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Why are translationally sub-optimal synonymous codons used in Escherichia coli?
1Centre for the Study of Evolution and School of Biological Sciences, University of Sussex, Brighton, BN1 9QG, UK.
Journal of Molecular Evolution
|August 28, 2001
Summary
Synonymous codons in Escherichia coli are influenced by multiple evolutionary forces. While translational selection favors optimal codons, suboptimal codons persist due to a balance of mutation, selection, drift, and alternative pressures.
Area of Science:
- Evolutionary Biology
- Molecular Biology
- Genomics
Background:
- Natural selection drives the preference for specific synonymous codons that enhance translation efficiency in Escherichia coli.
- Despite this, translationally suboptimal codons are observed, suggesting other evolutionary factors are at play.
Purpose of the Study:
- To investigate the reasons behind the persistence of translationally suboptimal codons in Escherichia coli.
- To test three hypotheses: weak selection (mutation-selection-drift balance), lack of selection at certain sites, and alternative selection pressures.
Main Methods:
- Analysis of frequency distributions of synonymous polymorphisms in Escherichia coli.
- Testing of three distinct models explaining the presence of suboptimal codons.
Main Results:
- When considering all data, a balance between mutation, selection, and drift (weak selection) best explains suboptimal codons.
- Models suggesting no selection or alternative selection pressures were rejected as sole explanations.
- Partitioning data by amino acid groups and gene regions revealed evidence supporting both alternative selection pressures and lack of selection.
Conclusions:
- The existence of translationally suboptimal codons in E. coli is a result of multiple evolutionary mechanisms.
- These include weak selection, lack of selection at specific sites, and alternative selection pressures, acting in concert.