Participation of Multifunctional RNA in Replication, Recombination and Regulation of Endogenous Plant Pararetroviruses (EPRVs) (original) (raw)
Virology, 2004
Carnation small viroid-like RNA (CarSV RNA) is unique among plant viroid-like RNAs in having a homologous DNA counterpart. In the present study, we found the most abundant CarSV DNA form (275 nt) coexisting with other smaller and longer-than-unit forms. Further analysis of PCR-amplified products revealed the presence of CarSV DNA-related sequences integrated in the plant genome, fused to microsatellite-like genomic sequences. Six to seven nucleotides at the boundaries in the CarSV DNA sequence could be found in the genomic sequences and also delimiting the boundaries of an enlarged version with partial duplication. This suggests that a common mechanism might have played a role in their emergence, namely, polymerase pausing and switching between stretches of homologous sequences. These plants also contained deleted CarSV DNA mutants with boundaries near those observed with fused sequences.
Journal of Virology - J VIROL, 2000
Carnation small viroid-like RNA (CarSV RNA) and its homologous DNA are the two forms of a unique plant retroviroid-like system. CarSV RNA is a 275-nucleotide noninfectious viroid-like RNA, present in certain carnation plants, which can adopt hammerhead structures in both polarity strands and self-cleave accordingly. CarSV DNA is organized as a series of head-to-tail multimers forming part of extrachromosomal elements in which CarSV DNA sequences are fused to sequences of carnation etched ring virus (CERV), a plant pararetrovirus. Analysis of more than 30 CarSV-CERV DNA junctions showed that distinct regions of the viral genome seem able to interact with CarSV DNA. All these junctions were short nucleotide stretches common to both CarSV and CERV DNAs. This suggests a polymerase-driven mechanism for their origin involving an enzyme with low processivity, most likely the viral reverse transcriptase. This view was further supported by the observation that most of CarSV sequences forming part of the junctions correspond either to strong secondary structure motifs in the conformation proposed for CarSV RNA or to its self-cleavage sites, which may have facilitated polymerase jumping. Accompanying the
Rearranged Endogenized Plant Pararetroviruses as Evidence of Heritable RNA-based Immunity
Molecular Biology and Evolution
Eukaryotic genomics frequently revealed historical spontaneous endogenization events of external invading nucleic acids, such as viral elements. In plants, an extensive occurrence of endogenous plant pararetroviruses (EPRVs) is usually believed to endow hosts with an additional layer of internal suppressive weaponry. However, an actual demonstration of this activity remains speculative. We analyzed the EPRV component and accompanying silencing effectors of Solanum lycopersicum, documenting that intronic/intergenic pararetroviral integrations bearing inverted-repeats fuel the plant's RNA-based immune system with suitable transcripts capable of evoking a silencing response. A surprisingly small set of rearrangements explained a substantial fraction of pararetroviral-derived endogenous small-interfering (si)RNAs, enriched in 22-nt forms typically associated with anti-viral post-transcriptional gene silencing. We provide preliminary evidence that such genetic and immunological signa...
Plant retroviruses: structure, evolution and future applications
Dna Sequence, 2005
Retroelements, which replicate by reverse transcription, have been detected in higher plants, higher animals, fungi, insects and bacteria. They have been classified into viral retroelements, eukaryotic chromosomal non-viral retroelements and bacterial chromosomal retroelements. Until recently, retroviruses were thought to be restricted to vertebrates. Plant sequencing projects revealed that plant genomes contain retroviral-like sequences. This review aims to address the structure and evolution of plant retroviruses. In addition, it proposes future applications for these important key components of plant genomes.
Genome Research, 2001
Retrotransposons and retroviruses share similar intracellular life cycles and major encoded proteins, but retrotransposons lack the envelope (env) critical for infectivity. Retrotransposons are ubiquitous and abundant in plants and active retroviruses are known in animals. Although a few env-containing retroelements, gypsy-like Athila, Cyclops, and Calypso and copia-like SIRE-1, have been identified in plants, the general presence and functionality of the domain remains unclear. We show here that env-class elements are present throughout the flowering plants and are widely transcribed. Within the grasses, we show the transcription of the env domain itself for Bagy-2 and related retrotransposons, all members of the Athila group. Furthermore, Bagy-2 transcripts undergo splicing to generate a subgenomic env product as do those of retroviruses. Transcription and the polymorphism of their insertion sites in closely related barley cultivars suggests that at least some are propagationally active. The putative ENV polypeptides of Bagy-2 and rice Rigy-2 contain predicted leucine zipper and transmembrane domains typical of retroviral ENVs. These findings raise the prospect of active retroviral agents among the plants.
Sequences and phylogenies of plant pararetroviruses, viruses, and transposable elements
2004
Abstract DNA elements found within cells that include the enzyme reverse transcriptase can be brought together within a unified taxonomic framework. The framework includes retroelements that are components of the nuclear genome, and recognized viruses where nuclear integration is unknown, occurs occasionally or is frequent. The classification probably has a natural basis and reflects aspects of the evolution and phylogeny of the elements.
