Tobraviruses—plant pathogens and tools for biotechnology

The tobraviruses, Tobacco rattle virus (TRV), Pea early‐browning virus (PEBV) and Pepper ringspot virus (PepRSV), are positive‐strand RNA viruses with rod‐shaped virus particles that are transmitted between plants by trichodorid nematodes. As a group, these viruses infect many plant species, with TRV having the widest host range. Recent studies have begun to dissect the interaction of TRV with potato, currently the most commercially important crop disease caused by any of the tobraviruses. As well as being successful plant pathogens, these viruses have become widely used as vectors for expression in plants of nonviral proteins or, more frequently, as initiators of virus‐induced gene silencing (VIGS). Precisely why tobraviruses should be so effective as VIGS vectors is not known; however, molecular studies of the mode of action of the tobravirus silencing suppressor protein are shedding some light on this process.     

The association between species of Trichodorus and Paratrichodorus vector nematodes and serotypes of tobacco rattle tobravirus

Virus transmission bait tests with single trichodorid nematodes from England, the Netherlands, Scotland or Sweden showed that a substantial degree of specificity occurs between trichodorid vector species and tobravirus serotypes. This specificity was more apparent with associations between Paratrichodorus vector species and tobravirus serotypes than with those between Trichodorus species and tobravirus serotypes. P. pachydermus transmitted PRN-serotype tobacco rattle virus (TRV) isolates, P. teres ORE-serotype isolates and P. anemones TRV isolates which did not react with any of the antisera used, but which could be distinguished from all other isolates by their symptomatology in Chenopodium test plants. T. viruliferus, T. primitivus and T. cylindricus transmitted RQ-serotype isolates and the latter species also transmitted TRV isolates reacting with TCB2 and pea early-browning SP5-antisera. Several TRV isolates transmitted by T. cylindricus failed to react with any of the antisera used.     

Rice stripe tenuivirus p2 may recruit or manipulate nucleolar functions through an interaction with fibrillarin to promote virus systemic movement

Rice stripe virus (RSV) is the type species of the genus Tenuivirus and represents a major viral pathogen affecting rice production in East Asia. In this study, RSV p2 was fused to yellow fluorescent protein (p2‐YFP) and expressed in epidermal cells of Nicotiana benthamiana. p2‐YFP fluorescence was found to move to the nucleolus initially, but to leave the nucleolus for the cytoplasm forming numerous distinct bright spots there at later time points. A bimolecular fluorescence complementation (BiFC) assay showed that p2 interacted with fibrillarin and that the interaction occurred in the nucleus. Both the nucleolar localization and cytoplasmic distribution of p2‐YFP fluorescence were affected in fibrillarin‐silenced N. benthamiana. Fibrillarin depletion abolished the systemic movement of RSV, but not that of Tobacco mosaic virus (TMV) and Potato virus X (PVX). A Tobacco rattle virus (TRV)‐based virus‐induced gene silencing (VIGS) method was used to diminish RSV NS2 (encoding p2) or NS3 (encoding p3) during RSV infection. Silencing of NS3 alleviated symptom severity and reduced RSV accumulation, but had no obvious effects on virus movement and the timing of symptom development. However, silencing of NS2 abolished the systemic movement of RSV. The possibility that RSV p2 may recruit or manipulate nucleolar functions to promote virus systemic infection is discussed.     

Increase in Plasmodesmatal Permeability during Cell-to-Cell Spread of Tobacco Rattle Virus from Individually Inoculated Cells

A microinjection technique was devised for inoculation of single Nicotiana clevelandii leaf trichome cells with virus particles. By removing inoculated trichomes at various times after microinjection, it was shown that at least 4 hr were required for tobacco rattle virus (TRV; tobravirus group) to move out of primarily inoculated cells. Effects of the early stages of TRV infection on plasmodesmatal permeability were examined by microinjection of fluorochrome-labeled molecules. Fluorescein-labeled insulin A chain (Mr, 2921) and fluorescein-labeled dextran (Mr, 4400) were observed to pass out of individual N. clevelandii trichome cells that had been inoculated with TRV by microinjection 5 hr previously. By contrast, Lucifer Yellow CH-labeled dextran (Mr, 10,000) was restricted to the inoculated cell. None of these fluorescent probes were able to move out of uninoculated cells or out of cells that had been inoculated with TRV only 2 hr previously. The movement of macromolecules through plasmodesmata, therefore, coincided with and probably resulted from cell-to-cell movement of TRV. The results are discussed with reference to the interaction of viruses and plasmodesmata and mechanisms of intercellular virus movement.     

