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, 365 (1552), 2495-501

Experimental Evolution of Viruses: Microviridae as a Model System

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Experimental Evolution of Viruses: Microviridae as a Model System

Holly A Wichman et al. Philos Trans R Soc Lond B Biol Sci.

Abstract

phiX174 was developed as a model system for experimental studies of evolution because of its small genome size and ease of cultivation. It has been used extensively to address statistical questions about the dynamics of adaptive evolution. Molecular changes seen during experimental evolution of phiX174 under a variety of conditions were compiled from 10 experiments comprising 58 lineages, where whole genomes were sequenced. A total of 667 substitutions was seen. Parallel evolution was rampant, with over 50 per cent of substitutions occurring at sites with three or more events. Comparisons of experimentally evolved sites to variation seen among wild phage suggest that at least some of the adaptive mechanisms seen in the laboratory are relevant to adaptation in nature. Elucidation of these mechanisms is aided by the availability of capsid and pro-capsid structures for phiX174 and builds on years of genetic studies of the phage life history.

Figures

Figure 1.
Figure 1.
Common sites of an amino acid substitution during experimental evolution. Histogram shows the number of times an amino acid substitution was seen at each residue among the 58 experimental lineages analysed. Only amino acid residues with three or more substitutions are included. Grey bars indicate sites that also vary among wild φX-like phages (Rokyta et al. 2006 and unpublished isolates). Black bars indicate substitutions that converge on the sequence at residues that are invariant among the wild φX-like phages. In most cases, the substitutions were parallel events of the same substitutions from a common ancestor, but reversions and alternate substitutions at the same residue were also counted. However, some lineages were extensions of other experiments and thus already carried amino acid substitutions relative to the ancestor, so, depending on the selective environment, not all substitutions have an equal opportunity of arising.
Figure 2.
Figure 2.
Structural location of select evolved sites. Images were rendered with VIPER using 1rb8_half.vdb from VIPERdb at http://viperdb.scripps.edu/. (a) Structure of the φX174 capsid. One of the 12 pentameric units is highlighted, with five copies of the major capsid protein F shown in red and five copies of the major spike protein G shown in blue. (b) Changes at sites of host recognition. Sites of host recognition in the major capsid protein F as suggested by experimental evolution on Salmonella are shown in yellow (F101, F102, F153 F336, F361, F364 and F388). The region of host recognition suggested by McKenna et al. (1994) based on the crystal structure are shown in aqua (F176, F178, F181, F205, F209 and F213). Amino acid number is based on GenBank accession AF176034. (c) Changes at sites of interaction between subunits of the major capsid protein. One copy of the major capsid protein F is highlighted in red. Experimentally evolved changes at or adjacent to sites of F–F interaction are shown in yellow (F2, F82, F115, F184, F188, F205, F227, F361 and F424).

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