Genome-Wide Association Mapping of Barley Yellow Dwarf Virus Tolerance in Spring Oat (Avena sativa L.)

Barley yellow dwarf viruses (BYDVs) are responsible for the disease barley yellow dwarf (BYD) and affect many cereals including oat (Avena sativa L.). Until recently, the molecular marker technology in oat has not allowed for many marker-trait association studies to determine the genetic mechanisms for tolerance. A genome-wide association study (GWAS) was performed on 428 spring oat lines using a recently developed high-density oat single nucleotide polymorphism (SNP) array as well as a SNP-based consensus map. Marker-trait associations were performed using a Q-K mixed model approach to control for population structure and relatedness. Six significant SNP-trait associations representing two QTL were found on chromosomes 3C (Mrg17) and 18D (Mrg04). This is the first report of BYDV tolerance QTL on chromosome 3C (Mrg17) and 18D (Mrg04). Haplotypes using the two QTL were evaluated and distinct classes for tolerance were identified based on the number of favorable alleles. A large number of lines carrying both favorable alleles were observed in the panel.

Mild and severe cereal yellow dwarf viruses differ in silencing suppressor efficiency of the P0 protein

Viral pathogenicity has often been correlated to the expression of the viral encoded-RNA silencing suppressor protein (SSP). The silencing suppressor activity of the P0 protein encoded by cereal yellow dwarf virus-RPV (CYDV-RPV) and -RPS (CYDV-RPS), two poleroviruses differing in their symptomatology was investigated. CYDV-RPV displays milder symptoms in oat and wheat whereas CYDV-RPS is responsible for more severe disease. We showed that both P0 proteins (P0(CY-RPV) and P0(CY-RPS)) were able to suppress local RNA silencing induced by either sense or inverted repeat transgenes in an Agrobacterium tumefaciens-mediated expression assay in Nicotiana benthamiana. P0(CY-RPS) displayed slightly higher activity. Systemic spread of the silencing signal was not impaired. Analysis of short-interfering RNA (siRNA) abundance revealed that accumulation of primary siRNA was not affected, but secondary siRNA levels were reduced by both CYDV P0 proteins, suggesting that they act downstream of siRNA production. Correlated with this finding we showed that both P0 proteins partially destabilized ARGONAUTE1. Finally both P0(CY-RPV) and P0(CY-RPS) interacted in yeast cells with ASK2, a component of an E3-ubiquitin ligase, with distinct affinities.

Environmental nutrient supply alters prevalence and weakens competitive interactions among coinfecting viruses

The rates and ratios of environmental nutrient supplies can determine plant community composition. However, the effect of nutrient supplies on within-host microbial interactions is poorly understood. Resource competition is a promising theory for understanding microbial interactions, because microparasites require nitrogen (N) and phosphorus (P) for synthesis of macromolecules such as nucleic acids and proteins. To better understand the effects of nutrient supplies to hosts on pathogen interactions, we singly inoculated and coinoculated Avena sativa with two virus species, barley yellow dwarf virus-PAV (BYDV-PAV) and cereal yellow dwarf virus-RPV (CYDV-RPV). Host plants were grown across a factorial combination of N and P supply rates that created a gradient of N : P supply ratios, one being replicated at low and high nutrient supply. Nutrient supply affected prevalence and the interaction strength among viruses. P addition lowered CYDV-RPV prevalence. The two viruses had a distinct competitive hierarchy: the coinoculation of BYDV-PAV lowered CYDV-RPV infection rate, but the reverse was not true. This antagonistic interaction occurred at low nutrient supply rates and disappeared at high N supply rate. Given the global scale of human alterations of N and P cycles, these results suggest that elevated nutrient supply will increase risks of virus coinfection with likely effects on virus epidemiology, virulence and evolution.

Genomic and proteomic analysis of Schizaphis graminum reveals cyclophilin proteins are involved in the transmission of cereal yellow dwarf virus

Yellow dwarf viruses cause the most economically important virus diseases of cereal crops worldwide and are transmitted by aphid vectors. The identification of aphid genes and proteins mediating virus transmission is critical to develop agriculturally sustainable virus management practices and to understand viral strategies for circulative movement in all insect vectors. Two cyclophilin B proteins, S28 and S29, were identified previously in populations of Schizaphisgraminum that differed in their ability to transmit the RPV strain of Cereal yellow dwarf virus (CYDV-RPV). The presence of S29 was correlated with F2 genotypes that were efficient virus transmitters. The present study revealed the two proteins were isoforms, and a single amino acid change distinguished S28 and S29. The distribution of the two alleles was determined in 12 F2 genotypes segregating for CYDV-RPV transmission capacity and in 11 genetically independent, field-collected S. graminum biotypes. Transmission efficiency for CYDV-RPV was determined in all genotypes and biotypes. The S29 isoform was present in all genotypes or biotypes that efficiently transmit CYDV-RPV and more specifically in genotypes that efficiently transport virus across the hindgut. We confirmed a direct interaction between CYDV-RPV and both S28 and S29 using purified virus and bacterially expressed, his-tagged S28 and S29 proteins. Importantly, S29 failed to interact with a closely related virus that is transported across the aphid midgut. We tested for in vivo interactions using an aphid-virus co-immunoprecipitation strategy coupled with a bottom-up LC-MS/MS analysis using a Q Exactive mass spectrometer. This analysis enabled us to identify a third cyclophilin protein, cyclophilin A, interacting directly or in complex with purified CYDV-RPV. Taken together, these data provide evidence that both cyclophilin A and B interact with CYDV-RPV, and these interactions may be important but not sufficient to mediate virus transport from the hindgut lumen into the hemocoel.