Analysis of the occurrence and distribution of tobacco rattle virus in field soil and disease in a subsequent tulip crop

The occurrence and distribution of tobacco rattle virus (TRV) in field plots was determined by soil bait-testing and disease incidence in tulips subsequently grown on these plots was studied. The virus occurred in patches, calculated as 1.5 m × 3.6 m. The presence of virus was not correlated with numbers of potential vector trichodorid nematodes. Of three trichodorid nematode species present, only Paratrichodorus teres transmitted TRV which, as with virus isolates obtained in bait-tests and from infected tulips, reacted in serological tests with an antiserum prepared against a Dutch isolate of pea-early browning virus (PEBV). Virus prevalence in a subsequent tulip crop was 0.8% and in a sample of tulip plants, virus was recovered only from plants showing virus symptoms. Plots from which TRV was recovered in bait-tests yielded significantly more virus diseased tulips than plots which tested negative for virus. Growing bait-plants in field-plots, as compared with greenhouse tests using soil collected as a series of sub-samples, resulted in an underestimate of the occurrence of TRV.     

cmv1 is a gate for Cucumber mosaic virus transport from bundle sheath cells to phloem in melon

Cucumber mosaic virus (CMV) has the broadest host range among plant viruses, causing enormous losses in agriculture. In melon, strains of subgroup II are unable to establish a systemic infection in the near‐isogenic line SC12‐1‐99, which carries the recessive resistance gene cmv1 from the accession PI 161375, cultivar ‘Songwhan Charmi’. Strains of subgroup I overcome cmv1 resistance in a manner dependent on the movement protein. We characterized the resistance conferred by cmv1 and established that CMV‐LS (subgroup II) can move from cell to cell up to the veins in the inoculated leaf, but cannot enter the phloem. Immunogold labelling at transmission electron microscopy level showed that CMV‐LS remains restricted to the bundle sheath (BS) cells in the resistant line, and does not invade vascular parenchyma or intermediary cells, whereas, in the susceptible line ‘Piel de Sapo’ (PS), the virus invades all vein cell types. These observations indicate that the resistant allele of cmv1 restricts systemic infection in a virus strain‐ and cell type‐specific manner by acting as an important gatekeeper for virus progression from BS cells to phloem cells. Graft inoculation experiments showed that CMV‐LS cannot move from the infected PS stock into the resistant cmv1 scion, thus suggesting an additional role for cmv1 related to CMV transport within or exit from the phloem. The characterization of this new form of recessive resistance, based on a restriction of virus systemic movement, opens up the possibility to design alternative approaches for breeding strategies in melon.     

Nanobody‐mediated resistance to Grapevine fanleaf virus in plants

Since their discovery, single‐domain antigen‐binding fragments of camelid‐derived heavy‐chain‐only antibodies, also known as nanobodies (Nbs), have proven to be of outstanding interest as therapeutics against human diseases and pathogens including viruses, but their use against phytopathogens remains limited. Many plant viruses including Grapevine fanleaf virus (GFLV), a nematode‐transmitted icosahedral virus and causal agent of fanleaf degenerative disease, have worldwide distribution and huge burden on crop yields representing billions of US dollars of losses annually, yet solutions to combat these viruses are often limited or inefficient. Here, we identified a Nb specific to GFLV that confers strong resistance to GFLV upon stable expression in the model plant Nicotiana benthamiana and also in grapevine rootstock, the natural host of the virus. We showed that resistance was effective against a broad range of GFLV isolates independently of the inoculation method including upon nematode transmission but not against its close relative, Arabis mosaic virus. We also demonstrated that virus neutralization occurs at an early step of the virus life cycle, prior to cell‐to‐cell movement. Our findings will not only be instrumental to confer resistance to GFLV in grapevine, but more generally they pave the way for the generation of novel antiviral strategies in plants based on Nbs.     

