ΦX174 Attenuation by Whole Genome Codon Deoptimization

Abstract

Natural selection acting on synonymous mutations in protein-coding genes influences genome composition and evolution. In viruses, introducing synonymous mutations in genes encoding structural proteins can drastically reduce viral growth, providing a means to generate potent, live attenuated vaccine candidates. However, an improved understanding of what compositional features are under selection and how combinations of synonymous mutations affect viral growth is needed to predictably attenuate viruses and make them resistant to reversion. We systematically recoded all non-overlapping genes of the bacteriophage ΦX174 with codons rarely used in its E. coli host. The fitness of recombinant viruses decreases as additional deoptimizing mutations are made to the genome, although not always linearly, and not consistently across genes. Combining deoptimizing mutations may reduce viral fitness more or less than expected from the effect size of the constituent mutations and we point out difficulties in untangling correlated compositional features. We test our model by optimizing the same genes and find that the relationship between codon usage and fitness does not hold for optimization, suggesting that wild-type ΦX174 is at a fitness optimum. This work highlights the need to better understand how selection acts on patterns of synonymous codon usage across the genome and provides a convenient system to investigate the genetic determinants of virulence.

Genome Modularization Reveals Overlapped Gene Topology Is Necessary for Efficient Viral Reproduction

“…To understand possible reasons for the large differences in protein expression between decompressed and wild-type φX174, we analyzed mRNA folding across gene 5′ termini and entire coding sequences (Figure S10). Other work focused only on synonymous codon changes within φX174 has found correlations between gene mRNA folding energy and viral fitness. , By contrast, our analyses showed predictive mRNA structure does not explain the difference in protein production between the strains, further emphasizing our current inability to accurately predict the effects of large-scale genome architectural changes.…”

Generating complex patterns of gene expression without regulatory circuits

“…Even smaller model systems are viruses and bacteriophages. Bacteriophages are useful from an engineering and genome-design standpoint because of their comparatively small size, genetic tractability, and potential uses in medical and biotechnological applications [20][21][22][23][24][25]. Despite the limited set of genes encoded by their genomes, phages are nevertheless capable of producing complex, time-varying patterns of gene expression [26].…”

Highlight—Evolution on the Outskirts: Virtual Issue on Viral Evolution

“…According to the resulting genotype–phenotype maps, codon composition influenced the translational robustness and evolvability of HAV, with adaptation to transcription shutoff involving mutations that significantly impacted translation efficiency. In order to gain a better understanding of what codons are desirable in what contexts and how combinations of synonymous mutations affect viral growth, Van Leuven et al. (2021) conducted a study in which they systematically recoded bacteriophage ΦX174 genes with codons that were rarely used in its E. coli host.…”