Translational Selection for Speed Is Not Sufficient to Explain Variation in Bacterial Codon Usage Bias

Area of Science:

• Microbiology
• Molecular Biology
• Genomics

Background:

• Bacterial growth rate drives selection for faster translation.
• This leads to increased tRNA gene copy number (GCN) and codon usage bias (CUB).
• A model suggests tRNA GCN and CUB coevolve with growth rate.

Purpose of the Study:

• To test the implication that translational selection favors higher tRNA GCN for frequent amino acids.
• To investigate the relationship between growth rate, tRNA GCN, and CUB in γ-proteobacteria.
• To explore factors beyond translational speed influencing CUB.

Main Methods:

• Analysis of bacterial growth rates.
• Quantification of tRNA gene copy numbers (GCN).
• Measurement of codon usage bias (CUB) across different bacterial species.

Main Results:

• CUB saturates with increasing growth rate, despite continued increases in tRNA gene copy number.
• tRNA GCN correlates with amino acid usage, but not with growth-rate-associated CUB changes.
• Certain amino acids show weak CUB independent of tRNA GCN variation.

Conclusions:

• Translational speed selection alone does not fully explain CUB.
• Amino acid-specific variations in CUB suggest other functional constraints are involved.
• Codon features and non-translational factors likely play a significant role in CUB.