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Synonymous codon usage is subject to selection in thermophilic bacteria.
David J Lynn1, Gregory A C Singer, Donal A Hickey
1Department of Biology, University of Ottawa, 30 Marie Curie, Ottawa, ON K1N 6N5, Canada.
Nucleic Acids Research
|October 5, 2002
Summary
Synonymous codon usage patterns in prokaryotes are influenced by genome G+C content and high-temperature growth. This study links specific codon usage in thermophiles to environmental adaptation, demonstrating a clear selective force.
Area of Science:
- Genomics
- Molecular Biology
- Evolutionary Biology
Background:
- Synonymous codon usage patterns have been studied for decades.
- Natural selection is known to influence codon usage, but specific external selective forces remain elusive.
- Previous studies lacked the comprehensive data to link codon usage to specific environmental factors.
Purpose of the Study:
- To investigate the factors affecting synonymous codon usage in prokaryotic genomes.
- To establish a link between codon usage patterns and specific external selective forces, particularly high-temperature growth.
- To analyze codon usage variations within and between 40 completely sequenced prokaryotic genomes.
Main Methods:
- Analysis of synonymous codon usage patterns across 40 prokaryotic genomes.
- Combining over 80,000 genes into a single dataset for comprehensive analysis.
- Eliminating phylogenetic history and lateral gene transfer as explanations for observed patterns.
Main Results:
- Synonymous codon usage is significantly affected by overall genome G+C content.
- Growth at high temperatures is a major factor shaping codon usage patterns.
- A characteristic pattern of codon usage among thermophiles is directly linked to high-temperature adaptation.
Conclusions:
- Synonymous codon usage in prokaryotes is driven by both intrinsic genomic properties and external selective pressures.
- High-temperature growth acts as a significant selective force, leading to distinct codon usage patterns in thermophiles.
- This study provides clear evidence linking a specific codon usage pattern to an external selective force, advancing our understanding of molecular evolution.