Avoidance of protein fold disruption in natural virus recombinants

Abstract

With the development of reliable recombination detection tools and an increasing number of available genome sequences, many studies have reported evidence of recombination in a wide range of virus genera. Recombination is apparently a major mechanism in virus evolution, allowing viruses to evolve more quickly by providing immediate direct access to many more areas of a sequence space than are accessible by mutation alone. Recombination has been widely described amongst the insect-transmitted plant viruses in the genus Begomovirus (family Geminiviridae), with potential recombination hot- and cold-spots also having been identified. Nevertheless, because very little is understood about either the biochemical predispositions of different genomic regions to recombine or what makes some recombinants more viable than others, the sources of the evolutionary and biochemical forces shaping distinctive recombination patterns observed in nature remain obscure. Here we present a detailed analysis of unique recombination events detectable in the DNA-A and DNA-A-like genome components of bipartite and monopartite begomoviruses. We demonstrate both that recombination breakpoint hot- and cold-spots are conserved between the two groups of viruses, and that patterns of sequence exchange amongst the genomes are obviously non-random. Using a computational technique designed to predict structural perturbations in chimaeric proteins, we demonstrate that observed recombination events tend to be less disruptive than sets of simulated ones. Purifying selection acting against natural recombinants expressing improperly folded chimaeric proteins is therefore a major determinant of natural recombination patterns in begomoviruses.

Figure 1. Recombination Region Count Matrix of Unique Recombination Events Detected amongst (A) DNA-A Sequences of Bipartite Begomoviruses and (B) DNA-A-Like Sequences of Monopartite Begomoviruses

Unique recombination events have been mapped onto the matrix based on their estimated breakpoint positions. The shades displayed are a function of the number of times pairs of nucleotides (plotted on the x- and y-axis) are separated during the observed set of unique recombination events. Diagrams indicating the positions of landmarks in begomovirus DNA-A/DNA-A-like sequences are shown on the top of the matrices. Positions were drawn in relative to EACMCV-[TZ] (AY795983) for bipartite sequences and ToLCYT-[Dem] (AJ865341) for monopartite sequences.

Figure 2. The Distribution of Recombination Breakpoints Detected within (A) DNA-A Sequences of Bipartite Begomovirus and (B) DNA-A-Like Sequences of Monopartite Begomoviruses

All estimated breakpoint positions are indicated by small vertical lines at the top of the graph. A 200-nucleotide window was moved along the alignment one nucleotide at a time and the number of breakpoints detected within the window region was counted and plotted (solid line). The horizontal lines at the top of each graph indicate 99% and 95% confidence thresholds for globally significant breakpoint clusters. Light and dark grey areas respectively indicate local 99% and 95% breakpoint clustering thresholds, taking into account local regional differences in sequence diversity that influence the ability of different recombination detection methods to identify recombination breakpoints. Red areas indicate recombination hot-spots, while blue areas represent recombination cold-spots. ORFs (horizontal arrows) and IR are represented on the top of the graph.