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Related Experiment Videos

Evolutionary lability of context-dependent codon bias in bacteria.

G A McVean1, G D Hurst

  • 1Institute of Cell, Animal and Population Biology, King's Buildings, West Mains Road, University of Edinburgh, Edinburgh EH9 3JT, UK. g.mcvean@ed.ac.uk

Journal of Molecular Evolution
|February 7, 2001
PubMed
Summary

Context-dependent codon bias is common in bacteria but rarely conserved across species. Selection and mutation shape synonymous codon usage, yet these forces vary significantly between bacterial genomes.

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Area of Science:

  • Genomics
  • Molecular Biology
  • Evolutionary Biology

Background:

  • Synonymous codon usage in bacteria is influenced by neighboring base composition.
  • Context-dependent biases may arise from selection against specific motifs or mutation biases.
  • Evolutionary conservation of these biases across diverse bacterial genomes is largely unexplored.

Purpose of the Study:

  • To investigate the evolutionary conservation of context-dependent codon biases in bacteria.
  • To examine biases like avoidance of out-of-frame stop codons and AGG motifs across 11 bacterial genomes.
  • To assess the impact of gene expression levels on codon bias in specific species.

Main Methods:

  • Comparative genomics analysis of 11 fully sequenced bacterial genomes.

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  • Identification of homologous genes across species to compare codon usage patterns.
  • Analysis of specific contextual biases, including stop codon and motif avoidance, in relation to gene expression.

    • Main Results:

    • Context-dependent codon biases are widespread in bacteria but show limited conservation across species.
    • Avoidance of out-of-frame stop codons is not universally conserved and is influenced by species-specific codon recognition (e.g., Mycoplasma spp.).
    • Avoidance of AGG motifs is somewhat conserved and linked to gene expression in E. coli, suggesting selection, but underlying causes vary by species.

    Conclusions:

    • Strong context-dependent forces, both selective and mutational, shape bacterial synonymous codon usage.
    • These forces exhibit significant variation across different bacterial genomes.
    • Understanding these species-specific forces is crucial for comprehending bacterial genome evolution.