Host adaptation by genome recombination
Genome recombination is important for its role in unlinking deleterious mutations from those that may be neutral or beneficial, allowing populations at least partial escape from the negative fitness effects of accumulating deleterious mutations. Similarly, recombination allows otherwise asexual organisms such as viruses and bacteria to avoid the evolution-retarding effects of “clonal interference”, which results from competition among distinct beneficial mutations that reside concurrently in multiple genomes – eventually one dominates within the population at the expense of the rest.
In viruses, where genetic exchange between different species or even unrelated taxa is possible, recombination is also capable of generating spectacular genetic diversity. While natural recombination between distantly related genomes has only rarely been shown to occur in double-stranded DNA and RNA viruses, it is apparently quite common amongst most reverse-transcribing, positive-sense single-stranded RNA and single-stranded DNA viruses.
Maize streak virus (MSV), the type strain of the genus Mastrevirus in the family Geminiviridae, has a simple genome consisting of virion sense movement protein (mp) and coat protein (CP) (cp) genes, and a complementary sense replication-associated protein (rep) gene that is expressed in two alternatively spliced isoforms. Separating the complementary and virion sense genes are a long intergenic region (LIR), containing the v-ori and transcriptional promoter elements, and a short intergenic region (SIR), containing the complementary sense ori and transcription termination elements. A recent paper describes a conceptually simple but powerful new experimental system to demonstrate how recombination in geminiviruses such as MSV can be a remarkably efficient mechanism capable of rapidly generating progeny genomes with increased fitness.
Rapid host adaptation by extensive recombination. 2009 J Gen Virol 90: 734-746
Experimental investigations into virus recombination can provide valuable insights into the biochemical mechanisms and the evolutionary value of this fundamental biological process. Here, we describe an experimental scheme for studying recombination that should be applicable to any recombinogenic viruses amenable to the production of synthetic infectious genomes. Our approach is based on differences in fitness that generally exist between synthetic chimaeric genomes and the wild-type viruses from which they are constructed. In mixed infections of defective reciprocal chimaeras, selection strongly favours recombinant progeny genomes that recover a portion of wild-type fitness. Characterizing these evolved progeny viruses can highlight both important genetic fitness determinants and the contribution that recombination makes to the evolution of their natural relatives. Moreover, these experiments supply precise information about the frequency and distribution of recombination breakpoints, which can shed light on the mechanistic processes underlying recombination. We demonstrate the value of this approach using the small single-stranded DNA geminivirus, maize streak virus (MSV). Our results show that adaptive recombination in this virus is extremely efficient and can yield complex progeny genomes comprising up to 18 recombination breakpoints. The patterns of recombination that we observe strongly imply that the mechanistic processes underlying rolling circle replication are the prime determinants of recombination breakpoint distributions found in MSV genomes sampled from nature.
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Tags: Biology, Genetics, Microbiology, Science, Virology
