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Related Experiment Videos

Synonymous codon usage in Bacillus subtilis reflects both translational selection and mutational biases.

D C Shields1, P M Sharp

  • 1Department of Genetics, Trinity College, Dublin, Ireland.

Nucleic Acids Research
|October 12, 1987
PubMed
Summary

Bacillus subtilis exhibits less codon bias than E. coli or S. cerevisiae, with highly expressed genes showing higher bias. Mutational bias, not translational selection, likely shapes codon usage in lowly expressed genes.

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Area of Science:

  • Microbial genomics and molecular evolution
  • Bacterial gene expression and regulation

Background:

  • Codon usage bias (CUB) reflects evolutionary pressures on gene expression.
  • Comparative analysis of CUB in Bacillus subtilis, Escherichia coli, and Saccharomyces cerevisiae is limited.
  • Understanding CUB drivers (translational selection vs. mutational bias) is crucial for interpreting genomic data.

Purpose of the Study:

  • To investigate the extent and patterns of synonymous codon usage bias in Bacillus subtilis.
  • To identify factors influencing codon usage bias, particularly the roles of translational selection and mutational bias.
  • To correlate codon bias with gene expression levels in B. subtilis.

Main Methods:

  • Analysis of codon usage data for 56 Bacillus subtilis genes.

Related Experiment Videos

  • Application of correspondence analysis and various codon bias indices.
  • Comparison of CUB patterns with gene expression levels and dinucleotide frequencies.

    • Main Results:

    • Bacillus subtilis shows less codon bias compared to Escherichia coli and Saccharomyces cerevisiae.
    • Highly expressed genes in B. subtilis exhibit a higher degree of codon bias.
    • Lowly expressed genes display minimal translational selection effects, with patterns likely dominated by mutational bias.

    Conclusions:

    • Codon usage bias in B. subtilis is generally lower but correlates with gene expression levels.
    • Mutational bias appears to be a significant factor shaping codon usage, especially in lowly expressed genes.
    • The prevalence of mutational bias may complicate the identification of functional open reading frames in B. subtilis.