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Mutagenesis and Functional Selection Protocols for Directed Evolution of Proteins in E. coli
Published on: March 16, 2011
Evolutionary lability of context-dependent codon bias in bacteria
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
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.
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.
- 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.
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