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At least 19 recordsLinked to original sources
PubMed2026

Characterization of endogenous pararetroviruses in yam (Dioscorea spp.) genomes revealed four pararetrovirus groups, including a dioscovirus-like lineage: implications for diagnostics and yam germplasm exchange.

Yams (Dioscorea spp.) are an important vegetatively propagated food security crop grown for their starchy tubers. Yams are susceptible to several viruses, and their genomes harbor a diverse array of endogenous pararetroviral sequences (EPRVs), which complicate diagnostics and germplasm exchange because of their similarity to episomal viruses. To better characterize EPRV diversity, we analyzed 86 publicly available whole-genome sequences from five Dioscorea species (D. rotundata, D. alata, D. praehensilis, D. abyssinica, and D. dumetorum). Assembled genomes were screened for endogenous pararetrovirus sequences (EPRVs) using the CAULIFINDER pipeline, targeting conserved RT/RNase H domains of the Caulimoviridae family. Our analyses revealed four major EPRV groups in D. rotundata: Yendovirus, Badnavirus, Yam Endovirus 1, and a Dioscovirus-like lineage. While most insertions were fragmented, we found full-length putative viral genomes corresponding to the Yam Badnavirus and Dioscovirus-like clades. These findings expand knowledge of yam EPRV diversity, contribute to the development of improved diagnostic tools to differentiate endogenous and episomal forms, and promote a science-based, risk-proportionate approach to yam phytosanitation that facilitates global germplasm exchange while maintaining biosecurity.

Dioscorea↗
PubMed1999

A short open reading frame terminating in front of a stable hairpin is the conserved feature in pregenomic RNA leaders of plant pararetroviruses.

In plant pararetroviruses, pregenomic RNA (pgRNA) directs synthesis of circular double-stranded viral DNA and serves as a polycistronic mRNA. By computer-aided analysis, the 14 plant pararetroviruses sequenced so far were compared with respect to structural organization of their pgRNA 5'-leader. The results revealed that the pgRNA of all these viruses carries a long leader sequence containing several short ORFs and having the potential to form a large stem-loop structure; both features are known to be inhibitory for downstream translation. Formation of the structure brings the first long ORF into the close spatial vicinity of a 5'-proximal short ORF that terminates 5 to 10 nt upstream of the stable structural element. The first long ORF on the pgRNA is translated by a ribosome shunt mechanism discovered in cauliflower mosaic (CaMV) and rice tungro bacilliform viruses, representing the two major groups of plant pararetroviruses. Both the short ORF and the structure have been implicated in the shunt process for CaMV pgRNA translation. The conservation of these elements among all plant pararetroviruses suggests conservation of the ribosome shunt mechanism. For some of the less well-studied viruses, the localization of the conserved elements also allowed predictions of the pgRNA promoter region and the translation start site of the first long ORF.

Badnavirus↗
PubMed1995

Characterization of cassava vein mosaic virus: a distinct plant pararetrovirus.

Cassava vein mosaic virus (CVMV) was found to be widespread throughout the north-eastern region of Brazil. The complete sequence of CVMV was determined, and the genome was 8158 bp in size. A cytosolic initiator methionine tRNA (tRNA met1)-binding site that probably acts as a primer for minus-strand synthesis was present. The genome contained five open reading frames that potentially encode proteins with predicted molecular masses of 186 kDa, 9 kDa, 77 kDa, 24 kDa and 26 kDa. The putative 186 kDa protein had regions with similarity to the zinc finger-like RNA-binding domain that is a common element in the capsid proteins and similarity to the intercellular transport domain of the plant pararetroviruses. The predicted 77 kDa protein had regions with similarity to aspartic proteases, reverse transcriptase and RNase H of pararetroviruses. This gene order was confirmed by the amplification of similar PCR products from total DNA extracted from CVMV-infected cassava plants. The genomic organization of CVMV was different from the organization of either the caulimoviruses or badnaviruses. In comparisons of the regions with the reverse transcriptase motif, CVMV was grouped between the caulimoviruses and badnaviruses. It appears that CVMV is distinct from the other well-characterized plant pararetroviruses.

Amino Acid Sequence↗
PubMed2001

Tetramerization is a conserved feature of the virion-associated protein in plant pararetroviruses.

