Why are translationally sub-optimal synonymous codons used in Escherichia coli?

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.