Comparison of nucleic acid hybridisation and other tests for detecting tobacco rattle virus in narcissus plants and potato tubers

All isolates of tobacco rattle virus (TRV) found in naturally infected narcissus leaves produced nucleoprotein particles, mostly in large concentrations but, because of antigenic diversity, less than half of the isolates were identified by immunosorbent electron microscopy (ISEM) and still fewer by enzyme-linked immunosorbent assay. All were identified by a nucleic acid hybridisation test in which DNA complementary to RNA-1 of strain PRN of TRV was allowed to react with nucleic acid extracted from leaf tissue. Spraing-affected tubers in some potato stocks yielded only NM isolates of TRV. These isolates do not produce virus particles and they were therefore not detected by ISEM. The infectivity of nucleic acid extracts from recently harvested tubers with spraing symptoms was much greater than that of extracts prepared from tubers after 8 months' storage. In other potato stocks, some spraing-affected tubers contained NM isolates and the rest contained particle-producing isolates (M isolates) of TRV. The infectivity of sap and of nucleic acid, extracted 7 months after harvest from tubers infected with M isolates, was much greater than that of nucleic acid extracted from comparable tubers infected with NM isolates. TRV was detected by nucleic acid hybridisation in extracts of almost all tubers containing either M or NM isolates, even when the tubers were not tested until 7–8 months after harvest. The probable sequence of events occurring after tubers are infected with TRV is outlined, and it is suggested that the virus will rarely become established in fields as a result of planting infected tubers.     

The incidence of viruses in wild Brassica nigra in Dorset (UK)

Using enzyme‐linked immunosorbent assays, the frequency of occurrence of six viruses was determined in Brassica nigra collected from five coastal sites in Dorset, spanning approximately 24 km. During 1998–2000, the viruses detected were: Turnip mosaic virus (genus Potyvirus) (TuMV), Turnip yellow mosaic virus (genus Tymovirus) (TYMV), Turnip crinkle virus (genus Carmovirus) (TCV), Turnip rosette virus (genus Sobemovirus) (TRoV), Beet western yellows virus (genus Polerovirus) (BWYV) and Cauliflower mosaic virus (genus Caulimovirus) (CaMV). Multiple infections were detected in some individuals (48/447). TuMV was detected infrequently over the three‐year period (5/597). A representative isolate of each virus was tested for its effects on glasshouse‐grown individuals from different half‐sib families of B. nigra from four of the sites. Whether inoculated manually or via aphids (Myzus persicae), TuMV caused a rapid (within 10 days) lethal systemic necrosis in the B. nigra seedlings except when they were near flowering at the time of inoculation. Each of the other viruses invaded systemically but were not lethal. Indeed, BWYV systemically invaded 13/19 glasshouse‐grown B. nigra seedlings but did not produce any visible symptoms. Otherwise, the isolates tested differed in their pathogenicity and in the symptoms they produced in infected B. nigra. With TYMV or TCV viral antigen concentration was closely linked to pathogenicity; for TRoV or CaMV, there was little or no difference in virus concentration between plants with and without symptoms. Substantial and reproducible differences were observed in sensitivity/susceptibility among B. nigra genotypes from different sites in Dorset challenged with the same virus isolate.     

Problems Encountered with the Selection of Cucumber Mosaic Virus (CMV) Isolates for Resistance Breeding Programs

Among the Chili breeding lines from the Asian Vegetable Research Center, two were chosen for the screening of a larger selection of Cucumber mosaic virus (CMV) isolates, mainly from Asian countries. The chili line (VC246) showed a resistance against several CMV‐isolates and was compared with chili line VC27a that was susceptible to CMV infection. Among the 28 CMV isolates, five were identified as resistance breaking (AN‐like) and non‐resistance breaking (P3613‐like) for the line VC246, whereas all isolates could establish a systemic infection on VC27a. However, further testing revealed that resistance in VC246 was also dependent on the way of inoculation and the inoculums itself. Graft inoculation could overcome the resistance, and the inoculation with isolated viral RNA resulted in no infection at all on the resistant chili line, independent of the virus isolate. Using a pseudo‐recombinant approach, we identified RNA2 of resistance breaking isolates as responsible for systemic infection and confined the area within RNA2 to the 3′ terminal part including the ORF 2b. Sequence alignments of that area revealed eight distinct mutations on amino acid level, which was present either in resistance or non‐resistance breaking isolates. A reversion from the P3613‐like to the AN‐like sequence of two of these mutations induced no effect on Capsicum sp., but induced symptoms on several tobacco species distinct from those induced by the wild‐type virus. However, pseudorecombinants, each generated from sets of two different AN‐like isolates, which were expected to infect VC246 systemically, did not indicating that probably RNA2 must be in a specific context to have the effect. In this case, a generalized attribution of functions to single amino acid exchanges might be impossible or at least extremely difficult.     

