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Journal of Molecular Evolution

, Volume 32, Issue 6, pp 504–510 | Cite as

Correlations between the compositional properties of human genes, codon usage, and amino acid composition of proteins

  • Giuseppe D'Onofrio
  • Dominique Mouchiroud
  • Brahim Aïssani
  • Christian Gautier
  • Giorgio Bernardi
Article

Summary

We have analyzed the correlation that exists between the GC levels of third and first or second codon position for about 1400 human coding sequences. The linear relationship that was found indicates that the large differences in GC level of third codon positions of human genes are paralleled by smaller differences in GC levels of first and second codon positions. Whereas third codon position differences correspond to very large differences in codon usage within the human genome, the first and second codon position differences correspond to smaller, yet very remarkable, differences in the amino acid composition of encoded proteins. Because GC levels of codon positions are linearly correlated with the GC levels of the isochores harboring the corresponding genes, both codon usage and amino acid composition are different for proteins encoded by genes located in isochores of different GC levels. Furthermore, we have also shown that a linear relationship with a unity slope and a correlation coefficient of 0.77 exists between GC levels of introns and exons from the 238 human genes currently available for this analysis. Introns are, however, about 5% lower in GC, on average, than exons from the same genes.

Key words

Human genome Amino acids Isochores Coding sequences Introns Codon positions 

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References

  1. Aïssani B, D'Onofrio G, Mouchiroud D, Gardiner K, Gautier C, Bernardi G (1991) The compositional properties of human genes. J Mol Evol 32:493–503PubMedGoogle Scholar
  2. Bernardi G (1989) The isochore organization of the human genome. Annu Rev Genet 23:637–661PubMedGoogle Scholar
  3. Bernardi G, Bernardi G (1985) Codon usage and genome composition. J Mol Evol 22:363–365PubMedGoogle Scholar
  4. Bernardi G, Bernardi G (1986) Compositional constraints and genome evolution. J Mol Evol 24:1–11PubMedGoogle Scholar
  5. Bernardi G, Bernardi G (1991) Compositional properties of nuclear genes from cold-blooded vertebrates. J Mol Evol (in press)Google Scholar
  6. Bernardi G, Olofsson B, Filipski J, Zerial M, Salinas J, Cuny G, Meunier-Rotival M, Rodier F (1985) The mosaic genome of warm-blooded vertebrates. Science 228:953–958PubMedGoogle Scholar
  7. Bulmer M (1987) A statistical analysis of nucleotide sequences of introns and exons in human genes. Mol Biol Evol 4:395–405PubMedGoogle Scholar
  8. Gouy M, Gautier C, Attimonelli N, Lanave C, Di Paola G (1985) ACNUC-portable retrieval system for nucleic acid sequence database: logical and physical design and usage. Cabios 1:167–172PubMedGoogle Scholar
  9. Grantham R (1980) Workings of the genetic code. Trends Biochem Sci 5:327–333Google Scholar
  10. Grantham R, Gautier C, Gouy M, Mercier R, Paré A (1980) Codon catalogue usage and the genome hypothesis. Nucleic Acids Res 8:r49-r62PubMedGoogle Scholar
  11. Sueoka N (1961) Correlation between base composition of deoxyribonucleic acid and amino acid composition of proteins. Proc Natl Acad Sci USA 47:1141–1149Google Scholar

Copyright information

© Springer-Verlag New York Inc 1991

Authors and Affiliations

  • Giuseppe D'Onofrio
    • 1
  • Dominique Mouchiroud
    • 2
  • Brahim Aïssani
    • 1
  • Christian Gautier
    • 2
  • Giorgio Bernardi
    • 1
  1. 1.Laboratoire de Génétique MoléculaireInstitut Jacques MonodParisFrance
  2. 2.Laboratoire de Biométrie, Génétique et Biologie des Populations, U.R.A. 243Université Claude BernardVilleurbanneFrance

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