RNA recombination in animal and plant viruses.

An increasing number of animal and plant viruses have been shown to undergo RNA-RNA recombination, which is defined as the exchange of genetic information between nonsegmented RNAs. Only some of these viruses have been shown to undergo recombination in experimental infection of tissue culture, animals, and plants. However, a survey of viral RNA structure and sequences suggests that many RNA viruses were derived form homologous or nonhomologous recombination between viruses or between viruses and cellular genes during natural viral evolution. The high frequency and widespread nature of RNA recombination indicate that this phenomenon plays a more significant role in the biology of RNA viruses than was previously recognized. Three types of RNA recombination are defined: homologous recombination; aberrant homologous recombination, which results in sequence duplication, insertion, or deletion during recombination; and nonhomologous (illegitimate) recombination, which does not involve sequence homology. RNA recombination has been shown to occur by a copy choice mechanism in some viruses. A model for this recombination mechanism is presented.     

Variability and evolution of the plant RNA virus pepper mild mottle virus

The RNA genomes of 26 isolates of pepper mild mottle virus were compared by their RNase T1 fingerprints. Twenty-three isolates came from epidemic outbreaks in greenhouse-grown peppers in Almería (southeastern Spain) from 1983 to 1987; three other isolates, from 1980, came from Sicily (Italy) and Zaragoza (central Spain). The 26 fingerprints can be classified into 10 different types; nucleotide substitution rates show them to be very similar. Cluster and cladistic analyses group types corresponding to the Almería isolates separate from those of 1980. Intraannual and interannual nucleotide differences were estimated. An evolutionary model for pepper mild mottle virus built on these data indicates a highly stable population, maintaining its diversity through time, with a main prevailing haplotype from which closely related variants arise that do not replace it. This high stability could be due to strong functional constraints on variation, as suggested by the high proportion of invariant versus polymorphic sites in fingerprints.     

Resistance in rice to Rice yellow mottle virus and evidence of non-seed transmission

Nine rice cultivars were evaluated under screenhouse conditions for resistance to Rice yellow mottle virus (RYMV) and possible seed transmission. Completely randomised design with three replications was used. In Experiment 1, the seedlings were inoculated with the virus at two weeks after planting. In Experiment 2, the seeds collected from Experiment 1 were dried for four weeks before planting. For each genotype, the seeds from healthy plants were planted as a control. Disease incidence and severity (scales 1–9), yield and yield components were recorded. Statistical analyses included Area Under the Disease Progress Curve (AUDPC) and independent t test. The cultivars FARO 37, FARO 52 and Gigante were highly resistant, whereas WAB189-B38HB was resistant. Paddy yield was highest (3.6 g) in FARO 37. There were no symptoms of virus disease in all the plants originating from the seeds of RYMV-infected plants. The differences between the seeds from infected and healthy plants for all the measured traits were not significant (p > 0.05). The number of days to seedling emergence was uniform (5.5 days) in all the cultivars. Plant height, number of tillers per plant, number of days to heading and paddy yield from the seeds of virus-infected plants varied from 54.8 to 68.4 cm, 17 to 21, 85.3 to 96 days and 2.7 to 4 g, respectively. Conversely, a range of 54.9–68.7 cm, 17–22, 83–95 days and 2.8–4.1 g was found in the seeds of healthy plants. Selection and cultivation of high-yielding, resistant and healthy seeds would enhance food security.     

