40 research outputs found

    Formation of a hypothetical EVE and relationship to modern viruses.

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    <p>1. An ancestral virus spreads in a host population, infecting and replicating in somatic tissue(s) of infected individuals. 2. Occasionally, a virion may encounter a germline cell (or any cell in the developmental pathway leading to germline tissue); in some cases viral sequence is inserted into chromosomal DNA. For retroviruses, integration is an essential step in viral replication; for other viruses, insertion is a rare by-product of replication and must be mediated by other mechanisms, such as retrotransposition <i>in trans</i> or recombination. In addition, any given virus may not efficiently infect or replicate well in such cells, reducing the probability of insertion. Likewise, infections or insertions that are deleterious to the cell or tissue will reduce the probability of vertical transmission. 3. If gametes bearing the insertion are formed and the chromosome bearing the viral sequence is inherited, the insertion initially exists as a rare allele (the majority of individuals lack the insertion) and the fate of the newborn EVE is similar to any other chromosomal mutation, subject to loss or fixation by random genetic drift (if the insertion has phenotypic consequences, natural selection may also play a role). 4. More often than not, EVEs are probably lost by chance. On rare occasions, an insertion may drift towards higher frequency. Early on, speciation events and incomplete lineage sorting can lead to fixation in some lineages but not others, and chance extinction of populations with the insertion can still lead to loss (only fixation is shown). 5. In descendant species that share the insertion, the orthologous EVE loci will evolve independently. 6. The genetic distance between orthologous EVEs in the genomes of modern species reflects the time passed since the last common ancestor of these species, and provides a lower bound estimate of the time since insertion. Divergence between EVE sequences and the sequences of their modern viral relatives is the combined result of EVE evolution (as part of the nuclear genome) and exogenous viral evolution, the rates of which can differ by several orders of magnitude.</p

    Estimated Minimum Age of Select EVEs.

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    <p>MY, millions of years.</p

    Accessory proteins are the most diverse of the primate lentivirus proteins.

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    <p>(A) Genomes of primate lentiviruses. Schematic representations of the three major types of genome organization found among primate lentiviruses. Genes encoding structural proteins (<i>gag</i>, <i>pol</i>, and <i>env</i>) are shown in gray. The regulatory genes, <i>tat</i> and <i>rev</i>, are in white. Accessory genes are color-coded to match the phylogenetic trees in the lower panel. (B) A comparison of genetic diversity among primate lentivirus proteins. Note that the accessory proteins are much more diverse than the structural proteins. Neighbor-Joining trees were generated using sequence alignments of primate lentiviruses available from Los Alamos National Labs (<a href="http://www.hiv.lanl.gov/" target="_blank">http://www.hiv.lanl.gov/</a>). The Vpx and Vpr proteins are paralogs that arose by duplication during evolution of the primate lentiviruses and were therefore combined into a single tree.</p

    Primate lentiviruses have an expanded repertoire of accessory genes.

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    <p>Abbreviatons: MLV, murine leukemia virus; HTLV-1, human T cell lymphotropic virus type 1; and MVV, maedi-visna virus.</p

    Elevated Rate of Fixation of Endogenous Retroviral Elements in Haplorhini <i>TRIM5</i> and <i>TRIM22</i> Genomic Sequences: Impact on Transcriptional Regulation

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    <div><p>All genes in the <i>TRIM6</i>/<i>TRIM34</i>/<i>TRIM5</i>/<i>TRIM22</i> locus are type I interferon inducible, with <i>TRIM5</i> and <i>TRIM22</i> possessing antiviral properties. Evolutionary studies involving the <i>TRIM6</i>/<i>34</i>/<i>5</i>/<i>22</i> locus have predominantly focused on the coding sequence of the genes, finding that <i>TRIM5</i> and <i>TRIM22</i> have undergone high rates of both non-synonymous nucleotide replacements and in-frame insertions and deletions. We sought to understand if divergent evolutionary pressures on <i>TRIM6/34/5/22</i> coding regions have selected for modifications in the non-coding regions of these genes and explore whether such non-coding changes may influence the biological function of these genes. The transcribed genomic regions, including the introns, of <i>TRIM6</i>, <i>TRIM34</i>, <i>TRIM5</i>, and <i>TRIM22</i> from ten Haplorhini primates and one prosimian species were analyzed for transposable element content. In Haplorhini species, <i>TRIM5</i> displayed an exaggerated interspecies variability, predominantly resulting from changes in the composition of transposable elements in the large first and fourth introns. Multiple lineage-specific endogenous retroviral long terminal repeats (LTRs) were identified in the first intron of <i>TRIM5</i> and <i>TRIM22</i>. In the prosimian genome, we identified a duplication of <i>TRIM5</i> with a concomitant loss of <i>TRIM22.</i> The transposable element content of the prosimian <i>TRIM5</i> genes appears to largely represent the shared Haplorhini/prosimian ancestral state for this gene. Furthermore, we demonstrated that one such differentially fixed LTR provides for species-specific transcriptional regulation of <i>TRIM22</i> in response to p53 activation. Our results identify a previously unrecognized source of species-specific variation in the antiviral TRIM genes, which can lead to alterations in their transcriptional regulation. These observations suggest that there has existed long-term pressure for exaptation of retroviral LTRs in the non-coding regions of these genes. This likely resulted from serial viral challenges and provided a mechanism for rapid alteration of transcriptional regulation. To our knowledge, this represents the first report of persistent evolutionary pressure for the capture of retroviral LTR insertions.</p></div

    The grey mouse lemur <i>TRIM6/34/5</i> genomic locus exhibits a novel architecture, while the genes largely maintain ancestral transposable element content.

