Biology and molecular biology of furoviruses

Coat protein of Chinese wheat mosaic virus upregulates and interacts with cytosolic glyceraldehyde-3-phosphate dehydrogenase, a negative regulator of plant autophagy, to promote virus infection

Autophagy is an intracellular degradation mechanism involved in antiviral defense, but the strategies employed by plant viruses to counteract autophagy-related defense remain unknown for the majority of the viruses. Herein, we describe how the Chinese wheat mosaic virus (CWMV, genus Furovirus) interferes with autophagy and enhances its infection in Nicotiana benthamiana. Yeast two-hybrid screening and in vivo/in vitro assays revealed that the 19 kDa coat protein (CP19K) of CWMV interacts with cytosolic glyceraldehyde-3-phosphate dehydrogenases (GAPCs), negative regulators of autophagy, which bind autophagy-related protein 3 (ATG3), a key factor in autophagy. CP19K also directly interacts with ATG3, possibly leading to the formation of a CP19K-GAPC-ATG3 complex. CP19K-GAPC interaction appeared to intensify CP19K-ATG3 binding. Moreover, CP19K expression upregulated GAPC gene transcripts and reduced autophagic activities. Accordingly, the silencing of GAPC genes in transgenic N. benthamiana reduced CWMV accumulation, whereas CP19K overexpression enhanced it. Overall, our results suggest that CWMV CP19K interferes with autophagy through the promotion and utilization of the GAPC role as a negative regulator of autophagy.

Root-specific role for Nicotiana benthamiana RDR6 in the inhibition of Chinese wheat mosaic virus accumulation at higher temperatures

Some viruses only infect plants at cool temperatures but the molecular mechanism underlying this low-temperature dependence remains unclear. Chinese wheat mosaic virus (CWMV, genus Furovirus) was able to infect wheat and Nicotiana benthamiana plants at 16 but not at 24°C. When CWMV-infected plants were transferred to 24°C for 2 weeks, the newly emerged leaves and roots became virus free. Co-infection with Potato virus Y rescued CWMV accumulation in N. benthamiana plants after a temperature shift to 24°C. In transgenic N. benthamiana plants silenced for the N. benthamiana RNA-dependent RNA polymerase 6 (NbRDR6), CWMV was able to accumulate in roots but not in leaves after a temperature shift to 24°C. Deep sequencing of small RNAs showed that, at 16°C, abundant CWMV small interfering (si)RNAs accumulated in infected N. benthamiana plants. Silencing of NbRDR6 increased the abundance of CWMV siRNAs and the generation of siRNAs from hotspots in the CWMV genome. In contrast, when shifted to 24°C for 1 week, CWMV siRNAs were markedly fewer in roots of NbRDR6-silenced than in roots of wild-type plants but were similar in the leaves of those plants. Our results demonstrate the root-specific role of NbRDR6 in the inhibition of CWMV accumulation and biogenesis of CWMV siRNAs at higher temperatures.

Progress towards the understanding and control of sugar beet rhizomania disease

Rhizomania is a soil-borne disease that occurs throughout the major sugar beet growing regions of the world, causing severe yield losses in the absence of effective control measures. It is caused by Beet necrotic yellow vein virus (BNYVV), which is transmitted by the obligate root-infecting parasite Polymyxa betae. BNYVV has a multipartite RNA genome with all natural isolates containing four RNA species, although some isolates have a fifth RNA. The larger RNA1 and RNA2 contain the housekeeping genes of the virus and are always required for infection, whereas the smaller RNAs are involved in pathogenicity and vector transmission. RNA5-containing isolates are restricted to Asia and some parts of Europe, and these isolates tend to be more aggressive. With no acceptable pesticides available to restrict the vector, the control of rhizomania is now achieved almost exclusively through the use of resistant cultivars. A single dominant resistance gene, Rz1, has been used to manage the disease worldwide in recent years, although this gene confers only partial resistance. More recently, new variants of BNYVV have evolved (both with and without RNA5) that are able to cause significant yield penalties on resistant cultivars. These isolates are not yet widespread, but their appearance has resulted in accelerated searches for new sources of resistance to both the virus and the vector. Combined virus and vector resistance, achieved either by conventional or transgenic breeding, offers the sugar beet industry a new approach in its continuing struggle against rhizomania.

