Replication slippage may cause parallel evolution in the secondary structures of mitochondrial transfer RNAs

Molecular Biology and Evolution

Volumn 14, Issue 1, 1997, Pages 30-39

  Macey, J Robert ^a   Larson, Allan ^a,d   Ananjeva, Natalia B ^b   Papenfuss, Theodore J ^c  

^a UNIVERSITY OF WASHINGTON   (United States)

^b ZOOLOGICAL INSTITUTE   (Russian Federation)

^c UNIVERSITY OF CALIFORNIA   (United States)

^d WASHINGTON UNIVERSITY   (United States)

Author keywords

cysteine transfer RNA; mitochondrial DNA; phylogenetic; reptile

Indexed keywords

CYSTEINE; MITOCHONDRIAL RNA; TRANSFER RNA;

ANIMAL TISSUE; ANTICODON; ARTICLE; EVOLUTION; GENE DELETION; GENE REPLICATION; GENE SEQUENCE; GENETIC ANALYSIS; GENOME; NONHUMAN; PHYLOGENY; PROTEIN SECONDARY STRUCTURE;

EID: 0031031728     PISSN: 07374038     EISSN: None     Source Type: Journal    
DOI: 10.1093/oxfordjournals.molbev.a025699     Document Type: Article

References (30)

1. ANDERSON, S., A. T. BANKIER, B. G. BARRELL et al. (14 co-authors). 1981. Sequence and organization of the human mitochondrial genome. Nature 290:457-465.
2. BOORE, J. L., and W. M. BROWN. 1994. Complete DNA sequence of the mitochondrial genome of the black chiton, Katharina tunicata. Genetics 138:423-443.
3. _. 1995. Complete sequence of the mitochondrial DNA of the annelid worm, Lumbricus terrestris. Genetics 141: 305-319.
4. BUROKER, N. E., J. R. BROWN, T. A. GILBERT, P. J. O'HARA, A. T. BECKENBACH, W. K. THOMAS, and M. J. SMITH. 1990. Length heteroplasmy of sturgeon mitochondrial DNA: an illegitimate elongation model. Genetics 124:157-163.
5. DE BRUIJN, M. H. L., and A. KLUG. 1983. A model for the tertiary structure of mammalian mitochondrial transfer RNAs lacking the entire "dihydrouridine" loop and stem. EMBO J. 2:1309-1321.
6. DESJARDINS, P., and R. MORAIS. 1990. Sequence and gene organization of the chicken mitochondrial genome. J. Mol. Biol. 212:599-634.
7. _. 1991. Nucleotide sequence and evolution of coding and noncoding regions of a quail mitochondrial genome. J. Mol. Evol. 32:153-161.
8. DIRHEIMER, G., G. KEITH, P. DUMAS, and E. WESTHOF. 1995. Primary, secondary, and tertiary structures of tRNAs. Pp. 93-126 in D. SÖLL and U. RAJBHANDARY, eds. tRNA: structure, biosynthesis, and function. American Society for Microbiology Press, Washington, D.C.
9. ESTES, R., K. DE QUEIROZ, and J. GAUTHIER. 1988. Phylogenetic relationships within squamata. Pp. 119-281 in R. ESTES and G. PREGILL, eds. Phylogenetics of the lizard families, essays commemorating Charles L. Camp. Stanford University Press, Stanford, Calif.
10. ETHERIDGE, R., and K. DE QUEIROZ. 1988. A phylogeny of Iguanidae. Pp. 283-367 in R. ESTES and G. PREGILL, eds. Phylogenetics of the lizard families, essays commemorating Charles L. Camp. Stanford University Press, Stanford, Calif.
11. GAUTHIER, J., R. ESTES, and K. DE QUEIROZ. 1988. A phylogenetic analysis of Lepidosauromorpha. Pp. 15-98 in R. ESTES and G. PREGILL, eds. Phylogenetics of the lizard families, essays commemorating Charles L. Camp. Stanford University Press, Stanford, Calif.
