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Analysis of codon usage: positional preference in various organisms

J Seetharaman1, R Srinivasan

  • 1Department of Crystallography and Biophysics, University of Madras, India.

Indian Journal of Biochemistry & Biophysics
|June 1, 1995
PubMed
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This study analyzed nucleotide preferences in gene codons across organisms. Guanine (G), Adenine (A), and Cytosine (C) show distinct positional preferences, influencing codon structure.

Area of Science:

  • Molecular Biology
  • Genetics
  • Bioinformatics

Background:

  • Codons, composed of three nucleotides, specify amino acids during protein synthesis.
  • Understanding nucleotide composition and positional preferences within codons is crucial for deciphering genetic code.
  • Previous analyses have explored codon usage bias, but detailed positional nucleotide preferences require further investigation.

Purpose of the Study:

  • To investigate the positional preferences of the four nucleotides (Cytosine - C, Guanine - G, Adenine - A, and Uracil - U) within codon positions (I, II, and III).
  • To analyze these preferences across a large dataset of genes from diverse organisms.
  • To identify patterns and correlations in nucleotide selection at specific codon positions.

Main Methods:

  • Utilized nucleotide sequence data from 15,137 genes sourced from the GenBank Genetic Sequence Data Bank (Release 65.0).

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  • Performed statistical analysis to determine the frequency and preference of each nucleotide (C, G, A, U) at the first, second, and third positions of codons.
  • Examined correlations between nucleotide preferences across adjacent and all three codon positions.

    • Main Results:

    • Guanine (G) is maximally preferred at the first codon position.
    • Adenine (A) is maximally preferred at the second codon position.
    • Cytosine (C) is maximally preferred at the third codon position.
    • Uracil (U), Guanine (G), and Adenine (A) are minimally preferred at the first, second, and third positions, respectively.
    • A significant correlation exists in positional base preferences, leading to a discrimination against codons with identical bases in all three or adjacent positions.

    Conclusions:

    • Specific nucleotides exhibit strong positional preferences within codons across a wide range of organisms.
    • These preferences contribute to non-random codon structures and influence the overall genetic code.
    • The observed patterns suggest evolutionary selection pressures shaping nucleotide composition at different codon positions.