptophan in Mycoplasma capricolum. Biochimie 73:11091112.
118. Oda, K.,, K. Yamato,, E. Ohta,, Y. Nakamura,, M. Takemura,, N. Nozato,, K. Akashi,, T. Kanegae,, Y. Ogura,, T. Kohchi,, and K. Ohyama. 1992. Gene organization deduced from the complete sequence of Liverwort Marchantía polymorpha mitochondrial DNA. J. Mol. Biol. 223:17.
119. Ohama, T.,, A. Muto,, and S. Osawa. 1989. Spectinomycin Operon of Micrococcus luteus: evolutionary implications of organization and novel codon usage. J. Mol. Evol. 29:381395.
120. Ohama, T.,, A. Muto,, and S. Osawa. 1990. Role of GC-biased mutation pressure on synonymous codon choice in Micrococcus luteus, a bacterium with a high genomic GC-content. Nucleic Acids Res. 18:15651569.
121. Ohama, T.,, S. Osawa,, K. Watanabe,, and T. H. Jukes. 1990. Evolution of the mitochondrial genetic code. IV. AAA as an asparagine codon in some animal mitochondria., J. Mol. Evol. 30:329332.
122. Ohama, T.,, T. Suzuki,, M. Mori,, S. Osawa,, T. Ueda,, K. Watanabe,, and T. Nakase. 1993. Non-universal decoding of the leucine codon CUG in several Candida species. Nucleic Acids Res. 21:40394045.
123. Ohama, T.,, E. Yamao,, A. Muto,, and S. Osawa. 1987. Organization and codon usage of the streptomycin operon in Micrococcus luteus, a bacterium with a high genomic G + C content. J. Bacteriol. 169:47704777.
124. Ohkubo, S.,, A. Muto,, Y. Kawauchi,, F. Yamao,, and S. Osawa. 1987. The ribosomal protein gene cluster of Mycoplasma capricolum. Mol. Gen. Genet. 210:314322.
125. Okimoto, R.,, H. M. Chamberlin,, J. L. Macfarlane,, and D. R. Wolstenholme. 1991. Repeated sequence sets in mitochondrial DNA molecules of root knot nematodes (Melo-idogyne): nucleotide sequences, genome location and potential for host-race identification. Nucleic Acids Res. 19:16191626.
126. Okimoto, R.,, J. L. Macfarlane,, D. O. Clary,, and D. R. Wolstenholme. 1992. The mitochondrial genomes of two nematodes, Caenorhabditis elegans and Ascaris suum. Genetics 130:471498.
127. Osawa, S.,, D. Collins,, T. Ohama,, T. H. Jukes,, and K. Watanabe. 1990. Evolution of the mitochondrial genetic code. III. Reassignment of CUN codons from leucine to threonine during evolution of yeast mitochondria. J. Mol. Evol. 30:322328.
128. Osawa, S.,, T. H. Jukes,, K. Watanabe,, and A. Muto. 1992. Recent evidence for evolution of the genetic code. Microbiol. Rev. 56:229264.
129. Ozeki, H.,, K. Ohyama,, H. Inokuchi,, H. Fukuzawa,, T. Kohchi,, T. Sato,, K. Nakahigashi,, and K. Umesono. 1987. Genetic system of chloroplasts. Cold Spring Harbor Symp. Quant. Biol. 52:791804.
130. Pape, L. K.,, and A. Tzagoloff. 1985. Cloning and characterization of the gene for the yeast cytoplasmic threonyl-tRNA synthetase. Nucleic Acids Res. 13:61716183.
131. Pollard, V. W.,, S. P. Rohrer,, E. F. Michelotti,, K. Hancock,, and S. L. Hajduk. 1990. Organization of minicircle genes for guide RNAs in Trypanosoma brucei. Cell 63:783790.
132. Powell, L. M.,, S. C. Wallis,, R. J. Pease,, Y. H. Edwards,, T. J. Knott,, and J. Scott. 1987. A novel form of tissue-specific RNA processing produces apolipoprotein-B48 in intestine. Cell 50:831840.
133. Pritchard, A. E.,, C. L. Sable,, S. E. Venuti,, and D. J. Cummings. 1990. Analysis of NADH dehydrogenase proteins, ATPase subunit 9, cytochrome b, and ribosomal protein L14 encoded in the mitochondrial DNA of Paramecium. Nucleic Acids Res. 18:163171.