Coat protein based molecular characterization of Barley yellow dwarf virus isolates identified on oat plants in Pakistan

Barley yellow dwarf virus (BYDV) is a potential threat to the agriculture production. The amplified complete coat protein sequences of the isolate M07 and M12 were determined to be 597 bp and 603bp, respectively. M07 showed maximum nucleotide sequence identity of 87.6% (84.3% amino acid sequence identity) to a Chinese isolate of BYDV-PAV. Whereas, the isolate M12 showed maximum nucleotide sequence identity of 94.5% (94.0% amino acid sequence identity) to French isolate BYDV-PAV. Since more than 10 o/o differences, among the amino acid level of any gene product, is the sole criterion to discriminate between species within the family Luteoviridae, the isolate M07 that shows maximum of 84.3% (less than 90%) amino acid sequence identity with previously known Luteovirus species, is thus, recommended to be a distinct PAV species within the genus Luteovirus.

Discovery and targeted LC-MS/MS of purified polerovirus reveals differences in the virus-host interactome associated with altered aphid transmission

Circulative transmission of viruses in the Luteoviridae, such as cereal yellow dwarf virus (CYDV), requires a series of precisely orchestrated interactions between virus, plant, and aphid proteins. Natural selection has favored these viruses to be retained in the phloem to facilitate acquisition and transmission by aphids. We show that treatment of infected oat tissue homogenate with sodium sulfite reduces transmission of the purified virus by aphids. Transmission electron microscopy data indicated no gross change in virion morphology due to treatments. However, treated virions were not acquired by aphids through the hindgut epithelial cells and were not transmitted when injected directly into the hemocoel. Analysis of virus preparations using nanoflow liquid chromatography coupled to tandem mass spectrometry revealed a number of host plant proteins co-purifying with viruses, some of which were lost following sodium sulfite treatment. Using targeted mass spectrometry, we show data suggesting that several of the virus-associated host plant proteins accumulated to higher levels in aphids that were fed on CYDV-infected plants compared to healthy plants. We propose two hypotheses to explain these observations, and these are not mutually exclusive: (a) that sodium sulfite treatment disrupts critical virion-host protein interactions required for aphid transmission, or (b) that host infection with CYDV modulates phloem protein expression in a way that is favorable for virus uptake by aphids. Importantly, the genes coding for the plant proteins associated with virus may be examined as targets in breeding cereal crops for new modes of virus resistance that disrupt phloem-virus or aphid-virus interactions.

Agrobacterium-mediated infection of whole plants by yellow dwarf viruses

Barley yellow dwarf virus-PAV (BYDV-PAV) and cereal yellow dwarf virus-RPV (CYDV-RPV) are only transmitted between host plants by aphid vectors and not by mechanical transmission. This presents a severe limitation for the use of a reverse genetics approach to analyze the effects of mutations in these viruses on plant infection and aphid transmission. Here we describe the use of agroinfection to infect plants with BYDV-PAV and CYDV-RPV. The cDNAs corresponding to the complete RNA genomes of BYDV-PAV and CYDV-RPV were cloned into a binary vector under the control of the cauliflower mosaic virus 35S promoter and the nopaline synthase transcription termination signal. The self-cleaving ribozyme from hepatitis virus D was included to produce a transcript in planta with a 3' terminus identical to the natural viral RNA. ELISA and RT-PCR analysis showed that the replicons of BYDV-PAV and CYDV-RPV introduced by Agrobacterium into Nicotiana benthamiana and N. clevelandii gave rise to a local infection in the infiltrated mesophyll cells. After several weeks systemic infection of phloem tissue was detected, although no systemic symptoms were observed. Three heterologous virus silencing suppressors increased the efficiency of agroinfection and accumulation of BYDV-PAV and CYDV-RPV in the two Nicotiana species. The progeny viruses purified from infiltrated tissues were successfully transmitted to oat plants by aphids, and typical yellow dwarf symptoms were observed. This study reports the first agroinfection of eudicot plants using BYDV-PAV and CYDV-RPV.

Modeling the competition between viruses in a complex plant-pathogen system

In this article, we propose a mathematical model that describes the competition between two plant virus strains (MAV and PAV) for both the host plant (oat) and their aphid vectors. We found that although PAV is transmitted by two aphids and MAV by only one, this fact, by itself, does not explain the complete replacement of MAV by PAV in New York State during the period from 1961 through 1976; an interpretation that is in agreement with the theories of A. G. Power. Also, although MAV wins the competition within aphids, we assumed that, in 1961, PAV mutated into a new variant such that this new variant was able to overcome MAV within the plants during a latent period. As shown below, this is sufficient to explain the swap of strains; that is, the dominant MAV was replaced by PAV, also in agreement with Power's expectations.

