Browsing by Subject "Viral genomics"

Now showing 1 - 4 of 4
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    Open Access
    Avoidance of Protein Fold Disruption in Natural Virus Recombinants
    (Public Library of Science, 2007) Lefeuvre, Pierre; Lett, Jean-Michel; Reynaud, Bernard; Martin, Darren P
    Author Summary The exchange of genetic material between different virus species, called inter-species recombination, has the potential to generate, within a single genome replication cycle, an almost unimaginable number of genetically distinct virus strains, including many that might cause deadly new human, animal, or plant diseases. Many fear that inter-species recombination could provide viruses with quick access to evolutionary innovations such as broader host ranges, altered tissue tropisms, or increased severities. However, mounting evidence suggests that recombination is not an unconstrained process and that most inter-species recombinants that occur in nature are probably defective. It is suspected that networks of coevolved interactions between different parts of virus genomes and their encoded proteins must be kept intact for newly formed inter-species recombinants to have any chance of out-competing their parents. One category of coevolved interaction is that between contacting amino acids within the 3-D structures of folded proteins. Here we examine the distributions of recombination events across the genomes of a group of rampantly recombining plant viruses and find very good evidence that this class of interaction tends to be preserved amongst recombinant sequences sampled from nature. This indicates that selection against misfolded proteins strongly influences the survival of natural recombinants.
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    Open Access
    Complex recombination patterns arising during geminivirus coinfections preserve and demarcate biologically important intra-genome interaction networks
    (Public Library of Science, 2011) Martin, Darren P; Lefeuvre, Pierre; Varsani, Arvind; Hoareau, Murielle; Semegni, Jean-Yves; Dijoux, Betty; Vincent, Claire; Reynaud, Bernard; Lett, Jean-Michel
    Author Summary Genetic recombination between viruses is a form of parasexual reproduction during which two parental viruses each contribute genetic information to an offspring, or recombinant, virus. Unlike with sexual reproduction, however, recombination in viruses can even involve the transfer of sequences between the members of distantly related species. When parental genomes are very distantly related, it is anticipated that recombination between them runs the risk of producing defective offspring. The reason for this is that the interactions between different parts of genomes and the proteins they encode (such as between different viral proteins or between viral proteins and the virus genomic DNA or RNA) often depend on particular co-evolved binding sites that recognize one another. When in a recombinant genome the partners in a binding site pair are each inherited from different parents there is a possibility that they will not interact with one another properly. Here we examine recombinant genomes arising during experimental mixed infections of two distantly related viruses to detect evidence that intra-genome interaction networks are broadly preserved in these genomes. We show this preservation is so strict that patterns of recombination in these viruses can even be used to identify the interacting regions within their genomes.
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    Open Access
    The Evolutionary Value of Recombination Is Constrained by Genome Modularity
    (Public Library of Science, 2005) Martin, Darren P; Walt, Eric van der; Posada, David; Rybicki, Edward P
    Genetic recombination is a fundamental evolutionary mechanism promoting biological adaptation. Using engineered recombinants of the small single-stranded DNA plant virus, Maize streak virus (MSV), we experimentally demonstrate that fragments of genetic material only function optimally if they reside within genomes similar to those in which they evolved. The degree of similarity necessary for optimal functionality is correlated with the complexity of intragenomic interaction networks within which genome fragments must function. There is a striking correlation between our experimental results and the types of MSV recombinants that are detectable in nature, indicating that obligatory maintenance of intragenome interaction networks strongly constrains the evolutionary value of recombination for this virus and probably for genomes in general.
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    Open Access
    Within-host dynamics of the emergence of tomato yellow leaf curl virus recombinants
    (Public Library of Science, 2013) Urbino, Cica; Gutiérrez, Serafin; Antolik, Anna; Bouazza, Nabila; Doumayrou, Juliette; Granier, Martine; Martin, Darren P; Peterschmitt, Michel
    Tomato yellow leaf curl virus (TYLCV) is a highly damaging begomovirus native to the Middle East. TYLCV has recently spread worldwide, recombining with other begomoviruses. Recent analysis of mixed infections between TYLCV and Tomato leaf curl Comoros begomovirus (ToLCKMV) has shown that, although natural selection preserves certain co-evolved intra-genomic interactions, numerous and diverse recombinants are produced at 120 days post-inoculation (dpi), and recombinant populations from different tomato plants are very divergent. Here, we investigate the population dynamics that lead to such patterns in tomato plants co-infected with TYLCV and ToLCKMV either by agro-inoculation or using the natural whitefly vector Bemisia tabaci . We monitored the frequency of parental and recombinant genotypes independently in 35 plants between 18 and 330 dpi and identified 177 recombinants isolated at different times. Recombinants were detected from 18 dpi and their frequency increased over time to reach about 50% at 150 dpi regardless of the inoculation method. The distribution of breakpoints detected on 96 fully sequenced recombinants was consistent with a continuous generation of new recombinants as well as random and deterministic effects in their maintenance. A severe population bottleneck of around 10 genomes was estimated during early systemic infection-a phenomenon that could account partially for the heterogeneity in recombinant patterns observed among plants. The detection of the same recombinant genome in six of the thirteen plants analysed beyond 30 dpi supported the influence of selection on observed recombination patterns. Moreover, a highly virulent recombinant genotype dominating virus populations within one plant has, apparently, the potential to be maintained in the natural population according to its infectivity, within-host accumulation, and transmission efficiency - all of which were similar or intermediate to those of the parent genotypes. Our results anticipate the outcomes of natural encounters between TYLCV and ToLCKMV.