134. Pritchard, A. E.,, J. J. Seilhamer,, R. Mahalingam,, C. L. Sable,, S. E. Venuti,, and D. J. Cummings. 1990. Nucleotide sequence of the mitochondrial genome of Paramecium. Nucleic Acids Res. 18:173180.
135. Randerath, K.,, H. P. Agrawal,, and E. Randerath. 1983. tRNA alterations in cancer. Recent Results Cancer Res. 84:103120.
136. Read, L. K.,, P. J. Myler,, and K. Stuart. 1992. Extensive editing of both processed and preprocessed maxicircle CR6 transcripts in Trypanosoma brucei. J. Biol. Chem. 267:11231128.
137. Renbaum, P.,, D. Abrahamove,, A. Fainsod,, G. G. Wilson,, S. Rottem,, and A. Razin. 1990. Cloning, characterization, and expression in Escherichia coli of the gene coding for the CpG DNA methylase from Spiroplasma sp. strain MQ1 (M-Sss1). Nucleic Acids Res. 18:11451152.
138. Roe, B. A.,, D.-P. Ma,, R. K. Wilson,, and J. F.-H. Wong. 1985. The complete nucleotide sequence of the Xenopus laevis mitochondrial genome. J. Biol. Chem. 260:97599774.
139. Roe, B. A.,, J. F. H. Wong,, E. Y. Chen,, and P. A. Armstrong,. 1981. Sequence analysis of mammalian mitochondrial tRNAs, p. 167176. In A. G. Walton (ed.), Recombinant DNA: Proceedings of the Third Cleveland Symposium on Macromolecules. Elsevier Scientific Publishing Co., Amsterdam.
140. Samuelsson, T.,, T. Axberg,, T. Boren,, and U. Lagerkvist. 1983. Unconventional reading of the glycine codons. J. Biol. Chem. 258:1317813184.
141. Samuelsson, T.,, Y. S. Guindy,, F. Lustig,, T. Boren,, and U. Lagerkvist. 1987. Apparent lack of discrimination in the reading of certain codons in Mycoplasma mycoides. Proc. Natl. Acad. Sci. USA 84:31663170.
142. Sangare, A.,, D. Lonsdale,, J.-H. Weil,, and J.-M. Grienen-berger. 1989. Sequence analysis of the tRNATyr and tRNALys genes and evidence for the transcription of a chloroplast-like tRNAMl!t in maize mitochondria. Curr. Genet. 16:195201.
143. Sasuga, J.,, S. Yokobori,, M. Kaifu,, T. Ueda,, K. Nishikawa,, and K. Watanabe. Unpublished data.
144. Schneider, S. U.,, M. B. Leible,, and X.-P. Yang. 1989. Strong homology between the small subunit of ribulose-l,5-bisphosphate carboxylase/oxygenase of two species of Acetabularia and the occurrence of unusual codon usage. Mol. Gen. Genet. 218:445452.
145. Schuster, W.,, and A. Brennicke. 1990. RNA editing of AT-Pase subunit 9 transcripts in Oenothera mitochondria. FEBS Lett. 268:252256.
145a. Schuster, W.,, J. M. Greinenberger,, J.-H. Weil,, and A. Brennicke. 1988. Comparison of tRNATrp and tRNAPro gene sequences in the chloroplast and mitochondrial genomes of Oenothera. Nucleic Acids Res. 16:7737.
146. Schuster, W.,, R. Hiesel,, B. Wissinger,, and A. Brennicke. 1990. RNA editing in the cytochrome b locus of the higher plant Oenothera berteriana includes a U-to-C transition. Mol. Cell Biol. 10:24282431.
147. Schuster, W.,, M. Unseld,, B. Wissinger,, and A. Brennicke. 1990. Ribosomal protein S14 transcripts are edited in Oenothera mitochondria. Nucleic Acids Res. 18:229233.
148. Sebald, W.,, E. Wachter,, and A. Tzagoloff. 1979. Identification of amino acid substitutions in the dicyclohexylcarbodiimide binding subunit of the mitochondrial ATPase complex from oligomycin resistant mutants of Saccharomyces cerevisiae. Eur. J. Biochem. 100:699707.