All plant pararetroviruses belong to the Caulimoviridae family. This family contains six genera of viruses with different biological, serological, and molecular characteristics. Although some important mechanisms of viral replication and host infection are understood, much remains to be discovered about the many functions of the viral proteins. The focus of this study, the virion-associated protein (VAP), is conserved among all members of the group and contains a coiled-coil structure that has been shown to assemble as a tetramer in the case of cauliflower mosaic virus. We have used the yeast two-hybrid system to characterize self-association of the VAPs of four distinct plant pararetroviruses, each belonging to a different genus of Caulimoviridae. Chemical cross-linking confirmed that VAPs assemble into tetramers. Tetramerization is thus a common property of these proteins in plant pararetroviruses. The possible implications of this conserved feature for VAP function are discussed.

Amino Acid Sequence↗
PubMed2005

Characterisation of pararetrovirus-like sequences in the genome of potato (Solanum tuberosum).

Three families of pararetrovirus-like sequences were isolated from the genome of potato using PCR of a characteristic fragment extending from the end of the transactivator domain. The potato pararetrovirus-like sequences are abundant in the nuclear genome of potato as demonstrated by their hybridisation to high-molecular weight DNA in Southern transfers and by fluorescence in situ hybridisation. Sequencing of cloned PCR products demonstrated that the potato pararetrovirus-like sequences were similar to other pararetroviral sequences and also to some expressed sequences from tobacco and tomato, notably from callus and Agrobacterium-infected tissue. It is possible that the potato pararetroviral sequences defend against viral genes via silencing mechanisms, although, as in Petunia or banana, their transcription and recombination may cause infection under stress conditions.

Base Sequence↗
PubMed1994

Splicing in a plant pararetrovirus.

Analysis of expression in rice cells of plasmids in which an ATG-less chloramphenicol acetyl transferase ORF was placed in frame with the coding sequence of the pararetrovirus rice tungro bacilliform virus (RTBV) ORF IV, and which contained much of the upstream full-length transcript sequence of RTBV, gave evidence to suggest that a splicing event occurred. Reverse transcription/PCR of RNA from transfected protoplasts and from RTBV-infected plants yielded a product which confirmed that the 5' end of ORF IV was spliced in frame to a short ORF (sORF) in the RTBV leader sequence removing an intron of about 6.3 kb. Most of the translation is initiated at the ATG codon in the sORF with only about 10% at the ORF IV ATG codon. The efficiency of splicing appears to be inversely related to the length of the intron. The finding of splicing in a pararetrovirus blurs the differences between them and retroviruses but is in accord with the hypothesis that retroelements acquire genes and sequences which adapt them to specific niches.

Base Sequence↗
PubMed2000

Characterization and genomic analysis of tobacco vein clearing virus, a plant pararetrovirus that is transmitted vertically and related to sequences integrated in the host genome.

A previously undescribed caulimo-like virus was identified in the hybrid tobacco species Nicotiana edwardsonii, and was named tobacco vein clearing virus (TVCV) after the symptoms associated with its occurrence in this plant. The virions of TVCV are 50 nm in diameter and are composed of a 45 kDa capsid protein and a 7767 bp dsDNA genome. Each strand of the genome is interrupted by a site-specific discontinuity. In genome sequence and arrangement of ORFs TVCV was most similar to cassava vein mosaic virus, indicating that TVCV is a pararetrovirus. No serological relationship was detected between TVCV and any other caulimoviruses, including petunia vein clearing virus, which has similar biological properties. In N. edwardsonii TVCV was seed-transmitted to 100% of progeny plants, but was not transmitted by mechanical inoculation, grafting or Myzus persicae to any of seven other Nicotiana spp. Genomic DNA of TVCV hybridized to genomic DNA of N. edwardsonii and of N. glutinosa, its male parent, but not to genomic DNA of N. clevelandii, the female parent. TVCV has 78% sequence identity with pararetrovirus-like sequences that are present in high copy number in the N. tabacum genome, and TVCV genomic DNA hybridized to genomic DNA of N. tabacum and N. rustica. These observations suggest that the episomal form of TVCV may arise from integrated pararetroviral elements present in N. edwardsonii, that these integrants were inherited from the male parent N. glutinosa, and that these elements are related but not identical to pararetroviral elements occurring in other Nicotiana spp.