Occurrence and relative incidence of viruses infecting papaya in Venezuela

A survey of the main papaya (Carica papaya L.) production fields in Venezuela during 1997, indicated that crops were heavily affected with various virus‐like symptoms. A total of 745 samples from papaya plants showing symptoms suggestive of virus infection were collected and analysed using electron microscopy and enzyme‐linked immunosorbent assay (ELISA). Papaya ringspot virus (PRSV) and Papaya mild yellowing virus (PMYV) were the most frequently found viruses, which also occurred, in mixed infections. Rhabdovirus‐like particles were found only in samples collected in Distrito Federal (D.F). Papaya mosaic virus (papMV) and Tomato spotted wild virus (TSW V) were not detected during the survey.     

Localisation and movement of Plum pox virus in apricot stem tissues

Localisation and movement of Plum pox virus (PPV), sharka disease, in stem tissues of susceptible and resistant apricot (Prunus armeniaca L.) cultivars was studied. Two different assays were performed. In the first assay, apricot cultivars were grafted on to a non‐inoculated GF305 peach rootstock and, after two months, the sprouted apricot was inoculated by chip‐grafting. In the second assay, apricot cultivars were grafted on to a previously chip‐inoculated GF305 showing strong PPV symptoms. Localisation of virus was studied in apricot stem by immuno‐tissue printing and sharka symptoms in GF305 and apricot leaves were also observed. Virus was mainly localised in the xylem, and sometimes in the cortex and pith. Results revealed that, while all the cultivars allowed limited virus movement from the inoculation point, only the susceptible cultivars (Screara, Bebeco and Colomer) allowed long distance movement and even showed symptoms in leaves.     

Identification and Characterization of a Potyvirus Isolated from Siratro Plants

The present work describes the identification and characterization of a potyvirus isolated from siratro (Macroptilium atropurpureum Urb.) in the north‐west region of the State of São Paulo, Brazil. The virus was transmitted by mechanical inoculation. Its host range was restricted mainly to members of the Fabaceae. A cDNA fragment of about 930 bp was amplified by RT/PCR, cloned and sequenced. The fragment, which included the coat protein gene, had amino acid identity percentages between 88 and 98% with isolates of Bean common mosaic virus (BCMV). Phylogenetic analysis grouped the siratro potyvirus and BCMV isolates in 99% of the replicates, including Azuki mosaic virus, Dendrobium mosaic virus, Blackeye cowpea mosaic virus and Peanut stripe virus, which have been classified as BCMV strains. This is the first citation on the presence of BCMV in siratro plants in Brazil.     

Properties of spinach yellow mottle, a distinctive strain of tobacco rattle virus

A virus (isolate SYM) obtained from spinach plants in England with a severe yellow mottle disease induced symptoms resembling those of tobacco rattle virus (TRV) in several indicator species but caused systemic necrosis in Chenopodium amaranticolor and C. quinoa. It was transmitted to bait plants grown in soil containing the nematode Trichodorus primitivus. Purified virus preparations contained rod-shaped particles that were predominantly of four modal lengths: 188 nm (L particles), 101 nm (S particles), 57 nm and 48 nm (together called VS particles), containing RNA with mol. wts of 2.4, 1.5, 0.7 and 0.6 million, respectively. L particles (s°₂₀= 300 S) and S particles (230 S) greatly outnumbered VS particles (c. 150 S). All particles contained a single polypeptide species with estimated mol wt of 24 700, slightly larger than those previously reported for tobraviruses. Purified L particles were infective but both L and S particles were needed to induce the production of virus nucleoprotein particles. VS particles were not infective and apparently had no qualitative or quantitative effect on infection by L or by L plus S particles. S particles carried determinants for serological specificity and ability to invade C. amaranticolor systemically. Isolate SYM produced pseudo-recombinants with isolate PRN of TRV. Also, isolates CAM, OR and PRN of TRV, and isolate SYM, were found to be distantly related by three kinds of serological test. No relationship was detected between these isolates and pea early-browning virus in gel-diffusion precipitin tests or electron microscope serological tests, but a distant relationship between isolate SYM and pea early-browning virus was found by micro-precipitin tests. Isolate SYM therefore has closer affinities with TRV than with pea early-browning virus and is considered to be a distinctive strain of TRV.     