Retrovirus-like elements in plants
2005
LTR retrotransposons with structures that are identical to those found in simple vertebrate retroviruses, including a putative env gene, have been discovered in plants. Those potential plant retroviruses can be classified into two classes. The first one is formed by the Arabidopsis thaliana Athila elements and many other closely related envcontaining elements. All of them belong to the Ty3/Gypsy group of LTR retrotransposons. The second class, in which the best-known element was first found in soybean and called SIRE1, belongs to the Ty1/Copia group. Thus, two distantly related lineages have convergent features that suggest that the transition between intracellular and infective ways of life may have occurred several times independently.
Cell, 2000
Norwich NR4 7UH standing of PTGS through the identification of short (25 nucleotide) RNAs that are invariably associated with United Kingdom PTGS in plants. These short RNAs of both sense and antisense polarity correspond to the target of PTGS (Hamilton and Baulcombe, 1999). Similar short RNA spe-Summary cies have been associated with RNA interference in Drosophila melanogaster. In in vitro extracts, they are pro-Posttranscriptional gene silencing is a defense mechduced by processing of larger dsRNAs (Zamore et al., anism in plants that is similar to quelling in fungi and 2000) and provide sequence specificity to a system of RNA interference in animals. Here, we describe four RNA degradation (Hammond et al., 2000). genetic loci that are required for posttranscriptional To shed more light on the mechanism of PTGS, we gene silencing in Arabidopsis. One of these, SDE1, is carried out a mutation analysis of PTGS in Arabidopsis a plant homolog of QDE-1 in Neurospora crassa that carrying two transgenes (Dalmay et al., 2000). One of encodes an RNA-dependent RNA polymerase. The these transgenes encodes a potato virus X:GFP vector sde1 mutation was specific for posttranscriptional (PVX:GFP) and is responsible for initiation of PTGS. The gene silencing induced by transgenes rather than by second transgene encodes a green fluorescent protein viruses. We propose that the role of SDE1 is to synthe-(GFP) reporter of silencing. In the absence of the size a double-stranded RNA initiator of posttranscrip-PVX:GFP transgene, this reporter gene was expressed tional gene silencing. According to this idea, when a at a high level and the Arabidopsis plants were green virus induces posttranscriptional gene silencing, the fluorescent under UV light. However, in the presence of virus-encoded RNA polymerase would produce the the PVX:GFP transgene, there was PTGS of the GFP double-stranded RNA and SDE1 would be redundant. reporter. This system was designed to combine elements of transgene-and virus-induced PTGS. Introduction We report here that at least four genetic loci are required for PTGS in Arabidopsis. Mutant, silencing defec-Posttranscriptional gene silencing (PTGS) in plants, tive (sde) plants differ from wild type in that they accuquelling in fungi, and RNA interference in animals are mulate high levels of GFP and PVX:GFP RNAs and low responses to various types of foreign nucleic acid inlevels of the 25 nt RNAs associated with PTGS. We show cluding viruses, transposons, transgenes, and doublethat one of these mutant loci (sde1) encodes an RdRPstranded (ds)RNA (Vaucheret et al., 1998; Sharp, 1999). related protein. This finding confirms the similarity of These processes represent natural systems of defense PTGS in plants with gene silencing phenomena in other against viruses (Ratcliff et al., 1997, 1999) and transpoorganisms because the SDE1 protein is similar to QDE-1 sons (Ketting et al., 1999) that were first discovered from of N. crassa and to EGO-1 of C. elegans, which are experiments with transgenes (Napoli et al., 1990; van required for quelling and RNAi, respectively (Cogoni and der Krol et al., 1990), virus vectors (Ruiz et al., 1998), or Macino, 1999a; Smardon et al., 2000). The SDE1 protein injected dsRNAs (Fire et al., 1998) in which the foreign is required for transgene silencing but not for virusnucleic acids were based on endogenous genes. The induced PTGS and, based on that finding, we propose foreign nucleic acids caused the defense system to be that the role of SDE1 is to produce a dsRNA activator targeted against these endogenous RNAs so that the of PTGS. According to this idea, SDE1 is not required for organism exhibits a phenocopy of loss-of-function muvirus-induced PTGS because the virus-encoded RdRP tations in the corresponding genes. produces dsRNA as an intermediate in the replication In Neurospora crassa and Caenorhabditis elegans, cycle. there is compelling evidence that the quelling and RNA interference mechanisms are related because both are Results abolished by mutations in homologs of a Werner's disease syndrome gene (Cogoni and Macino, 1999b; Ket-Mutation Analysis of PTGS in Arabidopsis ting et al., 1999), an eIF2C translation factor gene (Ta-To identify genes required for PTGS, we carried out bara et al., 1999; Catalanotto et al., 2000), and an RNAfast neutron mutagenesis of an Arabidopsis line dependent RNA polymerase (RdRP) gene (Cogoni and [GFP142xAmp243] (Dalmay et al., 2000). This line is de-Macino, 1999a; Smardon et al., 2000). In due course, rived from the F2 progeny of a cross between parental this list will be extended by characterization of other lines GFP142 and Amp243 carrying 35S-GFP and 35S-PVX:GFP transgenes, respectively. We refer here to [GFP142xAmp243] as "GxA" and the Amp243 and ‡ To whom correspondence should be addressed (e-mail: david. baulcombe@bbsrc.ac.uk).