Base Sequence↗
PubMed2006

Mechanism of ribosome shunting in Rice tungro bacilliform pararetrovirus.

In plant pararetroviruses, pregenomic RNA serves both as a template for replication through reverse transcription and a polysictronic mRNA. This RNA has a complex leader sequence preceding the first large ORF. The leader contains multiple short ORFs and strong secondary structure, both inhibiting ribosome scanning. Translation on this RNA is initiated by shunting, in which scanning ribosomes bypass a large portion of the leader with the inhibitory secondary structure and short ORFs. In Cauliflower mosaic virus (CaMV), the ribosome shunting mechanism involves translation of the 5'-proximal short ORF terminating in front of the secondary structure that appears to force ribosomes to take off and resume scanning at a landing site downstream of the structure. Using two plant protoplast systems and shunt-competent wheat-germ extracts, we demonstrate that in Rice tungro bacilliform virus (RTBV) shunting also depends on the first short ORF followed by strong secondary structure. Swapping of the conserved shunt elements between CaMV and RTBV revealed the importance of nucleotide composition of the landing sequence for efficient shunting. The results suggest that the mechanism of ribosome shunting is evolutionary conserved in plant pararetroviruses.

5' Untranslated Regions↗
PubMed1994

Analysis of figwort mosaic virus (plant pararetrovirus) polyadenylation signal.

Analysis of the cauliflower mosaic virus (CaMV) polyadenylation (poly(A)) signal has revealed several striking differences to poly(A) signals from animal genes such as the absence of activating sequences downstream from the cleavage site. Instead, upstream sequences were shown to induce recognition of an AAUAAA sequence. To test whether these features are representative of other plant pararetrovirus poly(A) signals, a characterization of the figwort mosaic virus (FMV) poly(A) signal is presented here. The FMV RNAs were isolated from infected plants and mapped, and the different elements composing the FMV poly(A) signal were identified. Multiple upstream sequences were found to be essential for efficient processing at the FMV poly(A) site and could be replaced by the CaMV upstream elements. The FMV upstream sequences showed homologies to other characterized upstream sequences from CaMV, from animal viruses, and from plant poly(A) signals. Surprisingly, neither the FMV nor the CaMV upstream elements could induce recognition of an AAUAAA sequence present in the FMV poly(A) signal, instead a UAUAAA sequence 55 nucleotides further downstream was utilized. It is proposed that additional features may be required for appropriate cleavage such as the context of the AAUAAA-like sequence or perhaps the cleavage site itself.

Base Sequence↗
PubMed1995

Comparison of packaging strategy in retroviruses and pararetroviruses.

Reverse transcription is not solely a retroviral mechanism. Animal hepadnaviruses, plant caulimoviruses, and badnaviruses have a RNA intermediate which is reverse transcribed into double-stranded DNA genome. Based on this fact, these three groups of viruses have been regrouped under the name of pararetroviruses. Although each one has developed its own strategy to assure an efficient packaging of their genome, it is clear that they have adopted a strategy where encapsidation prepares for initiation of reverse transcription. This is discussed in this review.

Caulimovirus↗
PubMed1996

Efficient translation of distal cistrons of a polycistronic mRNA of a plant pararetrovirus requires a compatible interaction between the mRNA 3' end and the proteinaceous trans-activator.

Caulimoviruses, a type of plant pararetrovirus, employ a highly unusual mechanism to express the multiple cistrons of their pregenomic RNA. It involves translation of a polycistronic mRNA utilizing cis-acting viral RNA sequences and a transacting virus-encoded protein (P6). In addition to its role in polycistronic translation, the translational trans-activator protein P6 also activates its own expression from a monocistronic subgenomic RNA. Using Nicotiana Edwardsonii cell suspension protoplasts, we analyzed the ability of P6 proteins from three different caulimoviruses to activate viral RNA-based reporter constructs. Cis-acting elements present in figwort mosaic caulimovirus (FMV) are functional not only in the presence of the cognate P6 activator protein, but also in the presence of the heterologous activators from cauliflower mosaic caulimovirus (CaMV) and peanut chlorotic streak caulimovirus (PCISV). However, when 3' cis-acting elements essential for efficient polycistronic expression of FMV are replaced by their counterparts from PCISV, reporter gene expression is only observed in the presence of PCISV P6. Derepression of monocistronic reporter constructs tailed with FMV or CaMV 3' proximal sequences is less efficient in the presence of PCISV P6 than with either FMV or CaMV P6, but more efficient when the constructs contain a cognate PCISV 3' cis-element. Efficient expression of polycistronic and monocistronic caulimovirus mRNAs in plant cells thus requires compatible interactions between P6, a translational trans-activator, and its cognate cis-element at the 3' end of the mRNA.