Further studies on a British form of pea early-browning virus

An isolate of pea early-browning virus from Britain (PEBV (B)) has tubular particles most of which are either about 103 or 212 mμ long with sedimentation coefficients of 210 and 286 S respectively. Both types show cross-banding at intervals of 2.5 mμ. Virus preparations containing only the shorter particles were not infective. PEBV (B) was transmitted to pea seedlings by both adult and juvenile Trichodorus primitivus (de Man) (Nematoda) and persisted for 32 days in T. primitivus kept without plants. In two experiments T. primitivus failed to transmit a Dutch isolate (PEBV (D)), which is distantly related serologically to PEBV (B). PEBV (B) was transmitted by nematodes to cucumber roots more readily in soil at 20d? than at 24d? C., and more readily at 24d? than at 29d? C. When transmitted by inoculation of sap, PEBV (B) and PEBV (D) caused similar symptoms in some pea varieties but differed in virulence towards others. Thirty-one varieties resistant to natural infection with PEBV in The Netherlands were susceptible to PEBV (B) when manually inoculated with sap or when grown in naturally infested soil from one site; twenty-six of these varieties did not become infected in soil from a second site, in which several other varieties that are susceptible in The Netherlands were infected. Varieties should therefore be tested for resistance by growing them on many infested fields. All but one of the pea varieties resistant to PEBV in The Netherlands became infected with the English form of tomato black ring virus when grown in soil containing infective Longidorus attenuatus Hooper.     

The leaky UGA termination codon of tobacco rattle virus RNA is suppressed by tobacco chloroplast and cytoplasmic tRNAs(Trp) with CmCA anticodon.

RNA-1 molecules from tobacco rattle virus (TRV) and pea early-browning virus (PEBV), two members of the tobravirus group, have recently been shown to contain internal, in-frame UGA termination codons which are suppressed in vitro. Our results suggest that a UGA stop codon also exists in RNA-1 of pepper ringspot virus (PRV), another tobravirus. UGA suppression may therefore be a universal feature of the expression of tobravirus genomes. We have isolated two natural suppressor tRNAs from uninfected tobacco plants on the basis of their ability to promote readthrough over the leaky UGA codon of TRV RNA-1 in a wheat germ extract depleted of endogenous mRNAs and tRNAs. Their amino acid acceptance and nucleotide sequences identify the two UGA-suppressor tRNAs as chloroplast (chl) and cytoplasmic (cyt) tryptophan-specific tRNAs with the anticodon CmCA. These are the first UGA suppressor tRNAs to be identified in plants. They have several interesting features. (i) Chl tRNA(Trp) suppresses the UGA stop codon more efficiently than cyt tRNA(Trp). (ii) Chl tRNA(Trp) contains an A24:U11 pair in the D-stem as does the mutated Escherichia coli UGA-suppressor tRNA(Trp) which is a more active suppressor than wild-type tRNA(Trp). (iii) The suppressor activity of chl tRNA(Trp) is dependent on the nucleotides surrounding the stop codon because it recognizes UGA in the TRV context but not the UGA in the beta-globin context.     

