Codon usage influences fitness through RNA toxicity

Area of Science:

• Molecular Biology
• Genetics
• Microbiology

Background:

• Organisms exhibit codon bias due to selective pressures, influencing synonymous codon usage.
• Understanding the mechanisms of selection on synonymous sites is crucial for gene expression studies.

Purpose of the Study:

• To investigate the impact of synonymous codon variants on bacterial fitness.
• To identify the mechanisms underlying toxicity associated with synonymous gene expression.

Main Methods:

• Generated and expressed hundreds of synonymous variants of the Green Fluorescent Protein (GFP) gene in Escherichia coli.
• Utilized quantitative growth and viability assays to measure bacterial fitness.
• Performed genome sequencing to identify genetic adaptations in suppressor strains.

Main Results:

• Discovered that many synonymous GFP variants were toxic to E. coli.
• Determined that toxicity is independent of translation and linked to toxic mRNA production.
• Identified RNA sequence features contributing to toxicity and evolved suppressor strains with promoter mutations reducing mRNA levels.

Conclusions:

• Translation-independent RNA toxicity is a previously unrecognized factor in bacterial gene expression.
• Codon bias can lead to detrimental effects beyond translational efficiency.
• Bacterial gene expression is subject to novel constraints imposed by mRNA structure and stability.