The Evolution of Molecular Compatibility between Bacteriophage ΦX174 and its Host

Abstract

Viruses rely upon their hosts for biosynthesis of viral RNA, DNA and protein. This dependency frequently engenders strong selection for virus genome compatibility with potential hosts, appropriate gene regulation and expression necessary for a successful infection. While bioinformatic studies have shown strong correlations between codon usage in viral and host genomes, the selective factors by which this compatibility evolves remain a matter of conjecture. Engineered to include codons with a lesser usage and/or tRNA abundance within the host, three different attenuated strains of the bacterial virus ФX174 were created and propagated via serial transfers. Molecular sequence data indicate that biosynthetic compatibility was recovered rapidly. Extensive computational simulations were performed to assess the role of mutational biases as well as selection for translational efficiency in the engineered phage. Using bacteriophage as a model system, we can begin to unravel the evolutionary processes shaping codon compatibility between viruses and their host.

Figure 1

Number of synonymous and nonsynonymous codon differences between the engineered lines and the Anc strain over the course of the selection experiment: (A) F coding region engineered lines S and E1, E2, E3, and E4. (B) J coding region engineered lines J1, J2, and J3.

Figure 2

Codon adaptiveness (CA) of each of the engineered lines: (A) F coding region engineered lines S and E1, E2, E3, and E4. (B) J coding region engineered lines J1, J2, and J3.

Figure 3

Codon changes observed within the engineered lines (relative to the codon in the Anc strain) over the course of the selection experiment. Synonymous mutations are indicated by triangles; those resulting in a codon more frequently used in the E. coli C HEGs are indicated by a “Δ” and the converse by a “∇”. If the mutation results in the codon present within the Anc strain, the triangle is solid black. Nonsynonymous mutations are indicated by ⊗.

Figure 4

Average CA values predicted over time from simulations under three different variations of the role of translational selection and random mutation. The CA values from the experimental assays are shown by the black line. Each of the engineered lines is shown separately, (A) S, (B) E1, and (C) J1.

Figure 5

Compensatory mutations observed in all engineered lines. Asterisks indicate a synonymous mutation was observed; all other changes in a residue resulted in a nonsynonymous mutation. The open block indicates the location of the excision which occurred in the E2, E3 and E4 lines. The black blocks indicate the location of the 66 bp and 69 bp regions targeted within the S and E and J engineered strains, respectively. “NC” indicates a mutation within the noncoding region of the genome.