First infectious clone of the propagatively transmitted Oat blue dwarf virus

Oat blue dwarf virus (OBDV) is a small, phloem-limited marafivirus that replicates in its leafhopper vector. We have developed complete cDNA clones of OBDV from which infectious transcripts may be derived--the first such clones for any propagatively transmitted plant virus. Prior to clone construction, the reported sequences of the 5' and 3' ends were confirmed using 5' RACE, primer extension, and ligation-anchored PCR. Using vascular puncture of maize seeds with capped transcripts, multiple clones were shown to be infectious at an average rate of 24.3% (range 14-36%). Aster leafhoppers successfully transmitted OBDV to oats and barley after feeding on detached, infected maize leaves. Proteins and RNAs consistent in size with those expected in OBDV infection were detected in young leaves via western and northern blotting, respectively. One construct, pOBDV-2r, was designated as the reference clone. An infectious clone of OBDV will be valuable in examining the interaction of this virus with both its insect and plant hosts.

Expression of the barley yellow dwarf virus-GAV movement protein and its detection in the infected and transgenic plants

Movement proteins (MPs) that facilitate virus movement in the plants were identified in a number of plant viruses. In this study, full-length MP gene of the Chinese isolate Barley yellow dwarf virus-GAV (BYDV-GAV) was cloned and expressed in Escherichia coli. About 32% of the expressed MP was soluble providing the concentration of isopropyl-beta-D-galactopyranoside (IPTG), time of the induction, temperature and shaking speed were optimized. The soluble MP was purified using nickel-affinity column. Immune serum prepared against purified MP was used for the detection of MP in the BYDV-GAV infected leaves of oat and in the leaves of transgenic wheat plants expressing the full-length and truncated MP gene.

An attempt to identify recombinants between two sobemoviruses in doubly infected oat plants

Recombination in RNA viruses is considered to play a major role as a driving force in virus variability to counterbalance loss in fitness that can be due to the accumulation of detrimental mutations. Studies on mixed infections are pertinent for understanding the role of recombination in virus evolution. They also provide important baseline information for studying the biosafety of plants expressing viral sequences. To investigate the possibility of RNA recombination occurrence between two sobemoviruses under little or no selection pressure, we co-infected test plants with Cocksfoot mottle virus (CfMV) and Ryegrass mottle virus (RGMoV). CfMV and RGMoV were selected because of their overlapping host range and geographical distribution. First, symptom development of both viruses in barley (Hordeum vulgare) and oat (Avena sativa) was examined. Both viruses generated quite strong infection symptoms in oat, but synergism was not detected. RGMoV was lethal for barley, whereas CfMV infection in barley was nearly symptomless. RT-PCR analysis revealed 100% infection with both viruses in oat but not in barley. Therefore, an RNA recombination study of CfMV and RGMoV was performed in oat. 105 plants were co-inoculated with both viruses and putative recombinational hot spot regions were screened for recombination events by RT-PCR analysis at a sensitivity level down to 0.1-100 pg of viral genomic RNA. No recombination events between the two sobemoviruses were detected.

In vitro synthesis of minus-strand RNA by an isolated cereal yellow dwarf virus RNA-dependent RNA polymerase requires VPg and a stem-loop structure at the 3' end of the virus RNA

Cereal yellow dwarf virus (CYDV) RNA has a 5'-terminal genome-linked protein (VPg). We have expressed the VPg region of the CYDV genome in bacteria and used the purified protein (bVPg) to raise an antiserum which was able to detect free VPg in extracts of CYDV-infected oat plants. A template-dependent RNA-dependent RNA polymerase (RdRp) has been produced from a CYDV membrane-bound RNA polymerase by treatment with BAL 31 nuclease. The RdRp was template specific, being able to utilize templates from CYDV plus- and minus-strand RNAs but not those of three unrelated viruses, Red clover necrotic mosaic virus, Cucumber mosaic virus, and Tobacco mosaic virus. RNA synthesis catalyzed by the RdRp required a 3'-terminal GU sequence and the presence of bVPg. Additionally, synthesis of minus-strand RNA on a plus-strand RNA template required the presence of a putative stem-loop structure near the 3' terminus of CYDV RNA. The base-paired stem, a single-nucleotide (A) bulge in the stem, and the sequence of a tetraloop were all required for the template activity. Evidence was produced showing that minus-strand synthesis in vitro was initiated by priming by bVPg at the 3' end of the template. The data are consistent with a model in which the RdRp binds to the stem-loop structure which positions the active site to recognize the 3'-terminal GU sequence for initiation of RNA synthesis by the addition of an A residue to VPg.

Synthesis of genomic and subgenomic RNAs by a membrane-bound RNA-dependent RNA polymerase isolated from oat plants infected with cereal yellow dwarf virus

A membrane-bound RNA-dependent RNA polymerase (RdRp) complex was isolated by differential sedimentation from oat plants infected with cereal yellow dwarf virus (CYDV). When incubated with 32P-labelled UTP, unlabelled ATP, CTP and GTP, and Mg2+ ions, the RdRp preparation catalysed the synthesis of double-stranded (ds) RNAs corresponding in size to the virus genomic RNA (5.7 kbp) and two putative subgenomic RNAs (2.8 and 0.7 kbp). Hybridisation using strand-specific hybridization targets showed that the 5.7-kbp dsRNA was labelled mainly in the plus strand, whereas the 2.8- and 0.7-kbp dsRNAs were labelled only in the minus strand. Genomic-length single-stranded, plus-strand RNA of 5.7 kb and single-stranded, plus-strand subgenomic RNAs of 2.8 and 0.7 kbp were detected in RNA isolated from oat plants infected with CYDV. Mapping experiments were consistent with the genomic and subgenomic RNAs having common 3' ends, but different 5' ends, whether produced in vitro or in vivo. The RdRp-encoding region of the CYDV genome was cloned and expressed in Escherichia coli, and the purified protein was used to raise antibodies in a rabbit. In immunoblots, the antibodies detected a protein of about 68 kDa in RdRp preparations from CYDV-infected oat plants, but not from equivalent preparations from healthy oats. As far as we are aware, this is the first report of an in vitro RNA synthesis system for a phloem-limited virus.

