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A complementary circular code in the protein coding genes

D G Arquès1, C J Michel

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

Journal of Theoretical Biology
|September 7, 1996
PubMed
Summary

Researchers identified three distinct sets of trinucleotides (three-nucleotide sequences) that consistently appear in specific reading frames within protein genes across prokaryotes and eukaryotes. These sets exhibit properties suggesting a role in gene evolution and the genetic code.

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Area of Science:

  • Genomics
  • Molecular Biology
  • Bioinformatics

Background:

  • Shifted periodicities of 1 and 2 modulo 3 have been observed in protein-coding genes.
  • Trinucleotides (three-nucleotide sequences) are fundamental units in gene reading frames.
  • Autocorrelation functions revealed patterns in trinucleotide usage.

Purpose of the Study:

  • To verify the hypothesis that trinucleotides are associated with specific reading frames in protein genes.
  • To analyze the distribution and properties of 64 possible trinucleotides in prokaryotic and eukaryotic genes.
  • To investigate the relationship between trinucleotide subsets and the genetic code.

Main Methods:

  • Analysis of trinucleotide frequencies within three distinct reading frames (0, 1, and 2).

Related Experiment Videos

  • Classification of each trinucleotide based on its preferential occurrence frame.
  • Comparison of identified trinucleotide subsets between prokaryotic and eukaryotic gene populations.

    • Main Results:

    • Three subsets of trinucleotides (Tzero, T1, T2) were consistently identified in the same frames (0, 1, 2 respectively) in both prokaryotes and eukaryotes.
    • These subsets possess properties including maximal circular code, DNA complementarity, circular permutation, rarity, and concatenation.
    • The RNY (Purine-Pyrimidine-Any) model closely aligns with the Tzero subset.
    • Trinucleotides in Tzero code for 13 specific amino acids, with observed correlations to amino acid frequencies in proteins.

    Conclusions:

    • The identified trinucleotide subsets (Tzero, T1, T2) represent a fundamental organizational principle in protein-coding genes.
    • These subsets exhibit properties that support their role in frame retrieval, DNA coding, and evolutionary processes.
    • The findings provide insights into the structure of the genetic code and its evolutionary origins.