The optimal temperature for RNA replication in cells infected by Soil-borne wheat mosaic virus is 17 degrees C

Systemic infection of wheat plants with Soil-borne wheat mosaic virus (SBWMV) requires temperatures below 20 degrees C. Here we examine the cause of the temperature sensitivity by inoculating infectious in vitro transcripts of SBWMV RNA1 and RNA2 to barley mesophyll protoplasts. After RNA inoculation, protoplasts were incubated at temperatures between 15 and 25 degrees C for up to 48 h. Western blot analysis showed that the capsid protein accumulated most abundantly at 17 degrees C but was not detectable at 25 degrees C. Northern blot analysis showed that the wild-type RNA1 and RNA2 and their subgenomic RNAs accumulated most abundantly at 17 degrees C but were barely detectable at 25 degrees C. An RNA1 mutant in which the p152 and p211 replicase genes were placed between the 5'- and 3'-untranslated regions also replicated most efficiently at 17 degrees C but not at 25 degrees C. Thus, the requirement for temperatures lower than 20 degrees C for SBWMV infection is primarily determined by replication of RNA1, which encodes the viral RNA replicase.

Ecology and epidemiology of benyviruses and plasmodiophorid vectors

Beet necrotic yellow vein virus (BNYVV) and Beet soilborne mosaic virus (BSBMV) are members of the genus Benyvirus, and Burdock mottle virus (BdMV) is a tentative member. BNYVV and BSBMV are vectored by the plasmodiophorid Polymyxa betae, which has a worldwide distribution. Polymyxa betae is morphologically indistinguishable from P. graminis, but recent molecular studies support separation of the two species. The geographic distribution of BNYVV is also worldwide, but BSBMV has been identified only in the United States. In Europe and Japan, several genotypic strains of BNYVV have been identified, and those with a fifth RNA appear to be more aggressive. No thorough survey of genotypic variability of BNYVV or BSBMV has been conducted in the United States. However, both viruses are widespread and frequently found in the same field, infecting the same beet plant. The implications of this close proximity, with regard to disease incidence and severity, and for recombination, are uncertain. Recent technological advances that permit improved detection and quantification of these viruses and their vector offer tremendous research opportunities.

Similarity and divergence among viruses in the genus Furovirus

Nucleotide sequences of RNAs 1 and 2 of a Japanese strain of soil-borne wheat mosaic virus (SBWMV), the type species of the genus Furovirus, and sorghum chlorotic spot virus (SCSV) were determined from cloned cDNA. The relationship among the Japanese and US strains of SBWMV, SCSV, oat golden stripe virus (OGSV), and recently proposed Chinese wheat mosaic and European wheat mosaic viruses (CWMV and EWMV) were examined at the nucleotide and amino acid levels. Pairwise comparisons of genome-encoded proteins among the six viruses showed that the US strains of SBWMV and CWMV were the most closely related pair in RNA 1 and the Japanese strains of SBWMV and EWMV were most closely related in RNA 2. SCSV was most distantly related to the other five viruses. Phylogenetic analysis indicated that there may have been an ancient reassortment between RNAs 1 and 2 of the four wheat-infecting viruses and OGSV, while SCSV was shown to have separated from the rest before the other five viruses diverged. The fact that CWMV and EWMV have almost identical biological properties as well as the sequence similarities to the two strains of SBWMV suggests that they be regarded as strains of SBWMV, considering that SBWMV consists of genetically diverged strains. OGSV and SCSV are distinct in biological properties in addition to genetic divergence in the genus Furovirus.