P1 Protein of Cocksfoot Mottle Virus is Indispensable for the Systemic Spread of the Virus

Cocksfoot mottle sobemovirus (CfMV) encodes a non-conserved protein P1 from the 5' ORF1 of genomic RNA. The functions of CfMV P1 are unknown. In the current study we show that P1-deficient CfMV can replicate both in oat leaves and barley suspension culture cells but can not infect oat plants systemically. However, the absence of P1 reduces the efficiency of virus accumulation considerably. The infectivity of the mutant virus restores as a result of the spontaneous transversion. CfMV P1:EGFP shows a very limited cell-to-cell movement in leaf epidermal cells. In Sf9 insect cells CfMV P1 localizes in the fraction of membranes and inclusions but not in soluble cytoplasmic protein fraction.

Complete deletion of Wheat streak mosaic virus HC-Pro: a null mutant is viable for systemic infection

A Wheat streak mosaic virus (WSMV) genome lacking HC-Pro was constructed and confirmed by reverse transcription-PCR to systemically infect wheat, oat, and corn. Coupled in vitro transcription/translation reactions indicated that WSMV P1 proteinase cleaved the polyprotein at the P1/P3 junction of the HC-Pro null mutant. The WSMV HC-Pro null mutant was competent for virion formation, but the virus titer was reduced 4.5-fold relative to that of the wild type. Collectively, these results indicate that WSMV HC-Pro is dispensable for replication and movement, two essential processes that are disrupted by point and small-insertion mutations introduced into potyvirus HC-Pro.

Maize and oat antixenosis and antibiosis against Delphacodes kuscheli (Homoptera: Delphacidae), vector of "Mal de Rio Cuarto" of maize in Argentina

"Mal de Rio Cuarto" (MRC) is the most important virus disease of maize, Zea mays L., in Argentina. Several maize lines show different levels of resistance to MRC in the field; however, no studies have been conducted to investigate resistance mechanisms against its insect vector, Delphacodes kuscheli Fennah (Homoptera: Delphacidae). Oat, Avena spp., is the main overwintering host of D. kuscheli and main source of populations that infest maize. Although oat varieties resistant to the greenbug, Schizaphis graminum (Rondani) (Homoptera: Aphididae) are commercially available, their effect on D. kuscheli is unknown. We conducted laboratory experiments to test for the presence of antixenosis and antibiosis resistance mechanisms on six maize lines with different levels of field resistance to MRC, and seven commercial oat cultivars that include two S. graminum-resistant varieties. We did not find antibiotic effects of maize lines on D. kuscheli longevity and survivorship patterns, but we obtained antixenotic effects from the LP2 line (field moderate) due to reduced settling preference and feeding. Oat 'Bonaerense Payé and 'Suregrain INTA' showed both antixenosis and antibiosis, with significantly less settling preference, oviposition in the no-choice test, and reduced total fecundity in comparison with the other varieties studied. The S. graminum-resistant 'Boyera F. A.' and 'Tambera F. A.' did not showed a consistent pattern of resistance versus D. kuscheli across all experiments. Our results indicate the presence of potential sources of insect resistance in the maize lines and oat cultivars tested that may be used in MRC integrated pest management programs.

Subgenomic RNA as a riboregulator: negative regulation of RNA replication by Barley yellow dwarf virus subgenomic RNA 2

Barley yellow dwarf virus (BYDV) generates three 3'-coterminal subgenomic RNAs (sgRNAs) in infected cells. Translation of BYDV genomic RNA (gRNA) and sgRNA1 is mediated by the BYDV cap-independent translation element (BTE) in the 3' untranslated region. sgRNAs 2 and 3 are unlikely to be mRNAs. We proposed that accumulation of sgRNA2, which contains the BTE in its 5' UTR, regulates BYDV replication by trans-inhibiting translation of the viral polymerase from genomic RNA (gRNA). Here, we tested this hypothesis and found that: (i) co-inoculation of the BTE or sgRNA2 with BYDV RNA inhibits BYDV RNA accumulation in protoplasts; (ii) Brome mosaic virus (BMV), engineered to contain the BTE, trans-inhibits BYDV replication; and (iii) sgRNA2 generated during BYDV infection trans-inhibits both GFP expression from BMV RNA and translation of a non-viral reporter mRNA. We conclude that sgRNA2, via its BTE, functions as a riboregulator to inhibit translation of gRNA. This may make gRNA available as a replicase template and for encapsidation. Thus, BYDV sgRNA2 joins a growing list of trans-acting regulatory RNAs.

