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Gene Duplication, Gene Conversion and Codon Bias

  • Donal A. Hickey
  • Shaojiu Wang
  • Charalambos Magoulas

Abstract

Within many genes, synonymous codons are found in very unequal frequencies. This observation of codon bias is often interpreted as a reflection of natural selection acting to mold the codon “choice” to match the frequency of corresponding tRNAs.1, 2, 3, 4, 5, 6 While the observation of codon bias is undeniable, the selective interpretation has been questioned. For instance, the fact that many different codons are biased toward the same nucleotide has led to the suggestion that codon bias may simply be a reflection of mutational bias.7,8 On the other hand, arguments against mutational bias are based on the observation that the level of codon bias can vary dramatically between different genes in a single genome5and between coding sequences and adjacent non-coding sequences.10 In this paper we consider the possibility that at least some cases of non-random codon usage are due to a bias in DNA repair. Furthermore, we point out that DNA repair enzymes do not affect all genes in a uniform manner. For instance, the effects of DNA repair are especially pronounced in duplicated genes that are undergoing concerted evolution, and such genes do show an extreme bias in the distribution of synonymous codons. In general, competing theories about the causes of codon bias can be tested based on the predictions they make about the patterns of longterm evolutionary trends at the non-silent codon positions.10, 11 Consequently, we will discuss the possible relationship between biased codon usage and the amino acid composition of proteins. We conclude that the interaction of biased DNA repair and mutation may influence, not only the difference in codon bias between species, but also the observed differences between genes within a single genome.

Keywords

Gene Conversion Synonymous Codon Codon Bias Bias Codon Usage Concerted Evolution 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.

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References

  1. 1.
    T. Ikemura. (1985).Mol. Biol. Evol.2, 13–34.PubMedGoogle Scholar
  2. 2.
    P. M. Sharp and W-H. Li. (1986).J. Mol. Evol.24, 28–38.PubMedCrossRefGoogle Scholar
  3. 3.
    W-H. Li. (1987).J. Mol. Evol.24, 337–345.PubMedCrossRefGoogle Scholar
  4. 4.
    M. Bulmer. (1987).Nature325, 728–730.PubMedCrossRefGoogle Scholar
  5. 5.
    D. C. Shields, P. M. Sharp, D. G. Higgins, and F. Wright. (1978).Mol. Biol. Evol.5, 704–716.Google Scholar
  6. 6.
    E. N. Moriyama and D. L. Hartl. (1993).Genetics134, 847–858.PubMedGoogle Scholar
  7. 7.
    N. Sueoka. (1988).Proc. Natl. Acad. Sci.(USA) 85, 2653–2657.PubMedCrossRefGoogle Scholar
  8. 8.
    K. H. Wolfe, P. M. Sharp, and W-H Li. (1989).Nature337, 283–285.PubMedCrossRefGoogle Scholar
  9. 9.
    J. P. Carulli, D. E. Krane, D. L. Hartl, and H. Ochman. (1993).Genetics134, 837–845.PubMedGoogle Scholar
  10. 10.
    N. Sueoka. (1993).J. Mol. Evol.37, 137–153.PubMedCrossRefGoogle Scholar
  11. 11.
    D. W. Collins, and J. H. Jukes. (1993). 36, 201–213.Google Scholar
  12. 12.
    N. Arnheim, M. Krystal, R. Schnickel, G. Wilson, O. Ryder, and E. Zimmer. (1980).Proc. Natl. Acad. Sci. (USA)77, 7323–7327.CrossRefGoogle Scholar
  13. 13.
    Y. Xiong, B. Sakaguchi, and T. H. Eickbush. (1988).Genetics120, 221–231.Google Scholar
  14. 14.
    D. A. Hickey, L. Bally-Cuif, S. Abukashawa, V. Payant, and B. F. Benkel. (1991).Proc. Natl. Acad. Sci. (USA)88, 1611–1615.CrossRefGoogle Scholar
  15. 15.
    K. K. Willis, and H. L. Klein. (1987).Genetics117, 633–643.PubMedGoogle Scholar
  16. 16.
    A. Letsou and R. M. Liskay.Genetics117, 759–769.Google Scholar
  17. 17.
    T. C. Brown, and J. Jiricny. (1988).Cell54, 705–711.PubMedCrossRefGoogle Scholar
  18. 18.
    V. Payant, S. Abukashawa, M. Sasseville, B. F. Benkel, D. A. Hickey, and J. David. (1988).Mol. Biol. Evol.5, 560–567.PubMedGoogle Scholar
  19. 19.
    C. A. Davis, D. C. Riddell, M. J. Higgins, J. J. A. Holden, and B. N. White. (1985).Nucl. Acids Res.13, 6605–6619.PubMedCrossRefGoogle Scholar
  20. 20.
    K. Wada, Y. Wada, H. Doi, I. Ishibashi, T. Gojobori, and T. Ikemura. (1991).Nucl. Acids Res.19 (Suppl), 1981–1985.PubMedCrossRefGoogle Scholar
  21. 21.
    N. Sueoka. (1961).Proc. Natl. Acad. Sci (USA)47, 1141–1149.CrossRefGoogle Scholar
  22. 22.
    G. D’Onofrio, D. Mouchiroud, B. Aissani, C. Gauthier, and G. Bernardi. (1991).J. Mol. Evol.32, 504–510.PubMedCrossRefGoogle Scholar
  23. 23.
    P. M. Sharp. (1991).J. Mol. Evol.33, 23–33.PubMedCrossRefGoogle Scholar
  24. 24.
    R. M. Kliman and J. Hey. (1993).Mol. Biol. Evol.(in press).Google Scholar
  25. 25.
    D. R. Wolstenholme and K. W. Jeon. (1992).Mitochondrial GenomesAcademic Press.Google Scholar
  26. 26.
    S. T. Aota, T. Gojobori, F. Ishibashi, T. Maruyama, and T. Ikemura. (1988).Nucl. Acids Res.16, 315–402.CrossRefGoogle Scholar
  27. 27.
    S. G. E. Andersson and C. G. Kurland. (1991).Mol. Biol. Evol.8, 530–544.PubMedGoogle Scholar
  28. 28.
    S. Osawa, D. Collins, T. Ohama, T. Jukes, and K. Watanabe. (1990).J. Mol. Evol.30,322–328.PubMedCrossRefGoogle Scholar
  29. 29.
    M. Hasegawa and T. HashimotoNature361, 23.Google Scholar
  30. 30.
    M. A. Steel, P. J. Lockhart, and D. Penny. (1993).Nature364, 440–442.PubMedCrossRefGoogle Scholar
  31. 31.
    D. A. Hickey, B. F. Benkel, P. H. Boer, Y. Genest, S. Abukashawa, and G. Ben-David. (1987).J. Mol. Evol.26, 252–256.PubMedCrossRefGoogle Scholar
  32. 32.
    P. H. Boer and D. A. Hickey. (1986).Nucl. Acids Res.14, 8399–8411.PubMedCrossRefGoogle Scholar
  33. 33.
    C. M. Long, M-J. Virolle, S-Y. Chang, S. Chang, and M. J. Bibb. (1987).J. Bacteriol.169, 5745–5754.PubMedGoogle Scholar

Copyright information

© Springer Science+Business Media Dordrecht 1994

Authors and Affiliations

  • Donal A. Hickey
  • Shaojiu Wang
  • Charalambos Magoulas

There are no affiliations available

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