Journal of Molecular Evolution

, Volume 22, Issue 1, pp 53–62

Amino acid composition and the evolutionary rates of protein-coding genes

  • Dan Graur
Article
  • 126 Downloads

Summary

Based on the rates of amino acid substitution for 60 mammalian genes of 50 codons or more, it is shown that the rate of amino acid substitution of a protein is correlated with its amino acid composition. In particular, the content of glycine residues is negatively correlated with the rate of amino acid substitution, and this content alone explains about 38% of the total variation in amino acid substitution rates among different protein families. The propensity of a polypeptide to evolve fast or slowly may be predicted from an index or indices of protein mutability directly derivable from the amino acid composition. The propensity of an amino acid to remain conserved during evolutionary times depends not so much on its being features prominently in active sites, but on its stability index, defined as the mean chemical distance [R. Grantham (1974) Science 185∶862–864] between the amino acid and its mutational derivatives produced by single-nucleotide substitutions. Functional constraints related to active and binding sites of proteins play only a minor role in determining the overall rate of amino acid substitution. The importance of amino acid composition in determining rates of substitution is illustrated with examples involving cytochrome c, cytochrome b5,ras-related genes, the calmodulin protein family, and fibrinopeptides.

Key words

Rate of amino acid substitution Amino acid composition Glycine Functional constraints 

Preview

Unable to display preview. Download preview PDF.

Unable to display preview. Download preview PDF.