Cis and trans requirements for rolling circle replication of a satellite RNA

Satellite RNAs usurp the replication machinery of their helper viruses, even though they bear little or no sequence similarity to the helper virus RNA. In Cereal yellow dwarf polerovirus serotype RPV (CYDV-RPV), the 322-nucleotide satellite RNA (satRPV RNA) accumulates to high levels in the presence of the CYDV-RPV helper virus. Rolling circle replication generates multimeric satRPV RNAs that self-cleave via a double-hammerhead ribozyme structure. Alternative folding inhibits formation of a hammerhead in monomeric satRPV RNA. Here we determine helper virus requirements and the effects of mutations and deletions in satRPV RNA on its replication in oat cells. Using in vivo selection of a satRPV RNA pool randomized at specific bases, we found that disruption of the base pairing necessary to form the non-self-cleaving conformation reduced satRPV RNA accumulation. Unlike other satellite RNAs, both the plus and minus strands proved to be equally infectious. Accordingly, very similar essential replication structures were identified in each strand. A different region is required only for encapsidation. The CYDV-RPV RNA-dependent RNA polymerase (open reading frames 1 and 2), when expressed from the nonhelper Barley yellow dwarf luteovirus, was capable of replicating satRPV RNA. Thus, the helper virus's polymerase is the sole determinant of the ability of a virus to replicate a rolling circle satellite RNA. We present a framework for functional domains in satRPV RNA with three types of function: (i) conformational control elements comprising an RNA switch, (ii) self-functional elements (hammerhead ribozymes), and (iii) cis-acting elements that interact with viral proteins.

Evaluation of oat cultivars and lines under infection with barley yellow dwarf virus

Thirteen domestic and foreign oat cultivars and eight breeding lines bred from the University of Illinois were evaluated for resistance to barley yellow dwarf (BYD) using artificial inoculation with Rhopalosiphum padi viruliferous for an isolate of Barley yellow dwarf virus-PAV endemic to Moscow region origin. Cultivar Blaze and six Illinois lines showed the best grain yields under disease pressure that resembled a BYD epidemic.

Complete nucleotide sequence of Oat necrotic mottle virus: a distinct Tritimovirus species (family Potyviridae) most closely related to Wheat streak mosaic virus

The RNA genome (9346 nucleotides) of Oat necrotic mottle virus (ONMV) was cloned and sequenced. Complete genome comparisons indicated that ONMV, currently classified as a rymovirus, was most closely related ( approximately 73% nucleotide, approximately 79% amino acid identity) to the tritimovirus Wheat streak mosaic virus (WSMV). ONMV encoded a single polyprotein, with proteinase cleavage sites very similar to those of WSMV. Pairwise comparison of ONMV and WSMV cistrons revealed that P3 was most conserved ( approximately 79% nucleotide, approximately 86% amino acid), whereas HC-Pro was most divergent ( approximately 67% nucleotide, approximately 69% amino acid). In contrast, the ONMV sequence was distantly related ( approximately 40% nt, approximately 26% amino acid identity) to that of the rymoviru s Ryegrass mosaic virus, with highest sequence conservation noted within the NIb cistron ( approximately 47% nucleotide, approximately 41% amino acid identity). These results firmly establish that ONMV is not a rymovirus but is instead a distinct species of the genus Tritimovirus.

Apoptotic cell death is a common response to pathogen attack in oats

We have examined the characteristics of cell death induced by pathogen infection in oats with respect to following hallmark apoptotic features: DNA laddering, chromatin condensation, and electron microscopic-terminal deoxynucleotidyl transferase-mediated UTP end labeling positive response. A wide range of plant pathogens representing different levels of parasitism in susceptible and resistant interactions were used for the inocula, which include (i) an obligate parasite, Puccinia coronata f. sp. avenae (the crown rust fungus); (ii) a facultative biotroph parasite, Magnaporthe grisea (the blast fungus); (iii) pathogenic bacteria, Pseudomonas syringae pv. atropurpurea and P. syringae pv. coronafaciens (the halo or stripe blights of oats); and (iv) Ryegrass mottle virus. Surprisingly, any of the pathogens used induced most of the apoptotic features in oat cells at and around the infection sites, indicating that apoptotic cell death is a common phenomenon in oats during pathogen attack. The localization and the timing of apoptotic cell death during a course of infection were, however, quite different depending on the interactions (compatible or incompatible) and the pathogens (fungi, bacteria, or viruses). Possible roles of apoptotic cell death in the susceptible and resistant interactions are discussed.

Phylogenetic relationships, strain diversity and biogeography of tritimoviruses

North American and Eurasian isolates of Wheat streak mosaic virus (WSMV; genus Tritimovirus) and Oat necrotic mottle virus (ONMV; genus Rymovirus) were examined. Nine WSMV isolates differentially infected oat, barley, inbred maize line SDp2 and sorghum line KS56. The WSMV isolates clustered into groups based on phylogenetic analyses of the capsid protein (CP) cistron and flanking regions. WSMV isolates from the United States (US) and Turkey were closely related, suggesting recent movement between continents. Although more divergent, WSMV from Iran (WSMV-I) also shared a most recent common ancestor with the US and Turkish isolates. Another group of WSMV isolates from central Europe and Russia may represent a distinct Eurasian population. Complete genome sequences of WSMV from the Czech Republic (WSMV-CZ) and Turkey (WSMV-TK1) were determined and comparisons based on complete sequences yielded relationships similar to those based on partial sequences. ONMV-Pp recovered from blue grass (Poa pratensis L.) in Germany displayed the same narrow host range as ONMV-Type from Canada. Western blots revealed a heterologous relationship among CP of WSMV and ONMV. Phylogenetic analyses of the capsid protein cistron and flanking genomic regions indicated that WSMV and ONMV are related species sharing 74.2-76.2% (nucleotide) and 79.2-81.0% (amino acid) identity. Thus, ONMV should be removed from the genus Rymovirus and designated a definitive member of the genus Tritimovirus. Phylogenetic analyses further suggest that Sugarcane streak mosaic virus is not a tritimovirus, and may represent a new genus within the family Potyviridae.

