Occurrence of a DNA sequence of a non-retro RNA virus in a host plant genome and its expression: Evidence for recombination between viral and host RNAs

Virus Laboratory, The Hebrew University of Jerusalem, Faculty of Agricultural, Food and Environmental Quality Sciences, Robert H. Smith Institute for Plant Sciences and Genetics, Rehovot 76100, Israel.
Virology (Impact Factor: 3.32). 03/2005; 332(2):614-22. DOI: 10.1016/j.virol.2004.11.007
Source: PubMed


This study demonstrates that sequences homologous to those of the non-retro RNA virus (Potato virus Y; PVY) are integrated into the genome of several grapevine varieties. The integrated PVY-coat-protein-like cistron is expressed in the grapevine as indicated by Southern and Western blot analyses as well as by RNase protection assay. In addition, genome-walking studies showed that one PVY-like sequence is flanked by 41-bp direct repeats and is embedded in authentic grapevine sequences, flanked by inverted repeats. Rearranged PVY-like sequences were also found in tobacco. It is suggested that nonhomologous recombination of a potyviral RNA with RNA of a retrotransposable element took place at some point in evolution. The initial integration locus was probably within a grapevine gene homologous to a pentatricopeptide repeat-carrying protein, and was later transposed to other locations. The current location is reminiscent of a MITE-type retroelement, indicating transposition history. Because grapevine cultivars are propagated asexually, without going through a meiotic phase, the chance for DNA recombination is minimal and the foreign integrated sequence may be better conserved, enabling it to be expressed correctly in the recipient genome.

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    • "Although pararetroviruses and geminiviruses normally form episomal minichromosomes, illegitimate integration of these viruses in the plant genome is well documented (Hohn et al., 2008; Staginnus and Richert-Poggeler, 2006). In addition, integrated cDNA sequences of RNA viruses have also been found in plant genomes (Chiba et al., 2011; Hohn et al., 2008; Tanne and Sela, 2005). Integrated viral sequences are usually present in multiple copies and are rearranged, frequently defective versions of the virus. "
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    ABSTRACT: The natural outcome of some plant–virus interactions is symptom recovery, which is characterized by the emergence of asymptomatic leaves following a systemic symptomatic infection. Symptom recovery is generally accompanied with reduced virus titers and sequence-specific resistance to secondary infection and has been linked with the induction of antiviral RNA silencing. Recent studies have revealed an unsuspected diversity of silencing mechanisms associated with symptom recovery in various host-virus interactions, including degradation or translation repression of viral RNAs and in the case of DNA viruses, transcriptional arrest of viral minichromosomes. RNA silencing may also contribute to symptom alleviation by regulating plant gene expression. In this review, we discuss the evidence supporting the role of various RNA silencing mechanisms in symptom recovery. We also discuss how a delicate equilibrium between RNA silencing and virus counter-defense responses in recovered leaves may help maintain virus titers at levels below the threshold required for symptom induction.
    Full-text · Article · Feb 2015 · Virology
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    • "Another potentially reliable source of minimum divergence times is endogenous paleoviral elements (Katzourakis et al., 2007). Over the last decade, evidence of the most unexpected class of paleoviral elements, Non-retroviral Endogenous RNA Viral Elements (NERVEs), has been provided for each major eukaryotic group by sequencing across the integration boundaries of putative viral elements and host genomes (Crochu et al., 2004; Horie et al., 2010; Liu et al., 2010; Tanne & Sela, 2005; Taylor & Bruenn, 2009; Taylor, Leach & Bruenn, 2010). BLAST searches of animal genome databases alone suggest that representatives of all known viral genome architectures are involved in the formation of paleoviral elements (Belyi, Levine & Skalka, 2010; Katzourakis & Gifford, 2010). "
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    ABSTRACT: An understanding of the timescale of evolution is critical for comparative virology but remains elusive for many RNA viruses. Age estimates based on mutation rates can severely underestimate divergences for ancient viral genes that are evolving under strong purifying selection. Paleoviral dating, however, can provide minimum age estimates for ancient divergence, but few orthologous paleoviruses are known within clades of extant viruses. For example, ebolaviruses and marburgviruses are well-studied mammalian pathogens, but their comparative biology is difficult to interpret because the existing estimates of divergence are controversial. Here we provide evidence that paleoviral elements of two genes (ebolavirus-like VP35 and NP) in cricetid rodent genomes originated after the divergence of ebolaviruses and cuevaviruses from marburgviruses. We provide evidence of orthology by identifying common paleoviral insertion sites among the rodent genomes. Our findings indicate that ebolaviruses and cuevaviruses have been diverging from marburgviruses since the early Miocene.
    Full-text · Article · Sep 2014 · PeerJ
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    • "Horizontal gene transfer (HGT), which is also known as lateral gene transfer, refers to the movement of genetic information across distinct evolutionary lineages. At present, the occurrence of HGT is recognized as frequent events from cells to viruses (Bratke and McLysaght, 2008; Filée et al., 2008; Forterre, 2006; Koonin et al., 2006), from viruses to viruses (Koonin and Dolja, 2006; Liu et al., 2012a; Moreira and López-García, 2009), and from viruses to cells (Geuking et al., 2009; Horie et al., 2010; Koonin, 2010; Liu et al., 2010; Tanne and Sela, 2005; Taylor and Bruenn, 2009). However, transfer from viruses to cells was primarily found in DNA viruses and retroviruses (Bejarano et al., 1996; Kunii et al., 2004; Monier et al., 2009), and transfer has only rarely been shown to occur in non-retroviruses (Chare et al., 2003; Geuking et al., 2009; Hon et al., 2008). "
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    ABSTRACT: In this study, we describe a novel mycovirus isolated from Ustilaginoidea virens, which was designated Ustilaginoidea virens nonsegmented virus 1 (UvNV-1). The sequence analysis revealed that UvNV-1 has two open reading frames (ORFs). ORF1 encodes an unknown protein, which is similar to the hypothetical protein BN7_5177 of Wickerhamomyces ciferrii. ORF2 encodes a putative RNA-dependent RNA polymerase (RdRp), which is most closely related to Bryopsis mitochondria-associated dsRNA (BDRM) and is likely expressed by a +1 ribosomal frameshift within the sequence CCC_UUU_CGA. The phylogenetic analysis of the RdRp of UvNV-1 showed that UvNV-1 represents a new virus taxon of mycoviruses with a partitivirus-like lineage that is classified into the family of picorna-like viruses. Based on northern hybridization, UvNV-1 was found to be common to U. virens from different geographic locations in China. The biological comparison of virus-free and infected fungal strains revealed that UvNV-1 is likely to be cryptic to its host.
    Full-text · Article · Jul 2014 · Virology
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