References

  1. Baba ML, Darga LL, Goodman M, Czelusniak J (1981) Evolution of cytochrome c investigated by the maximum parsimony method. J. Mol Evol 17:197–213PubMedGoogle Scholar
  2. Baba ML, Goodman M, Berger-Cohn J, Demaille JG, Matsuda G (1984) The early adaptive evolution of calmodulin.Mol Biol Evol 1:442–455PubMedGoogle Scholar
  3. Clarke B (1970) Selective constraints on amino-acid substitutions during the evolution of proteins. Nature 228:159–160PubMedGoogle Scholar
  4. Dayhoff MO (ed) (1972) Atlas of protein sequence and structure, vol 5. National Biomedical Research Foundation, Silver Spring, MarylandGoogle Scholar
  5. Dayhoff MO (ed) (1976) Atlas of protein sequence and structure, vol 5, suppl 2. National Biomedical Research Foundation, Washington, DCGoogle Scholar
  6. Dayhoff MO (ed) (1978) Atlas of protein sequence and structure vol 5, suppl 3. National Biomedical Research Foundation, Washington, DCGoogle Scholar
  7. Dayhoff MO, Hunt LT, Barker WC, Orcutt BC, Yeh LS, Chen HR, George DG, Blomquist MC, Johnson GC (1983) Protein sequence database (June release). National Biomedical Research Foundation. Washington, DCGoogle Scholar
  8. DeFeo-Jones D, Scolnick EM, Koller R, Dhar R (1983)ras-Related gene sequences identified and isolated fromSaccharomyces cerevisiae. Nature 306:707–709PubMedGoogle Scholar
  9. Dickerson RE (1971) The structure of cytochrome c and the rates of molecular evolution. J Mol Evol 1:26–45PubMedGoogle Scholar
  10. Doolittle RF (1979) Protein evolution. In: Neurath HD (ed) The proteins. Academic Press, New York, pp 1–118Google Scholar
  11. French S, Robson B (1983) What is a conservative substitution? J Mol Evol 19:171–175Google Scholar
  12. Gallwitz D, Donath C, Sander C (1983) A yeast gene encoding a protein homologous to the human c-has/has proto-oncogene product. Nature 306:704–707PubMedGoogle Scholar
  13. Gojobori T, Nei M (1984) Concerted evolution of the immunoglobulin VH gene family. Mol Biol Evol 1:195–212PubMedGoogle Scholar
  14. Gojobori T, Li W-H, Graur D (1982) Patterns of nucleotide substitution in pseudogenes and functional genes. J Mol Evol 18:360–369PubMedGoogle Scholar
  15. Grantham R (1974) Amino acid difference formula to help explain protein evolution. Science 185:862–864PubMedGoogle Scholar
  16. Graur D (1985) Pattern of nucleotide substitution and the extent of purifying selection in retroviruses. J Mol Evol 21:221–231Google Scholar
  17. Grütter MG, Hawkes RB (1983) Mutation and the conformational stability of globular proteins. Naturwissenschaften 70:434–438PubMedGoogle Scholar
  18. Jukes TH, King JL (1971) Deleterious mutations and neutral substitutions. Nature 231:114–115PubMedGoogle Scholar
  19. Jukes TH, King JL (1979) Evolutionary nucleotide replacements in DNA. Nature 281:605–606PubMedGoogle Scholar
  20. Kimura M (1983) The neutral theory of molecular evolution. Cambridge University Press. CambridgeGoogle Scholar
  21. Kimura M, Ohta T (1974) On some principles governing molecular evolution. Proc Natl Acad Sci USA 71:2848–2852PubMedGoogle Scholar
  22. Lehninger AL (1975) Biochemistry. Worth Publishers, New YorkGoogle Scholar
  23. Li W-H, Gojobori T, Nei M (1981) Pseudogenes as a paradigm of neutral evolution. Nature 292:237–239PubMedGoogle Scholar
  24. Li W-H, Wu, C-I, Luo C-C (1985) A new method for estimating synonymous and nonsynonymous rates of nucleotide substitution considering the relative likelihood of nucleotide and codon changes. Mol Biol Evol 2, in pressGoogle Scholar
  25. Marshall DR, Brown AHD (1975) The charge-state model of protein polymorphism in natural populations. J Mol Evol 6: 149–163PubMedGoogle Scholar
  26. Miyata T, Miyazawa S, Yasunaga T (1979) Two types of amino acid substitution in protein evolution. J Mol Evol 12:219–236PubMedGoogle Scholar
  27. Miyata T, Yasunaga T, Nishida T (1980) Nucleotide sequence divergence and functional constraint in mRNA evolution. Proc Natl Acad Sci USA 77:7328–7332PubMedGoogle Scholar
  28. Nei M (1975) Molecular population genetics and evolution. North-Holland, AmsterdamGoogle Scholar
  29. Nei M, Koehn RK (1983) Evolution of genes and proteins. Sinauer, Sunderland, MassachusettsGoogle Scholar
  30. Newmark P (1983) Morerasmatazz. Nature 306:642PubMedGoogle Scholar
  31. Nie NH, Hull CH, Jenkins JG, Steinbrenner K, Bent DH (1975) SPSS. McGraw-Hill, New YorkGoogle Scholar
  32. Shilo B-Z, Weinberg RA (1981) DNA sequences homologous to vertebrate oncogenes are conserved inDrosophila melanogaster. Proc Natl Acad Sci USA 78:6789–6791PubMedGoogle Scholar
  33. Sneath PHA (1966) Relations between chemical structure and biological activity in peptides. J Theor Biol 12:157–195PubMedGoogle Scholar
  34. Sokal RR, Rohlf FJ (1969) Biometry. WH Freeman, San FranciscoGoogle Scholar
  35. Taniguchi T, Mantei N, Schwarzstein M, Nagata S, Muramatsu M, Weissmann C (1980) Human leukocyte and fibroblast interferons are structurally related. Nature 285:547–549PubMedGoogle Scholar
  36. Valenzuela D, Weber H, Weissmann C (1985) Is sequence conservation in interferons due to selection for functional proteins? Nature 313:698–700PubMedGoogle Scholar
  37. Wu C-I, Li W-H (1985) Evidence for higher rates of nucleotide substitution in rodents than in man. Proc Natl Acad Sci USA 82:1741–1745PubMedGoogle Scholar
  38. Zuckerkandl E (1976) Evolutionary processes and evolutionary noise at the molecular level. I. Functional density in proteins. J Mol Evol 7:167–183PubMedGoogle Scholar

Copyright information

© Springer-Verlag 1985

Authors and Affiliations

  • Dan Graur
    • 1
  1. 1.Center for Demographic and Population GeneticsUniversity of Texas Health Science CenterHoustonUSA
  2. 2.Lehrstuhl für PopulationsgenetikInstitut für Biologie II der Universität TübingenTübingen 1West Germany

Personalised recommendations