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    <p>Panel (A) depicts the relative location and orientation of genes and pseudogenes present in the <i>TRIM5</i> genomic locus of the grey mouse lemur. Similar to <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0058532#pone-0058532-g005" target="_blank">Figures 5</a> and <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0058532#pone-0058532-g006" target="_blank">6</a>, RepeatMasker was used to identify repetitive elements present in genes of this locus and graphical representations overlaying the identified transposable elements on the exon/intron structure of <i>TRIM6</i> (B), <i>TRIM34-2</i> (C), and <i>TRIM5-1</i> and <i>TRIM5-2</i> (D). Symbols representing non-conserved transposable elements as well as 1 kb scale bars are presented in the panel with which they are associated, while symbols common to all genes are shown at the bottom of the figure.</p

    Number and orientation of unique <i>Alu</i> and LTR elements captured during primate evolution.

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    <p>Number and orientation of unique <i>Alu</i> and LTR elements captured during primate evolution.</p

    <i>TRIM5</i> and <i>TRIM22</i> contain more transposable elements than <i>TRIM6</i> or <i>TRIM34</i>.

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    <p>The absolute number of transposable elements present in each TRIM gene was tallied for each species and the results are depicted in panel (A). Black dots represent the number of transposable elements found in a given primate species and the black bar represents the mean value. The quantitation shown in (A) was performed without regard for identity or conservation of the elements present, therefore the number of novel transposable elements was considered. In panel (B), the number of unique transposable elements present in pairwise comparisons of each TRIM gene is shown. The black dots indicate number of elements in an individual pairwise sequence comparison and the black bar represents the mean value. In panels (A) and (B), statistical significance was calculated using the Friedman test, a one-way repeated measures ANOVA without assuming Gaussian distributions and using the Dunn’s post-test to compare all genes against one another. A p-value of less than 0.05 is denoted by *, a p-value less than 0.01 is denoted by **, a p-value less than 0.001 is denoted by ***. Correlations between average indel size and the number of unique transposable elements were examined <i>TRIM6</i> (C), <i>TRIM34</i> (D), <i>TRIM22</i> (E), and <i>TRIM5</i> (F). Statistical significance was assessed using Spearman’s rank correlation the r and p-values resulting from this analysis are indicated in each panel. Comparisons involving colobus <i>TRIM6</i>, which contains a 6-kb LINE L1 element insertion, are indicated with red dots.</p

    Graphical depiction of the genomic structure and location of transposable elements in the TRIM6, TRIM34, and TRIM22 genes.

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    <p>RepeatMasker was used to identify repetitive elements present in the genomic TRIM gene sequences and these elements were mapped onto the multiple sequence alignments. Graphical representations of the exon/intron structure as well as the various transposable elements found in <i>TRIM6</i> (A), <i>TRIM34</i> (B), or <i>TRIM22</i> (C) are shown. Figures are drawn to approximate scale, with a 1 kb scale bar shown in the legend of each panel. Symbols common to all genes analyzed are shown at the bottom of the figure, while symbols representing non-conserved transposable elements are shown in the panel in which they are present.</p

    Evolutionary history of <i>TRIM5</i> and the primate species involved in this study.

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    <p>(A) Graphical depiction of the <i>TRIM6/34/5/22</i> genomic locus of primates as well as a depiction of the hypothetical ancestral mammalian genomic locus. (B) Phylogenetic tree showing the evolutionary relationship of primate species representative of the most prominent genera of primate evolution. The following species were examined in this study: human (<i>Homo sapiens</i>), chimpanzee (<i>Pan troglodytes</i>), white-cheeked gibbon (<i>Nomascus leucogenys</i>), olive baboon (<i>Papio anubis</i>), rhesus macaque (<i>Macaca mulatta</i>), guereza colobus (<i>Colobus guereza</i>), Peruvian red-necked owl monkey (<i>Aotus nancymaae</i>), common marmoset (<i>Callithrix jacchus</i>), Bolivian squirrel monkey (<i>Saimiri boliviensis boliviensis</i>), dusky titi (<i>Callicebus moloch</i>), and grey mouse lemur (<i>Microcebus murinus</i>). These species are highlighted using ‘*’ as well as bold lettering. This phylogenetic tree was adapted from Bininda-Emonds et al. 2007, and uses the revised dates published with the corrigendum on the original article.</p
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