149. Seilhamer, J. J.,, and D. J. Cummings. 1982. Altered genetic code in Paramecium mitochondria: possible evolutionary trends. Mol. Gen. Genet. 187:236239.
150. Shibutani, S.,, M. Takeshita,, and A. P. Grollman. 1991. Insertion of specific bases during DNA synthesis past the oxidation-damaged base 8-oxoG. Nature (London) 349:431434.
151. Shimayama, T.,, H. Himeno,, J. Sasuga,, S. Yokobori,, T. Ueda,, and K. Watanabe. 1990. The genetic code of a squid mitochondrial gene. Nucleic Acids Res. Symp. Ser. 22:7374.
152. Shinozaki, K.,, M. Ohme,, M. Tanaka,, T. Wakasugi,, N. Hayashi,, T. Matsubayashi,, N. Zaita,, J. Chunwongse,, J. Obokata,, K. Yamaguchi-Shinozaki,, C. Ohto,, K. Torazawa,, E. Y. Meng,, M. Sugita,, H. Deno,, T. Kamogashira,, K. Yamada,, J. Kusuda,, F. Takaiwa,, A. Kato,, N. Tohdoh,, H. Shimada,, and M. Sugiura. 1986. The comlete nucleotide sequence of the tobacco chloroplast genome: its gene organization and expression. EMBO J. 5:20432049.
153. Sibler, A.-P.,, R. Bordonne,, G. Dirheimer,, and R. Martin. 1980. Structure primaire d'un tryptophane-tRNA de mitochondrie de Levure capable de traduire le codon de terminaison U-G-A. C. R. Acad. Sci. Paris. D 290:695698.
154. Sibler, A. P.,, G. Dirheimer,, and R. P. Martin. 1985. Yeast mitochondrial tRNAIle and tRNAMetm: nucleotide sequence and codon recognition patterns. Nucleic Acids Res. 13:13411345.
155. Sibler, A. P.,, G. Dirheimer,, and R. P. Martin. 1986. Codon reading patterns in Saccharomyces cerevisiae mitochondria based on sequences of mitochondrial tRNAs. FEBS Lett. 194:131138.
156. Simpson, L.,, and J. Shaw. 1989. RNA editing and the mitochondrial cryptogenesis of kinetoplastid protozoa. Cell 57:355366.
157. Smith, M. J.,, D. K. Banfield,, K. Doteval,, S. Gorski,, and D. J. Klowbel. 1990. Nucleotide sequence of nine protein-coding genes and 22 tRNAs in the mitochondrial DNA of the sea star Pisaster ochraceus. J. Mol. Evol. 31:195204.
158. Sollner-Webb, B. 1991. RNA editing. Curr. Opinion Cell Biol. 3:10561061.
159. Sommer, B.,, M. Kohler,, R. Sprengel,, and P. H. Seeburg. 1991. RNA editing in brain controls: a determinant of ion flow in glutamate-gated channels. Cell 67:1119.
160. Steinberg, S.,, A. Misch,, and M. Sprinzl. 1993. Compilation of tRNA sequences and sequences of tRNA genes. Nucleic Acids Res. 21:30113015.
161. Stuart, K. 1991. RNA editing in mitochondrial mRNA of trypanosomatides. Trends Biochem. Sci. 16:6872.
162. Stuart, K. 1991. RNA editing in trypanosomatid mitochondria. Annu. Rev. Microbiol. 45:327344.
163. Suyama, Y. 1985. Nucleotide sequences of three tRNA genes encoded in Tetrahymena mitochondrial DNA. Nucleic Acids Res. 13:32733284.
164. Suzuki, T.,, T. Ueda,, T. Yokogawa,, K. Nishikawa,, and K. Watanabe. 1994. Characterization of serine and leucine tRNAs in an asporogenic yeast Candida cylindracea and evolutionary implications of genes for tRNASerCAG responsible for translation of a non-universal genetic code. Nucleic Acids Res. 22:115123.
165. Tanaka, Y.,, K. Kuroe,, K. Angata,, and K. Yanagisawa. 1990. ORF209 of Dictyosterium discoideum mitochondrial DNA has a homologue in chloroplast DNA. Plant Mol. Biol. 15:659660.
165a. Tanaka, Y.,, K. Kuroe,, K. Angata,, and K. Yanagisawa. Unpublished data.