Caulimovirus↗
PubMed1997

Petunia vein-clearing virus: a plant pararetrovirus with the core sequences for an integrase function.

Petunia vein-clearing virus (PVCV) is a plant pararetrovirus that has some features of retrotransposons. It encapsidates dsDNA and has isometric particles and inclusion bodies similar to those of caulimoviruses. The PVCV genome of 7205 bp has two large ORFs in the transcribed strand and a methionine tRNA primer-binding site in its 663-bp intergenic region. The N-terminal position of the large protein (126 kDa) encoded by ORF I has similarity to the movement protein of caulimoviruses. Toward the C-terminus of this same polyprotein are the two distinctive sequence elements [HHCC and DD(35)E] of the integrase function of retroviruses and retrotransposons. ORF II of PVCV encodes a protein of 125 kDa with domains for an RNA-binding element, common to the gag gene of retroelements, followed by consensus sequences for an acid protease, reverse transcriptase, and ribonuclease H. Hence, the gag equivalent (capsid protein) and pol gene of PVCV are part of the same polyprotein. Phylogenetic comparison of the reverse transcriptase of PVCV with that of various other retroelements grouped PVCV between caulimoviruses and the Ty3/gypsy retrotransposons, suggesting that PVCV is a divergent member of the caulimoviruses.

Amino Acid Sequence↗
PubMed2006

Endogenous pararetroviruses: two-faced travelers in the plant genome.

Endogenous plant pararetroviruses (EPRVs) were identified as integrated counterparts of most members of the plant virus family Caulimoviridae and represent repetitive elements that are ubiquitous in the plant kingdom. They are often located in pericentromeric regions of plant chromosomes in the vicinity of retrotransposon sequences. Depending on their structure and sequence integrity, some EPRVs are able to replicate and to initiate viral infection. However, conservation of integrated sequences in plant genomes might indicate benefits for the host during evolution. Understanding EPRV activation and control by the host could have important implications for plant breeding strategies to prevent viral disease caused by EPRVs in newly generated cultivars.

Caulimoviridae↗
PubMed2003

Detection of petunia vein-clearing virus: model for the detection of DNA viruses in plants with homologous endogenous pararetrovirus sequences.

A number of cases of plant virus sequence integration into host plant genome have been reported. In at least two cases, endogenous pararetrovirus sequences are correlated strongly with subsequent episomal virus infection and there is circumstantial evidence that this also occurs for Petunia vein-clearing virus (PVCV). The detection of viruses is a critical component of plant health and therefore, it is important to have diagnostic procedures that differentiate between the detection of encapsidated viral DNA and homologous sequences in the host genome. PCR-based detection methods targeted at PVCV DNA have been tested and particular attention was paid to design controls that would indicate the existence of host DNA in the reaction. The use of ion-exchange chromatography for the partial purification of plant viruses from other cellular components, including chromosomal DNA, is described. The methods tested for PVCV detection are used to illustrate general principles for the specific detection of virus infections in host plants that carry homologous virus sequences in their genomes.

Chromatography, Ion Exchange↗
PubMed1991

An analysis of the sequence of an infectious clone of rice tungro bacilliform virus, a plant pararetrovirus.

The nucleotide sequence of an infectious clone of rice tungro bacilliform virus (RTBV) DNA has been determined. The circular genome has 8002 bp and one strand contains four open reading frames (ORFs). One ORF is potentially capable of encoding a protein of 24 kD (P24) and has no initiation (ATG) codon. The other three ORFs potentially encode proteins of 12 kD, 194 kD and 46 kD (P12, P194, P46) respectively. The functions of P24, P12 and P46 are unknown. Comparative analyses with retroviruses and Commelina yellow mottle virus suggest that the 194 kD putative product is a polyprotein that is proteolytically cleaved to yield the virion coat protein, a protease and replicase (reverse transcriptase and RNase H) characteristic of retroelements. The DNA sequence reveals other features which strongly support our belief that RTBV is a pararetrovirus. These include sequences at the mapped positions of two discontinuities in the virion DNA which are complementary to tRNA metinit and purine-rich, and may be the priming sites for minus- and plus-strand DNA synthesis respectively. As the positions of likely transcriptional signals suggest, a full-length viral transcript is observed by northern analysis. The predicted folding of the 645 bp 5'-region of this RNA resembles that of caulimoviruses. Comparisons with other reverse transcribing elements are discussed.

