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Codon usage in bacteria: correlation with gene expressivity.

M Gouy, C Gautier

    Nucleic Acids Research
    |November 25, 1982
    PubMed
    Summary
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    This study analyzes codon frequencies in prokaryotic genes, particularly within Escherichia coli. It confirms a link between codon composition, gene expression, and protein yield, offering evolutionary insights into genetic code selection.

    Area of Science:

    • Genomics
    • Molecular Biology
    • Bioinformatics

    Background:

    • The nucleic acid sequence bank includes over 600 protein-coding genes, with 107 from prokaryotic organisms.
    • Previous research has explored codon usage but lacked comprehensive analysis integrating gene expressivity, regulation, and tRNA dynamics.

    Purpose of the Study:

    • To analyze genetic code usage in 83 sequenced genes of the Escherichia coli genome.
    • To investigate the relationship between codon composition, mRNA expressivity, peptide elongation rate, and protein yield.
    • To explore the evolutionary aspects of codon selection in mRNA sequences.

    Main Methods:

    • Analysis of codon frequencies and composition in prokaryotic genes, including Escherichia coli.
    • Development of two indexes to summarize codon composition based on iso-tRNA usage and third-base choice (Cytosine vs. Uracil).

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  • Integration of data on gene expressivity, regulation, iso-tRNA specificity, and cellular concentration.

    • Main Results:

    • A strong correlation between codon composition and mRNA expressivity was confirmed, even within the same operon.
    • The study provides codon frequencies for new prokaryotic genes and detailed analysis for Escherichia coli.
    • The influence of codon usage on peptide elongation rate and protein yield was discussed.

    Conclusions:

    • Codon usage is a significant factor influencing gene expression efficiency and protein production in prokaryotes.
    • The findings support the role of evolutionary pressures in shaping codon selection in mRNA sequences.
    • This research provides a deeper understanding of the intricate relationship between genetic code and biological function.