Transfer RNA mimicry in a new group of positive-strand RNA plant viruses, the furoviruses: differential aminoacylation between the RNA components of one genome

Recent sequencing of the genomes of several furoviruses--fungus-transmitted rod-shaped positive-strand plant viruses--has suggested the presence of tRNA-like structures (TLSs) at the 3' ends of the genomic RNAs. We show here that the genomic RNAs of soil-borne wheat mosaic virus (SBWMV), beet soil-borne virus (BSBV), potato mop-top virus (PMTV), peanut clump virus (PCV), and Indian peanut clump virus (IPCV) all possess functional TLSs that are capable of high-efficiency valylation. While the SBWMV, BSBV, and PMTV TLSs are similar to those found in tymoviruses, the PCV and IPCV TLSs harbor an insertion of about 40 nucleotides between the two halves of the TLS. The valylated SBWMV and BSBV RNAs formed tight complexes with wheat germ EF-1 alpha.GTP (Kd = 2 to 11 nM), whereas valylated PMTV, PCV, and IPCV RNAs bound EF-1 alpha.GTP weakly (Kd > or = 50 nM). The TLS of PCV RNA2 differs from PCV RNA1 in lacking the major valine identity nucleotide in the anticodon and consequently is capable of only very inefficient valylation. This is the first case of differential aminoacylation between the RNA components of one genome.

The nucleotide sequence of RNA-1 of Indian peanut clump furovius

The nucleotide sequence of RNA-1 of an isolate of the H serotype of Indian peanut clump virus (IPCV-H) was shown to comprise 5,841 nucleotides. The RNA contains three open reading frames (ORF) which are between nucleotides 133 and 3,522, nucleotides 3,526 and 5,103 (assuming expression by suppression of the ORF 1 termination codon) and nucleotides 5,168 and 5,539. The encoded polypeptides have M(r), of 129,687 (p130), 60,188 (p60) and 14,281 (p14). ORF 2 is thought to be expressed by suppression of the termination codon of ORF 1 to produce a M(r) 189,975 product (p190). p130 contains sequences characteristic of proteins with methyl transferase and NTP-binding properties and p190 contains these and sequences characteristic of RNA-dependent RNA polymerases. The nucleotide sequence of IPCV RNA-1 is similar to that of peanut clump virus (PCV) and corresponding encoded polypeptides are 88% (p130), 95% p60 and 75% (p14) identical. The sequences of the translation products are also similar to those of soil-borne wheat mosaic virus and barley stripe mosaic virus. Oligonucleotide primers, designed on the basis of the sequences of RNA-1 of IPCV and PCV, were effective in reverse transcription-PCR amplification of these RNAs and that of IPCV isolates of the serologically distinct L and T serotypes.

Characteristics of Beet Soilborne Mosaic Virus, a Furo-like Virus Infecting Sugar Beet

Beet soilborne mosaic virus (BSBMV) is a rigid rod-shaped virus transmitted by Polymyxa betae. Particles were 19 nm wide and ranged from 50 to over 400 nm, but no consistent modal lengths could be determined. Nucleic acids extracted from virions were polyadenylated and typically separated into three or four discrete bands of variable size by agarose-formaldehyde gel electrophoresis. RNA 1 and 2, the largest of the RNAs, consistently averaged 6.7 and 4.6 kb, respectively. The sizes and number of smaller RNA species were variable. The molecular mass of the capsid protein of BSBMV was estimated to be 22.5 kDa. In Northern blots, probes specific to the 3' end of individual beet necrotic yellow vein virus (BNYVV) RNAs 1-4 hybridized strongly with the corresponding BNYVV RNA species and weakly with BSBMV RNAs 1, 2, and 4. Probes specific to the 5' end of BNYVV RNAs 1-4 hybridized with BNYVV but not with BSBMV. No cross-reaction between BNYVV and BSBMV was detected in Western blots. In greenhouse studies, root weights of BSBMV-infected plants were significantly lower than mock-inoculated controls but greater than root weights from plants infected with BNYVV. Results of serological, hybridization, and virulence experiments indicate that BSBMV is distinct from BNYVV. However, host range, capsid size, and the number, size, and polyadenylation of its RNAs indicate that BSBMV more closely resembles BNYVV than it does other members of the genus Furovirus.