Internal point mutations of the capsid modify the serotype of Rice yellow mottle virus

Rice yellow mottle virus is classified in five major serotypes; the molecular diversity of the coat protein (CP) is well established, but the amino acids involved in the recognition by discriminant monoclonal antibodies (MAbs) remain unknown. Reconstruction of a phylogenetic tree and sequence alignment of the CP gene of a sample representative of the continental-large diversity were used to identify 10 serospecific amino acids (i.e., conserved in all isolates belonging to the same serotype and distinct in other serotypes). Positions occupied by serospecific residues were localized on the crystal structure of the CP monomer and on modeled capsomers. Structural, molecular, and serological properties of each serotype were analyzed, and subsequently, hypotheses on the potential role of amino acids in discriminating reactions with antibodies were formulated. The residues 114 and 115 (serospecific of Sr1) and 190 (serospecific of Sr2) were localized on the outer surface of the capsid and might be directly involved in the immunoreactivity with MAb D and MAb A, respectively. In contrast, residues 180 (Sr3) and 178 (Sr5) lay within the inner surface of the capsid. To understand the role of these internal positions in the recognition with the antibodies, two substitutions (T180K and G178D) were introduced in the CP of an infectious clone. These mutations modified the antigenicity with MAb G and MAb E discriminating Sr3 and Sr5, respectively, while the reaction with MAb D remained unaffected. This result suggests an indirect effect of these two internal mutations on local immunostructure while the global structure was maintained.     

Diversity of Rice yellow mottle virus in Benin and Togo and Screening for Resistant Accessions

Surveys were conducted in rice fields in Benin, Cote d'Ivoire, Mali, Nigeria, Togo and Niger to assess the importance of Rice yellow mottle virus (RYMV). Diseased leaf samples were collected. In Togo, surveys were made mainly in the southern part of the country, and in Benin, all areas where rice is grown were covered. Leaf samples were serologically confirmed by ACP ELISA as bearing RYMV, propagated and all conserved. One hundred and forty‐eight (148) Beninese and 27 Togolese strains were serotyped. They were also phenotyped on three susceptible accessions including IR 64, four resistant lines with known alleles on RYMV 1 gene namely TOG 5681 (rymv 1‐3), TOG 5672 (rymv 1‐4 and RYMV 2), TOG 5674 (rymv 1.5) and Gigante (rymv 1‐2). RYMV spots with 9–100% incidences were identified. Serotyping by triple antibody sandwich (TAS) ELISA indicated that two main groups S1 and S2 coexisted in Benin with S1 being prevalent. In Togo, 26 strains were S1 and only one was S2. Phenotyping of the 148 Beninese and 27 Togolese indicated that they all attacked the three susceptible accessions, while TOG 5681 (rymv 1‐3), TOG 5672 (rymv 1‐4 and RYMV 2), TOG 5674 (rymv 1‐5) and Gigante (rymv 1‐2) remained symptomless. The use of the genes/alleles above in these countries against the disease is discussed. Three representative Beninese strains were selected to screen 48 accessions for disease resistance. Nine accessions were as susceptible as IR 64 to all strains while six (NERICA 9, NERICA 12, NERICA 13, TOG 7291, WAB56‐50, CG 14 and Moroberekan) were very resistant. Susceptibility of the six ARICA and resistance of some NERICA lines could be explained by the fact that one or both parental lines were, respectively, susceptible or resistant to the strains.     

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.     

Diversification of rice yellow mottle virus and related viruses spans the history of agriculture from the neolithic to the present

The mechanisms of evolution of plant viruses are being unraveled, yet the timescale of their evolution remains an enigma. To address this critical issue, the divergence time of plant viruses at the intra- and inter-specific levels was assessed. The time of the most recent common ancestor (TMRCA) of Rice yellow mottle virus (RYMV; genus Sobemovirus) was calculated by a Bayesian coalescent analysis of the coat protein sequences of 253 isolates collected between 1966 and 2006 from all over Africa. It is inferred that RYMV diversified approximately 200 years ago in Africa, i.e., centuries after rice was domesticated or introduced, and decades before epidemics were reported. The divergence time of sobemoviruses and viruses of related genera was subsequently assessed using the age of RYMV under a relaxed molecular clock for calibration. The divergence time between sobemoviruses and related viruses was estimated to be approximately 9,000 years, that between sobemoviruses and poleroviruses approximately 5,000 years, and that among sobemoviruses approximately 3,000 years. The TMRCA of closely related pairs of sobemoviruses, poleroviruses, and luteoviruses was approximately 500 years, which is a measure of the time associated with plant virus speciation. It is concluded that the diversification of RYMV and related viruses has spanned the history of agriculture, from the Neolithic age to the present.     