The complete sequence of Oat mosaic virus and evidence for deletion and duplication in RNA2

The complete nucleotide sequence of a UK isolate of oat mosaic virus (OMV) was determined. RNA1 was 7550 nt long with one large open reading frame potentially encoding a polyprotein of 262.8 kDa with features typical of bymoviruses. RNA2 was 2284 nt in length, substantially smaller than those of other bymoviruses sequenced. It appeared that most of the P2 region had been deleted during repeated mechanical transmission of the isolate. The 3'-UTR of RNA2 was very long (> 1.25 kb) and proved to have a 532 nt slightly overlapping repeat. Phylogenetic analysis confirmed that OMV is an independent member of the genus Bymovirus.

The 3prime prime or minute-terminal structure required for replication of Barley yellow dwarf virus RNA contains an embedded 3prime prime or minute end

We determined the 3prime prime or minute-terminal primary and secondary structures required for replication of Barley yellow dwarf virus (BYDV) RNA in oat protoplasts. Computer predictions, nuclease probing, phylogenetic comparisons, and replication assays of specific mutants and chimeras revealed that the 3prime prime or minute-terminal 109 nucleotides (nt) form a structure with three to four stem-loops followed by a coaxially stacked helix incorporating the last four nt [(A/U)CCC]. Sequences upstream of the 109-nt region also contributed to RNA accumulation. The base-pairing but not the sequences or bulges in the stems were essential for replication, but any changes to the 3prime prime or minute-terminal helix destroyed replication. The two 3prime prime or minute-proximal tetraloops tolerated all changes, but the two 3prime prime or minute-distal tetraloops gave most efficient replication if they fit the GNRA consensus. A mutant lacking the 3prime prime or minute-proximal stem-loop produced elevated levels of less-than-full-length minus strands, and no (+) strand. We propose that a "pocket" structure is the origin of (minus sign)-strand synthesis, which is negatively regulated by the inaccessible conformation of the 3prime prime or minute terminus, thus favoring a high (+)/(minus sign) ratio. This 3prime prime or minute structure and the polymerase homologies suggest that genus Luteovirus is more closely related to the Tombusviridae family than to other Luteoviridae genera.

A sequence required for -1 ribosomal frameshifting located four kilobases downstream of the frameshift site

Programmed ribosomal frameshifting allows one mRNA to encode regulate expression of, multiple open reading frames (ORFs). The polymerase encoded by ORF 2 of Barley yellow dwarf virus (BYDV) is expressed via minus one (-1) frameshifting from the overlapping ORF 1. Previously, this appeared to be mediated by a 116 nt RNA sequence that contains canonical -1 frameshift signals including a shifty heptanucleotide followed by a highly structured region. However, unlike known -1 frameshift signals, the reporter system required the zero frame stop codon and did not require a consensus shifty site for expression of the -1 ORF. In contrast, full-length viral RNA required a functional shifty site for frameshifting in wheat germ extract, while the stop codon was not required. Increasing translation initiation efficiency by addition of a 5' cap on the naturally uncapped viral RNA, decreased the frameshift rate. Unlike any other known RNA, a region four kilobases downstream of the frameshift site was required for frameshifting. This included an essential 55 base tract followed by a 179 base tract that contributed to full frameshifting. The effects of most mutations on frameshifting correlated with the ability of viral RNA to replicate in oat protoplasts, indicating that the wheat germ extract accurately reflected control of BYDV RNA translation in the infected cell. However, the overall frameshift rate appeared to be higher in infected cells, based on immunodetection of viral proteins. These findings show that use of short recoding sequences out of context in reporter constructs may overlook distant signals. Most importantly, the remarkably long-distance interaction reported here suggests the presence of a novel structure that can facilitate ribosomal frameshifting.

A universal PCR primer to detect members of the Potyviridae and its use to examine the taxonomic status of several members of the family

A universal primer (Sprimer: 5'-GGX AAY AAY AGY GGX CAZ CC-3', X = A, G, C or T; Y = T or C; Z = A or G), designed from the consensus sequences that code for the conserved sequence GNNSGQP in the NIb region of members of the family Potyviridae, was used to amplify by RT-PCR the 3'-terminal genome regions from infected plant samples representing 21 different viruses in the family. Sequencing of some of the fragments (c. 1.7 kb) showed that the type strain (ATTC PV-107) of Oat necrotic mottle virus is not a distinct species in the genus Rymovirus, but is synonymous with Brome streak mosaic virus (genus Tritimovirus) and that Celery mosaic virus is a distinct member of the genus Potyvirus not closely related to any other sequenced species. Potyviruses infecting crops in China were also investigated, showing that viruses on cowpea and maize in Hangzhou, Zhejiang province were respectively Bean common mosaic virus and Sugarcane mosaic virus and that one on garlic in Nanjing, Jiangsu province was Onion yellow dwarf virus. Fragments were also sequenced from Chinese isolates of Lettuce mosaic virus and Soybean mosaic virus (from Hangzhou), Turnip mosaic virus (2 different isolates from Zhejiang province) and RNA1 of Wheat yellow mosaic virus (from Rongcheng, Shandong province).