Age-related Resistance in Bell Pepper to Cucumber mosaic virus

We demonstrated the occurrence of mature plant resistance in Capsicum annuum‘Early Calwonder’ to Cucumber mosaic virus (CMV) under greenhouse conditions. When Early Calwonder plants were sown at 10 day intervals and transplanted to 10‐cm square pots, three distinct plant sizes were identified that were designated small, medium and large. Trials conducted during each season showed that CMV accumulated in inoculated leaves of all plants of each size category. All small plants (with the exception of the winter trial) developed a systemic infection that included accumulation of CMV in uninoculated leaves and severe systemic symptoms. Medium plants had a range of responses that included no systemic infection to detection of CMV in uninoculated leaves with the systemically infected plants being either symptomless or expressing only mild symptoms. None of the large plants contained detectable amounts of CMV in uninoculated leaves or developed symptoms. When plants were challenged by inoculation of leaves positioned at different locations along the stem or different numbers of leaves were inoculated, large plants continued to accumulate CMV in inoculated leaves but no systemic infection was observed. When systemic infection of large plants did occur, e.g. when CMV‐infected pepper was used as a source of inoculum, virus accumulation in uninoculated leaves was relatively low and plants remained symptomless. A time‐course study of CMV accumulation in inoculated leaves revealed no difference between small and large plants. Analyses to examine movement of CMV into the petiole of inoculated leaves and throughout the stem showed a range in the extent of infection. While all large plants contained CMV in inoculated leaves, some had no detectable amounts of virus beyond the leaf blade, whereas others contained virus throughout the length of the stem but with limited accumulation relative to controls.     

Ultrastructural Impact of Tobacco Rattle Virus on Tobacco and Pepper Ovary and Anther Tissues

The one‐third of plant viruses are seed transmitted, and this has significant economic consequences. Tobacco rattle virus (TRV), belonging to the genus Tobravirus and family Virgaviridae, has one of the widest host range of any known plant viruses. TRV infects vegetative organ and effects seed and pollen development that results in a decrease in crop yield. The mechanisms by which Tobravirus is transmissible to seeds are still poorly understood. The presence of the virus in pollen grains and inside ovaries is linked with seed transmission and can have effects on virus particles' transport during the pollination and fertilization process. This paper focuses on the significant impact of TRV on pepper and tobacco anthers and ultrastructure changes in ovaries. The presence of two types of TRV particles in ovary wall parenchyma and vascular tissues as well as in placenta cells was demonstrated via ultrastructural analysis. For the first time, the regular inclusion of virus particles was reported in both ovule integuments and nucellus parenchyma cells. Immunolocalization of TRV capsid proteins indicated the deposition of TRV CP epitope in ovary vascular bundles and in placenta cells. Moreover, the presence of virus particles was demonstrated inside pepper seeds in endothelium and integument parenchyma layers as well as on the embryo cell wall. Virus particles were found not only on the surface of pollen grains but also inside pepper pollen protoplasts in mature anthers. Also, this is the first time where TRV particles are reported in both differentiated endothecium cells and the remaining tapetum cells. Moreover, the detection of TRV capsid protein epitope in tobacco and pepper vascular anther tissues as well as in tapetum and endothecium cells was correlated with TRV distribution in infected anthers. Demonstrated analyses indicated that pollen grains and ovaries with ovules as well as could be a natural source of TRV transmission.     

Molecular characterisation of Onion yellow dwarf virus (OYDV) infecting garlic (Allium sativum L.) in Israel: Thermotherapy inhibits virus elimination by meristem tip culture

Garlic (cv. Shani) was tested using single step RT‐PCR and digoxygenin (DIG) labelled dot‐blot for a number of viruses. Following sequence analysis it was shown that at least three different polymorphs of the potyvirus Onion yellow dwarf virus (OYDV) infect the same plant simultaneously, together with the potyvirus Leek yellow stripe virus (LYSV), the carlavirus Garlic common latent virus (GCLV) and a multitude of allexiviruses (Shallot virus X (ShVX) related viruses]. Several garlic plants free of all the viruses tested were obtained through meristem‐tip culture. Plants infected with single viruses or with different combinations of viruses were similarly obtained. Meristem‐tip culture was confirmed as a satisfactory method of virus eradication, while thermotherapy treatment given to mother plantlets before meristem excision was found to specifically antagonise OYDV eradication. This work uses molecular methods for the first time to examine the effectiveness of meristem‐tip culture for the eradication of multiple viruses from garlic.