Advertisement

Inverse correlation between the GC content of bacterial genomes and their level of preterminal codon usage

  • E. V. Barkovsky
  • V. V. Khrustalev
Article

Abstract

The aim of this work was to determine the character of the dependence between the GC content of the genes and the level of their usage of preterminal codons (PTCs), i.e., codons that are converted to the terminal codons as a result of single nucleotide substitution. 84 codon usage tables were used as the material, each of which contains average frequencies of codon usage for all encoding sequences belonging to that bacterial specie. Nucleotide sequences encoding for active centers of bacterial adenylate cyclases were used as well. The inverse correlation between the GC content and the total level of PTC usage was observed (R = −0.97). For nucleotide sequences that encode the active centers from class-I adenylate cyclases, the coefficient of correlation between G+C and PTC is −0.75. For sequences that encode for active centers from class-III adenylate cyclases, the coefficient of correlation between G+C and PTC is −0.91. The most of preterminal codons are absolutely GC poor and GC poor relatively to codons synonymous to them. The cause of the inverse correlation between G+C and the level of preterminal codon usage is an increase in the frequencies of their usage due to mutational AT pressure and the decrease of their frequencies of usage due to mutational GC pressure. Evidence was found of the frequent fixation of nonsense mutations in GC poor bacteria. The practical conclusion is as follows: by increasing the GC content of a genome or gene, the probability of a nonsense mutation is decreased.

Keywords

Codon Codon Usage Adenylate Cyclase Nonsense Mutation Bacterial Genome 
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.

Preview

Unable to display preview. Download preview PDF.

Unable to display preview. Download preview PDF.

References

  1. 1.
    Barkovsky, E.V. and Achinovich, O.V., Membranosvyazannye adenilattsiklazy: Monografiya (Membrane-Bound Adenylyl Cyclases: A Monograph), Minsk, 2005.Google Scholar
  2. 2.
    Kimura, M., Molekulyarnaya evolyutsiya: teoriya neitral’nosti (Molecular Evolution: The Neutrality Theory), Moscow, 1985.Google Scholar
  3. 3.
    Khrustalev, V.V. and Barkovsky, E.V., Zdravookhranenie, 2006, no. 2, pp. 17–20.Google Scholar
  4. 4.
    Khrustalev, V.V. and Barkovsky, E.V., Med. Zh., 2007, no. 1, pp. 92–96.Google Scholar
  5. 5.
    Danchin, A., Adv. Second Messenger Phosphoprotein Res., 1993, vol. 27, pp. 109–162.PubMedGoogle Scholar
  6. 6.
    Fryxell, K.J. and Zuckerkandl, E., Mol. Biol. Evol., 2000, vol. 17, pp. 1371–1383.PubMedGoogle Scholar
  7. 7.
    Fu, L.H., Wang, X., Eyal, Y., et al., J. Biol. Chem., 2002, vol. 277, pp. 25983–25991.PubMedCrossRefGoogle Scholar
  8. 8.
    Gros, L., Saparbaev, M.K., and Laval, J., Oncogene, 2002, vol. 21, pp. 8905–8925.PubMedCrossRefGoogle Scholar
  9. 9.
    Modiano, G., Baffistuzzi, G., and Motulsky, A.G., Proc. Natl. Acad. Sci. USA, 1981, vol. 78, pp. 1110–1114.PubMedCrossRefGoogle Scholar
  10. 10.
    Nakamura, Y., Gojobori, T., and Ikemura, T., Nucleic Acids Res., 2000, vol. 28, p. 292.PubMedCrossRefGoogle Scholar
  11. 11.
    Neuberger, M.S., Di Noia, J.M., Beale, R.C.L., et al., Nat. Rev. Immunol., 2005, vol. 5, pp. 171–178.PubMedCrossRefGoogle Scholar
  12. 12.
    Osawa, S., Jukes, T.H., Watanabe, K., and Muto, A., Microbiol. Rev., 1992, vol. 56, no. 1, pp. 229–264.PubMedGoogle Scholar
  13. 13.
    Sueoka, N., Proc. Natl. Acad. Sci. USA, 1988, vol. 85, pp. 2653–2657.PubMedCrossRefGoogle Scholar
  14. 14.
    Sueoka, N., Gene, 2002, vol. 300, pp. 141–154.PubMedCrossRefGoogle Scholar

Copyright information

© Allerton Press, Inc. 2009

Authors and Affiliations

  • E. V. Barkovsky
    • 1
  • V. V. Khrustalev
    • 1
  1. 1.Belarussian State Medical UniversityMinskBelarus

Personalised recommendations