Satellite cereal yellow dwarf virus-RPV (satRPV) RNA requires a douXble hammerhead for self-cleavage and an alternative structure for replication

The 110 nt hammerhead ribozyme in the satellite RNA of cereal yellow dwarf virus-RPV (satRPV RNA) folds into an alternative conformation that inhibits self-cleavage. This alternative structure comprises a pseudoknot with base-pairing between loop (L1) and a single-stranded bulge (L2a), which are located in hammerhead stems I and II, respectively. Mutations that disrupt this base-pairing, or otherwise cause the ribozyme to more closely resemble a canonical hammerhead, greatly increase self-cleavage. In a more natural multimeric sequence context containing the full-length satRPV RNA and two copies of the hammerhead, wild-type RNA cleaves much more efficiently than in the 110 nt context. Mutations in the upstream hammerhead, including a knock-out in the catalytic core, affect cleavage at the downstream cleavage site, indicating that multimers of satRPV RNA cleave via a double hammerhead. The double hammerhead includes base-pairing between two copies of the L1 sequence which extends stem I. Disruption of L1-L1 base-pairing slows cleavage of the multimer. L1-L2a base-pairing is required for efficient replication of satRPV RNA in oat protoplasts. Mutations that affect self-cleavage of the multimer do not correlate with replication efficiency, indicating that the ability to self-cleave is not a primary determinant of replication. We present a replication model in which multimeric satRPV RNA folds into alternative conformations that cannot form in the monomer. One potential metastable intermediate conformation involves L1-L2a base-pairing that may facilitate formation of the double hammerhead. However, we conclude that L1-L2a also performs some other essential function in the satRPV RNA replication cycle, because the L1-L2a base-pairing is more important than efficient self-cleavage for replication.

The sugarcane bacilliform badnavirus promoter is active in both monocots and dicots

Regions of the sugarcane bacilliform badnavirus genome were tested for promoter activity. The genomic region spanning nucleotides 5999-7420 was shown to possess promoter activity as exemplified by its ability to drive the expression of the coding region of the uidA gene of Escherichia coli, in both Avena sativa and Arabidopsis thaliana. In A. sativa, the promoter was active in all organs examined and, with the exception of the anthers where the expression was localized, this activity was constitutive. In A. thaliana, the promoter activity was constitutive in the rosette leaf, stem, stamen, and root and limited primarily to vascular tissue in the sepal and the silique. The transgene was inherited and active in progeny plants of both A. sativa and A. thaliana.

The characterization of a subgenomic RNA and in vitro translation products of oat chlorotic stunt virus

Oat chlorotic stunt virus (OCSV) is a 35 nm icosahedral plant virus comprising of a single capsid protein with a Mr of 48.2 kDa and a 4.1 kb single stranded, positive sense genomic RNA. Northern blot analysis detected a single 3' terminal subgenomic RNA in extracts from infected plants, which was also found to be encapsidated. Virion RNA directs the synthesis of a 23 kDa polypeptide in a rabbit reticulocyte in vitro translation system. Primer extension analysis has been used to map the end of both the genomic and subgenomic RNA's, and has shown the genomic size to be 4115 nucleotides in length. The results have enabled a model for the genome expression to be proposed.

Taxonomic characteristics of fijiviruses based on nucleotide sequences of the oat sterile dwarf virus genome

Sequence determination of full-length cDNA clones of genomic segments 7-10 (S7-S10) of oat sterile dwarf fijivirus (OSDV) revealed that the 5' and 3' ends of the plus strands of these segments had the same conserved terminal sequences, 5' AACGAAAAA and UUUUUUUAGUC 3'. These sequences are similar, but not identical, to the conserved terminal nucleotide sequences of the genomic segments of rice black streaked dwarf fijivirus (RBSDV) and maize rough dwarf fijivirus (MRDV). The coding strands of S7 and S10 each contained two large nonoverlapping open reading frames (ORFs), as do RBSDV S7 and S9, MRDV S6 and S8 and Nilaparvata lugens reovirus (NLRV; a putative member of Fijivirus) S9. These results strongly suggest that the dicistronic nature of certain genomic segments is characteristic of fijiviruses. Computer analyses revealed sequence homology between RBSDV S7 ORF2, MRDV S6 ORF2 and OSDV S7 ORF2, suggesting that this protein is conserved among plant fijiviruses. No counterparts were found in the genome of NLRV, which is a nonphytopathogenic insect reovirus. Furthermore, phylogenetic trees derived from multiple sequence alignments of each of the homologous proteins from OSDV, RBSDV, MRDV and NLRV suggest that NLRV did not evolve from either Fijivirus group 2 (RBSDV and MRDV) or group 3 (OSDV).