Identification of a second major resistance gene to Rice yellow mottle virus, RYMV2, in the African cultivated rice species, O. glaberrima

Rice yellow mottle virus (RYMV) is the most damaging rice-infecting virus in Africa. However, few sources of high resistance and only a single major resistance gene, RYMV1, are known to date. We screened a large representative collection of African cultivated rice (Oryza glaberrima) for RYMV resistance. Whereas high resistance is known to be very rare in Asian cultivated rice (Oryza sativa), we identified 29 (8%) highly resistant accessions in O. glaberrima. The MIF4G domain of RYMV1 was sequenced in these accessions. Some accessions possessed the rymv1-3 or rymv1-4 recessive resistance alleles previously described in O. glaberrima Tog5681 and Tog5672, respectively, and a new allele, rymv1-5, was identified, thereby increasing the number of resistance alleles in O. glaberrima to three. In contrast, only a single allele has been reported in O. sativa. Markers specific to the different alleles of the RYMV1 gene were developed for marker-assisted selection of resistant genotypes for disease management. In addition, the presence of the dominant susceptibility allele (Rymv1-1) in 15 resistant accessions suggests that their resistance is under different genetic control. An allelism test involving one of those accessions revealed a second major resistance gene, i.e., RYMV2. The diversity of resistance genes against RYMV in O. glaberrima species is discussed in relation to the diversification of the virus in Africa.     

Inferring the evolutionary history of rice yellow mottle virus from genomic, phylogenetic, and phylogeographic studies

Fourteen isolates of Rice yellow mottle virus (RYMV) were selected as representative of the genetic variability of the virus in Africa from a total set of 320 isolates serologically typed or partially sequenced. The 14 isolates were fully sequenced and analyzed together with two previously reported sequences. RYMV had a genomic organization similar to that of Cocksfoot mottle sobemovirus. The average nucleotide diversity among the 16 isolates of RYMV was 7%, and the maximum diversity between any two isolates was 10%. A strong conservative selection was apparent on both synonymous and nonsynonymous substitutions, through the amino acid replacement pattern, on the genome size, and through the limited number of indel events. Furthermore, there was a lack of positive selection on single amino acid sites and no evidence of recombination events. RYMV diversity had a pronounced and characteristic geographic structure. The branching order of the clades correlated with the geographic origin of the isolates along an east-to-west transect across Africa, and there was a marked decrease in nucleotide diversity moving westward across the continent. The insertion-deletion polymorphism was related to virus phylogeny. There was a partial phylogenetic incongruence between the coat protein gene and the rest of the genome. Overall, our results support the hypothesis that RYMV originated in East Africa and then dispersed and differentiated gradually from the east to the west of the continent.     

Identification of an RNA silencing suppressor from a plant double-stranded RNA virus

RNA silencing is a mechanism which higher plants and animals have evolved to defend against viral infection in addition to regulation of gene expression for growth and development. As a counterdefense, many plant and some animal viruses studied to date encode RNA silencing suppressors (RSS) that interfere with various steps of the silencing pathway. In this study, we report the first identification of an RSS from a plant double-stranded RNA (dsRNA) virus. Pns10, encoded by S10 of Rice dwarf phytoreovirus (RDV), exhibited RSS activity in coinfiltration assays with the reporter green fluorescent protein (GFP) in transgenic Nicotiana benthamiana line 16c carrying GFP. The other gene segments of the RDV genome did not have such a function. Pns10 suppressed local and systemic silencing induced by sense RNA but did not interfere with local and systemic silencing induced by dsRNA. Expression of Pns10 also increased the expression of beta-glucuronidase in transient assays and enhanced Potato virus X pathogenicity in N. benthamiana. Collectively, our results establish Pns10 as an RSS encoded by a plant dsRNA virus and further suggest that Pns10 targets an upstream step of dsRNA formation in the RNA silencing pathway.     