12. HOELZEL, A. R., J. V. LOPEZ, G. A. DOVER, and S. J. O'BRIEN. 1994. Rapid evolution of a heteroplasmic repetitive sequence in the mitochondrial DNA control region of carnivores. J. Mol. Evol. 39:191-199.
13. JANKE, A., G. FELDMAIER-FUCHS, W. K. THOMAS, A. VON HAESELER, and S. PÄÄBO. 1994. The marsupial mitochondrial genome and the evolution of placental mammals. Genetics 137:243-256.
14. KLUGE, A. G. 1987. Cladistic relationships in the Gekkonoidea (Squamata, Sauria). Misc. Publ. Mus. Zool. Univ. Mich. 173:1-54.
15. KUMAZAWA, Y., and M. NISHIDA. 1993. Sequence evolution of mitochondrial tRNA genes and deep-branch animal phylogenetics. J. Mol. Evol. 37:380-398.
16. _. 1995. Variations in mitochondrial tRNA gene organization of reptiles as phylogenetic markers. Mol. Biol. Evol. 12:759-772.
17. LEVINSON, G., and G. A. GUTMAN. 1987. Slipped-strand mispairing: a major mechanism for DNA sequence evolution. Mol. Biol. Evol. 4:203-221.
18. LYNCH, M. 1996. Mutation accumulation in transfer RNAs: molecular evidence for Muller's ratchet in mitochondrial genomes. Mol. Biol. Evol. 13:209-220.
19. MACEY, J. R., A. LARSON, N. B. ANANJEVA, Z. FANG, and T. J. PAPENFUSS. 1997. Two novel gene orders and the role of light-strand replication in rearrangement of the vertebrate mitochondrial genome. Mol. Biol. Evol. 14:82-95.
20. MACEY, J. R., and A. VERMA. 1997. Homology in phylogenetic analysis: alignment of transfer RNA genes and the phylogenetic position of snakes. Mol. Phyl. Evol. (in press).
21. MADDISON, W. P., and D. R. MADDISON. 1992. MacClade: analysis of phylogeny and character evolution. Version 3.0. Sinauer, Sunderland, Mass.
22. MANIATIS, T., E. F. FRITSCH, and J. SAMBROOK. 1982. Molecular cloning: a laboratory manual. Cold Spring Harbor Laboratory, Cold Spring Harbor, N.Y.
23. RAMIREZ, V., P. SAVOIE, and R. MORAIS. 1993. Molecular characterization and evolution of a duck mitochondrial genome. J. Mol. Evol. 37:296-310.
24. ROE, B. A., D.-P. MA, R. K. WILSON, and J. F.-H. WONG. 1985. The complete sequence of the Xenopus laevis mitochondrial genome. J. Biol Chem. 260:9759-9774.
25. SCHWENK, K. 1988. Comparative morphology of the lepidosaur tongue and its relevance to squamate phylogeny. Pp. 569-598 in R. ESTES and G. PREGILL, eds. Phylogenetics of the lizard families, essays commemorating Charles L. Camp. Stanford University Press, Stanford, Calif.
26. SEUTIN, G., B. F. LANG, D. P. MINDELL, and R. MORAIS. 1994. Evolution of the WANCY region in amniote mitochondrial DNA. Mol. Biol. Evol. 11:329-340.
27. Ser to common three-dimensional constraints. J. Mol. Biol. 236: 982-989.
28. WOLSTENHOLME, D. R. 1992. Animal mitochondrial DNA: structure and evolution. Int. Rev. Cytol. 141:173-216.
29. 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 84:1324-1328.
30. WOLSTENHOLME, D. R., R. OKIMOTO, and J. L. MACFARLANE. 1994. Nucleotide correlations that suggest tertiary interactions in the TV-replacement loop-containing mitochondrial tRNAs of the nematodes, Caenorhabditis elegans and Ascaris suum. Nucleic Acids Res. 22:4300-4306.