Oat blue dwarf marafivirus resembles the tymoviruses in sequence, genome organization, and expression strategy

The complete nucleotide sequence and genome organization of oat blue dwarf marafivirus (OBDV) were determined. The 6509 nucleotide RNA genome encodes a putative 227-kDa polyprotein (p227) with sequence motifs similar to the methyltransferase, papain-like protease, helicase, and polymerase motifs present in the nonstructural proteins of other positive strand RNA viruses. The 3' end of the open reading frame (ORF) that encodes p227 (ORF 227) also encodes the two capsid proteins: a 24-kDa capsid protein is presumably cleaved from the p227 polyprotein, whereas the 21-kDa capsid protein appears to be translated from a subgenomic RNA (sgRNA). Encoded amino acid and nucleotide sequence comparisons, as well as the OBDV genome expression strategy, show that OBDV closely resembles the tymoviruses. OBDV differs from the tymoviruses in its general biology, in its lack of a putative movement gene that overlaps the replication-associated genes, and in its fusion of the capsid gene sequences to the major ORF. OBDV also possesses a 3' poly(A) tail, as compared to the tRNA-like structures found in most tymoviral genomes. Due to the strong similarities in genome sequence and expression strategy, OBDV, and presumably the other marafiviruses, should be considered a member of the tymovirus lineage of the alpha-like plant viruses.

Sequence analysis of wheat and oat furovirus capsid protein genes suggests that oat golden stripe virus is a strain of soil-borne wheat mosaic virus

In northern blots, cDNA probes prepared to soil-borne wheat mosaic virus (SBWMV) RNA-1 and RNA-2 hybridized to RNA-1 and RNA-2, respectively, from a UK isolate of oat golden stripe virus (OGSV), as well as to their homologous RNAs. RT-PCR was used to amplify, clone and sequence a region of about 750 nucleotides spanning the capsid protein gene and part of the readthrough protein on RNA-2 from OGSV, a French isolate of SBWMV and two stable deletion mutants (Lab1 and Okl-7) of SBWMV isolates from Nebraska and Oklahoma respectively. There was very high (96.7-99.1%) nucleotide homology between all these sequences and the wild-type SBWMV sequences from Nebraska and Oklahoma. OGSV was more similar to SBWMV from France and Nebraska than were any of the isolates to SBWMV from Oklahoma. Of the few differences in the deduced amino acid sequences of the capsid proteins from the different isolates, OGSV differed from all SBWMV isolates only in one amino acid (isoleucine for valine at position 88). The high degree of similarity suggests that OGSV may best be classified as an oat strain of SBWMV.

A single nucleotide substitution in the alpha a gene confers oat pathogenicity to barley stripe mosaic virus strain ND18

A 236-nucleotide region from the alpha a gene of strain CV42 (pathogenic to oat), when substituted for the homologous region in strain ND18 (nonpathogenic to oat), was shown previously to confer a near wild-type oat pathogenicity to this strain (Weiland and Edwards, 1994, Virology 201: 116-126). The data suggested that six amino acid substitutions in the alpha a gene were responsible for the differences in oat pathogenicity, and that threonine-724, encoded by CV42, might be a critical amino acid in determining pathogenicity of barley stripe mosaic virus (BSMV) to oat. In the present work, codons specifying T-724, I-764, and N-785 (encoded by CV42 RNA alpha) were substituted individually and in combination for those coding for P-724, T-764, and K-785 (encoded by ND18 RNA alpha), respectively, by site-directed mutagenesis. The core K-733, T-734, and K-736 positions (CV42) were substituted for Q-733, S-734, and Q-736 (ND18) as a single block. The results of inoculations with these mutants indicate that the C2261-->A2261 nucleotide substitution (P-724-->T-724) by itself is sufficient to enable strain ND18 to infect oat plants, although poorly. Additional substitution of CV42 codons into ND18 RNA alpha at the remaining five positions altered symptom type, decreased the timing of the appearance of symptoms, and increased the percentage of plants infected per inoculation. Nonetheless, all mutants accumulated to similar levels in inoculated oat protoplasts after a 24-h period. Using a recombinant RNA beta from which beta-glucuronidase could be expressed, results were obtained suggesting that the multiplication of strain ND18 and the nonpathogenic variants generated in the study was restricted in the inoculated leaf. The data indicate a potential pathway by which pathogenicity to oat evolved in BSMV.

The nucleotide sequence and proposed genome organization of oat chlorotic stunt virus, a new soil-borne virus of cereals

The complete genomic sequence of a new virus, first found infecting oats in Wales, UK, has been determined. The genome is a positive-sense ssRNA molecule, 4114 nucleotides in length, examination of which indicates the presence of four ORFs. The first ORF initiating at the 5' terminus (ORF1) encodes a protein with a predicted M(r) of 23476 (p23). ORF2 extends through the amber termination codon of ORF1 to give a protein with a predicted M(r) of 84355 (p84). The readthrough domain of p84 contains amino acid sequence similarities with a number of putative RNA-dependent RNA polymerases. ORF3 is in a different reading frame from ORF1/2 and encodes a protein with an M(r) of 48231 (p48), identified as the coat protein by direct peptide sequencing. ORF4 nests within ORF3 but is in a different frame from it and codes for a protein with a predicted M(r) of 8220 (p8). Comparisons of peptide sequence, particularly within the putative polymerase region and within the S domain of the coat protein, highlight similarities with members of both the tombusvirus and carmovirus groups. The coat protein region shows most similarity with members of the tombusvirus group, whilst the size and predicted strategy of the genome seem to be intermediate between that of the carmovirus and tombusvirus groups. These features highlight possible evolutionary links with each group whilst being distinct from both. We propose the name of oat chlorotic stunt for this new virus.