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An evolutionary model of a complementary circular code

D G Arquès1, J P Fallot, C J Michel

  • 1Université de Marne-la-Vallée, Institut Gaspard Monge, France.

Journal of Theoretical Biology
|March 21, 1997
PubMed
Summary
This summary is machine-generated.

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A specific set of 20 trinucleotides, known as the C3 code, preferentially occurs in frame 0 of protein genes. This code

Area of Science:

  • Genomics and Molecular Biology
  • Bioinformatics
  • Evolutionary Biology

Background:

  • Protein-coding genes in prokaryotes and eukaryotes exhibit a non-random distribution of trinucleotides.
  • A specific subset of 20 trinucleotides, termed the C3 code (X0), shows preferential occurrence in frame 0.
  • The C3 code possesses unique properties as a maximal circular code, with related codes X1 and X2 in frames 1 and 2.

Purpose of the Study:

  • To quantitatively analyze the occurrence frequencies of trinucleotide subsets (X0, X1, X2) across different reading frames in eukaryotic protein genes.
  • To investigate the positional constancy of these frequencies within coding regions and their variability in non-coding regions.
  • To explain observed frequency asymmetries within frames using a novel property of the C3 code related to substitutions.

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Main Methods:

  • Quantitative analysis of trinucleotide subset frequencies (X0, X1, X2) in frame 0, 1, and 2 of eukaryotic protein genes.
  • Comparison of frequencies within coding regions versus 5' and 3' non-coding regions.
  • Development and application of a three-parameter evolutionary model (p, q, k) simulating codon mixing and substitutions.

Main Results:

  • Frequencies of X0, X1, and X2 are constant functions of trinucleotide position within eukaryotic protein gene frames (48.5%, 29%, 22.5% in frame 0).
  • These frequencies vary around the random value (1/3) in 5' and 3' non-coding regions.
  • An evolutionary model incorporating equiprobable codon mixing and substitutions accurately reproduces observed frequencies and explains asymmetries.

Conclusions:

  • The C3 code and its frame-shifted variants exhibit non-random, positionally constant frequencies within protein-coding genes, suggesting functional or evolutionary constraints.
  • Observed frequency asymmetries are explained by a model of codon evolution involving specific substitution patterns.
  • These findings provide insights into the evolutionary pressures shaping gene sequences and codon usage.