Examples of expression systems based on animal RNA viruses: alphaviruses and influenza virus.

Successful recovery of RNA viruses and functional RNA replicons from cDNA has greatly facilitated molecular genetic analyses of viral proteins and cis-regulatory elements. This technology allows the use of RNA virus replication machinery to express heterologous sequences. Both positive-strand and negative-strand animal RNA viruses have been engineered to produce chimeric viruses expressing protective epitopes from other pathogens and for transient expression of heterologous sequences.     

An encapsidated,subgenomic messenger RNA encodes the coat protein of carnation mottle virus

The translation strategy of carnation mottle virus (CarMV) in vitro has been generally assumed to involve internal initiation events on full-length, genomic RNA (4.3 kb). We suggest that this is, at least in part, incorrect. Encapsidated RNA, fractionated on denaturing sucrose gradients, or total RNA from CarMV-infected leaves, fractionated under non-denaturing conditions, was translated in an mRNA-dependent rabbit reticulocyte cell-free system. Evidence for subgenomic RNAs which encode a polypeptide of M_r 38 000 was found. This product was shown to be related to authentic CarMV coat protein by partial proteolysis with -chymotrypsin and SDS/polyacrylamide-gel electrophoresis.     

Isolation of an asymmetric RNA uncoating intermediate for a single-stranded RNA plant virus

We have determined the three-dimensional structures of both native and expanded forms of turnip crinkle virus (TCV), using cryo-electron microscopy, which allows direct visualization of the encapsidated single-stranded RNA and coat protein (CP) N-terminal regions not seen in the high-resolution X-ray structure of the virion. The expanded form, which is a putative disassembly intermediate during infection, arises from a separation of the capsid-forming domains of the CP subunits. Capsid expansion leads to the formation of pores that could allow exit of the viral RNA. A subset of the CP N-terminal regions becomes proteolytically accessible in the expanded form, although the RNA remains inaccessible to nuclease. Sedimentation velocity assays suggest that the expanded state is metastable and that expansion is not fully reversible. Proteolytically cleaved CP subunits dissociate from the capsid, presumably leading to increased electrostatic repulsion within the viral RNA. Consistent with this idea, electron microscopy images show that proteolysis introduces asymmetry into the TCV capsid and allows initial extrusion of the genome from a defined site. The apparent formation of polysomes in wheat germ extracts suggests that subsequent uncoating is linked to translation. The implication is that the viral RNA and its capsid play multiple roles during primary infections, consistent with ribosome-mediated genome uncoating to avoid host antiviral activity.     

Mutations in the eIF(iso)4G translation initiation factor confer high resistance of rice to Rice yellow mottle virus

We report here evidence of the role that the isoform of the eukaryotic translation initiation factor 4G (eIF(iso)4G) plays in naturally occurring resistance in plant/virus interactions. A genetic and physical mapping approach was developed to isolate the Rymv1 locus controlling the high recessive resistance to Rice yellow mottle virus (RYMV) in the rice (Oryza sativa) variety Gigante. The locus was mapped to a 160-kb interval containing a gene from the eIF(iso)4G family. The stable transformation of a resistant line with the cDNA of this gene, derived from a susceptible variety, resulted in the loss of resistance in transgenic plants. The allelic variability of this gene was analysed in three resistant and 17 susceptible varieties from different cultivated rice species or subspecies. Compared with susceptible varieties, resistant varieties present specific alleles, characterized by either amino acid substitutions or short amino-acid deletions in the middle domain of the protein. The structure of this domain was modelled and showed that the substitutions were clustered on a small surface patch. This suggests that this domain may be involved in an interaction with the virus.