ΦX174 Attenuation by Whole-Genome Codon Deoptimization.

Area of Science:

• Virology
• Molecular Biology
• Evolutionary Genetics

Background:

• Natural selection on synonymous mutations impacts genome composition and evolution.
• Synonymous mutations in viral structural genes can attenuate viral growth, aiding live-attenuated vaccine development.
• Predicting viral attenuation and resistance to reversion requires understanding selection on compositional features and mutation combinations.

Purpose of the Study:

• To systematically investigate the impact of synonymous codon usage on viral fitness.
• To determine how combinations of synonymous mutations affect viral growth.
• To explore the relationship between codon usage optimization and fitness.

Main Methods:

• Systematic recoding of bacteriophage ΦX174 genes using rare codons from its host, Escherichia coli.
• Assessing the fitness of recombinant viruses with varying numbers of deoptimizing mutations.
• Testing the effect of gene optimization on fitness to evaluate the wild-type's fitness optimum.

Main Results:

• Viral fitness decreased with increasing deoptimizing mutations, but not always linearly or consistently across genes.
• Combined deoptimizing mutations had unpredictable effects on viral fitness, greater or lesser than expected.
• Optimizing genes did not improve fitness, suggesting wild-type ΦX174 is already at a fitness optimum.

Conclusions:

• Synonymous codon usage significantly influences viral fitness and genome evolution.
• The effects of multiple synonymous mutations are complex and not always additive.
• Bacteriophage ΦX174 serves as a valuable model for studying codon usage, viral attenuation, and virulence determinants.