166. Tanaka, R.,, A. Muto,, and S. Osawa. 1989. Nucleotide sequence of tryptophan tRNA gene in Acholeplasma laidlawii. Nucleic Acids Res. 17:5842.
167. van de Spek, H.,, G.-J. Arts,, R. R. Zwaal,, J. Van den Burg,, P. Sloop,, and R. Benne. 1991. Conserved genes encode guide RNAs in mitochondria of Critbidia fasciculata. EMBO J. 10:12171224.
168. Walbot, V. 1991. RNA editing fixes problems in plant mitochondrial transcripts. Trends Genet. 7:3739.
169. Waring, R. B.,, R. W. Davies,, S. Lee,, E. Grisi,, M. M. Berks,, and C. Scazzocchino. 1981. The mosaic organization of the apocytochrome b gene of Aspergillus nidulans revealed by DNA sequencing. Cell 27:411.
170. Williams, K. R.,, and G. Herrick. 1991. Expression of the gene encoded by a family of macronuclear chromosomes generated by alternative DNA processing in Oxytricha fallax. Nucleic Acids Res. 19:47174724.
171. Wissinger, B.,, W. Schuster,, and A. Brennicke. 1990. Species-specific RNA editing patterns in the mitochondrial rpsl3 transcripts of Oenothera and Daucus. Mol. Gen. Genet. 224:389395.
172. Wissinger, B.,, W. Schuster,, and A. Brennicke. 1991. Trans splicing in Oenothera mitochondria: nad 1 mRNAs are edited in exon and trans-splicing group II intron sequences. Cell 65:473482.
173. Wolstenholme, D. R. 1992. Animal mitochondrial DNA: structure and evolution. Int. Rev. Cytol. 141:173216.
174. Wolstenholme, D. R.,, J. L. Macfarlane,, R. Okimoto,, D. O. Clary,, and J. A. Wahleithner. 1987. Bizarre tRNAs inferred from DNA sequences of mitochondrial genomes of nematode worms. Proc. Natl. Acad. Sci. USA 84:13241328.
175. Wolstenholme, D. R.,, R. Okimoto,, J. L. Macfarlane,, G. A. Pont,, H. M. Chamberlin,, J. R. Garey,, and N. A. Okada,. 1990. Unusual features of lower invertebrate mitochondrial genomes, p. 103106. In E. Quagliariello,, S. Papa,, F. Palmieri,, and C. Saccone (ed.), Structure, Function, and Biogenesis of Energy Transfer Systems. Elsevier, Amsterdam.
176. Yamao, E.,, S. Iwagami,, Y. Azumi,, A. Muto,, S. Osawa,, N. Fujita,, and A. Ishihama. 1988. Evolutionary dynamics of tryptophan tRNAs in Mycoplasma capricolum. Mol. Gen. Genet. 212:364369.
177. Yamao, E.,, A. Muto,, Y. Kawauchi,, M. Iwami,, S. Iwagami,, Y. Azumi,, and S. Osawa. 1985. UGA is read as tryptophan in Mycoplasma capricolum. Proc. Natl. Acad. Sci. USA 82:23062309.
178. Yang, A. J.,, and R. M. Mulligan. 1991. RNA editing intermediates of cox 2 transcripts in maize mitochondria. Mol. Cell. Biol. 11:42784281.
179. Yokobori, S.,, T. Ueda,, and K. Watanabe. 1993. Codons AGA and AGG are read as glycine in Ascidian mitochondria. J. Mol. Evol. 36:18.
179a. Yokobori, S.,, T. Ueda,, and K. Watanabe. Unpublished data.
180. Yokogawa, T.,, T. Suzuki,, T. Ueda,, M. Mori,, T. Ohama,, Y. Kuchino,, S. Yoshinari,, I. Motoki,, K. Nishikawa,, S. Osawa,, and K. Watanabe. 1992. Serine tRNA complementary to the non-universal codon CUG in Candida cylindracea: evolutionary implications. Proc. Natl. Acad. Sci. USA 89:74087411.
181. Yokoyama, S.,, T. Watanabe,, K. Murao,, H. Ishikura,, Z. Yamaizumi,, S. Nishimura,, and T. Miyazawa. 1985. Molecular mechanism of codon recognition of tRNA species with modified uridine in the first position of the anticodon. Proc. Natl. Acad. Sci. USA 82: 49054909.