Amino Acid Sequence↗
PubMed2004

A distinct endogenous pararetrovirus family in Nicotiana tomentosiformis, a diploid progenitor of polyploid tobacco.

A distinct endogenous pararetrovirus (EPRV) family corresponding to a previously unknown virus has been identified in the genome of Nicotiana tomentosiformis, a diploid ancestor of allotetraploid tobacco (Nicotiana tabacum). The putative virus giving rise to N. tomentosiformis EPRVs (NtoEPRVs) is most similar to tobacco vein clearing virus, an episomal form of a normally silent EPRV family in Nicotiana glutinosa; it is also related to a putative virus giving rise to the NsEPRV family in Nicotiana sylvestris (the second diploid progenitor of tobacco) and in the N. sylvestris fraction of the tobacco genome. The copy number of NtoEPRVs is significantly higher in N. tomentosiformis than in tobacco. This suggests that after the polyploidization event, many copies were lost from the polyploid genome or were accumulated specifically in the diploid genome. By contrast, the copy number of NsEPRVs has remained constant in N. sylvestris and tobacco, indicating that changes have occurred preferentially in the NtoEPRV family during evolution of the three Nicotiana species. NtoEPRVs are often flanked by Gypsy retrotransposon-containing plant DNA. Although the mechanisms of NtoEPRV integration, accumulation, and/or elimination are unknown, these processes are possibly linked to retrotransposon activity.

Base Sequence↗
PubMed1996

Roles of the 35S promoter and multiple overlapping domains in the pathogenicity of the pararetrovirus cauliflower mosaic virus.

Elements associated with the 35S promoter involved in generating the pregenomic RNA (35S RNA) of the pararetrovirus cauliflower mosaic virus have been extensively studied in heterologous systems, but little is known about their role in viral pathogenicity. To investigate these elements, premature termination codons were progressively inserted into the 3' end of the adjacent gene VI to dissect it from colinear 35S enhancer sequences. The ability to cause a systemic infection in plants was retained with loss of up to 40 amino acids from the gene VI polypeptide, but truncations into a putative zinc finger proved lethal. In the 35S promoter, removal of the TATA box also abolished infectivity. However, upstream deletions encompassing the 35S enhancer showed that the sequence between -207 and -56 from the cap site comprised nonessential elements, although complete removal of this fragment caused loss of infectivity even when domain spacing was restored by linker insertion. Two separate enhancer domains (-207 to - 150 and -95 to -56) were identified, of which either one or the other, but not both, was required for infectivity. Some mutations affected the cellular levels of viral RNAs in unexpected ways, as with removal of the as-1 enhancer element causing an increase in 35S RNA. Others altered the relative abundance of nuclear and cytoplasmic viral DNAs. Mutations in promoter domains thought to be involved in regulating tissue-specific expression did not significantly affect virus accumulation in leaves versus roots, whereas gene VI mutants showed reduced root accumulation. We conclude that elements associated with the cauliflower mosaic virus 35S promoter contain extensive nonessential regions that can behave differently in their proper context than as isolated elements.

Base Sequence↗
PubMed2000

The DNA of a plant retroviroid-like element is fused to different sites in the genome of a plant pararetrovirus and shows multiple forms with sequence deletions.

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 most-abundant CarSV RNA, a series of CarSV RNAs with sequence deletions were previously characterized. Here we have identified some of their corresponding DNA forms, together with other CarSV DNA forms with deletions not found in any CarSV RNA species identified so far. Some of these CarSV DNA forms have also been detected fused to CERV sequences. The existence of these shortened CarSV DNA versions may provide a continuous input of their corresponding transcripts and explain the persistence of CarSV RNAs with defective hammerhead structures for which an RNA-RNA model of amplification seems unlikely.

Base Sequence↗