Tables

Generic image for table
Table 1

Current Status of codon-anticodon pairing rules

Adapted from reference .

For modified bases, see chapter 12.

Citation: Watanabe K, Osawa S. 1995. tRNA Sequences and Variations in the Genetic Code, p 225-250. In tRNA. ASM Press, Washington, DC. doi: 10.1128/9781555818333.ch13
Generic image for table
Table 2

Variations in mitochondrial genetic code

ND = not determined; — = same as universal code.

Citation: Watanabe K, Osawa S. 1995. tRNA Sequences and Variations in the Genetic Code, p 225-250. In tRNA. ASM Press, Washington, DC. doi: 10.1128/9781555818333.ch13
Generic image for table
Table 3

Summary of the correlation between altered codons and the corresponding tRNA anticodons in mitochondrial systems of various organisms

Citation: Watanabe K, Osawa S. 1995. tRNA Sequences and Variations in the Genetic Code, p 225-250. In tRNA. ASM Press, Washington, DC. doi: 10.1128/9781555818333.ch13
Generic image for table
Table 4

Variations in eubacterial and in nuclear genetic code from “universal” genetic code

— = same as universal code, or not determined; N = not known; *U - cmnm5Um.

Determined for Mycoplasma capricolum ( ). Gene for tRNA with anticodon UCA was found in , , and ( ).

Determined for , , , , , and ( ).

Determined for ( ).

Citation: Watanabe K, Osawa S. 1995. tRNA Sequences and Variations in the Genetic Code, p 225-250. In tRNA. ASM Press, Washington, DC. doi: 10.1128/9781555818333.ch13
Generic image for table
Table 5

Effeet of genomic G+C content on eubacterial tRNA anticodon compositions and codon-anticodon pairing patterns

Table shows the general tendency of anticodon compositions in eubacteria with various genomic G+C contents and does not necessarily indicate that all boxes and sets actually have these compositions. Modification of U is not indicated (see Table 1 ). Reprinted from reference .

The bacteria are arranged in descending order of G+C content. c D = deletion.

Citation: Watanabe K, Osawa S. 1995. tRNA Sequences and Variations in the Genetic Code, p 225-250. In tRNA. ASM Press, Washington, DC. doi: 10.1128/9781555818333.ch13
Generic image for table
Table 6

Unassigned or nonsense codons

Yeast mitochondria

Citation: Watanabe K, Osawa S. 1995. tRNA Sequences and Variations in the Genetic Code, p 225-250. In tRNA. ASM Press, Washington, DC. doi: 10.1128/9781555818333.ch13
Generic image for table
Table 7

Examples of RNA editing occurring in plant mitochondria

+, RNA ediring in mitochondria.

Citation: Watanabe K, Osawa S. 1995. tRNA Sequences and Variations in the Genetic Code, p 225-250. In tRNA. ASM Press, Washington, DC. doi: 10.1128/9781555818333.ch13

This is a required field
Please enter a valid email address
Please check the format of the address you have entered.
Approval was a Success
Invalid data
An Error Occurred
Approval was partially successful, following selected items could not be processed due to error