The coat protein of Indian peanut clump virus: relationships with other furoviruses and with barley stripe mosaic virus

The 5'-most open reading frame of the c.4kb RNA-2 of Indian peanut clump furovirus (IPCV) encodes a protein of 208 amino acids. This protein is thought to be the coat protein of IPCV because its amino acid composition and M(r) closely resemble those reported for IPCV coat protein and because its amino acid sequence is 61% identical to that of the coat protein of peanut clump virus (PCV) from West Africa. The extent of the sequence identity between IPCV and PCV coat proteins confirms previous conclusions that the viruses are distinct rather than strains of one virus. The sequences of the coat proteins of IPCV and PCV were between 18% and 26% identical to those of other furoviruses and those of unrelated tobamoviruses and tobraviruses. In contrast, the coat protein sequences were 37% (IPCV) and 36% (PCV) identical to that of the coat protein of barley stripe mosaic hordeivirus (BSMV). This similarity between the coat proteins of viruses from different groups (= genera) is unusual but is consistent with previous reports of sequence relatedness in various genes between certain furoviruses and BSMV.

In vitro mutagenesis of biologically active transcripts of beet necrotic yellow vein virus RNA 2: evidence that a domain of the 75-kDa readthrough protein is important for efficient virus assembly

RNA 2 of the multipartite genome of beet necrotic yellow vein virus carries the cistron for 21-kDa viral coat protein at its 5' extremity. The amber termination codon of the coat protein cistron undergoes suppression approximately 10% of the time so that translation continues into an adjacent 54-kDa open reading frame, yielding a 75-kDa readthrough protein. The roles of coat protein and the readthrough protein in infection were investigated with biologically active transcripts of RNA 2. Much of the coat protein cistron of the RNA 2 transcript could be deleted without interfering with viral replication and local lesion formation on leaves, although formation of the rod-shaped virions did not occur. Mutants in which the amber coat protein termination codon was replaced with an ochre codon or a tyrosine codon were also viable. The ochre codon was suppressed both in vitro and in planta. The mutant containing the tyrosine substitution produced only the 75-kDa read-through protein and was deficient in viral assembly. Deletions in the 54-kDa readthrough domain were also viable in planta but had different effects on virus assembly. A deletion in the C-terminal portion of the readthrough domain did not interfere with RNA packaging but, unexpectedly, deletions in the N-terminal portion were assembly deficient, although 21-kDa coat protein was produced in planta. Thus, the 75-kDa protein can apparently intervene in virion assembly even though it has not been detected in purified virions.

Viruses and viruslike particles of eukaryotic algae

Until recently there was little interest or information on viruses and viruslike particles of eukaryotic algae. However, this situation is changing. In the past decade many large double-stranded DNA-containing viruses that infect two culturable, unicellular, eukaryotic green algae have been discovered. These viruses can be produced in large quantities, assayed by plaque formation, and analyzed by standard bacteriophage techniques. The viruses are structurally similar to animal iridoviruses, their genomes are similar to but larger (greater than 300 kbp) than that of poxviruses, and their infection process resembles that of bacteriophages. Some of the viruses have DNAs with low levels of methylated bases, whereas others have DNAs with high concentrations of 5-methylcytosine and N6-methyladenine. Virus-encoded DNA methyltransferases are associated with the methylation and are accompanied by virus-encoded DNA site-specific (restriction) endonucleases. Some of these enzymes have sequence specificities identical to those of known bacterial enzymes, and others have previously unrecognized specificities. A separate rod-shaped RNA-containing algal virus has structural and nucleotide sequence affinities to higher plant viruses. Quite recently, viruses have been associated with rapid changes in marine algal populations. In the next decade we envision the discovery of new algal viruses, clarification of their role in various ecosystems, discovery of commercially useful genes in these viruses, and exploitation of algal virus genetic elements in plant and algal biotechnology.

cDNAs of beet necrotic yellow vein virus RNAs 3 and 4 are rendered biologically active in a plasmid containing the cauliflower mosaic virus 35S promoter

cDNAs of beet necrotic yellow vein virus RNAs 3 and 4 could be rendered biologically active when they were placed under the control of the cauliflower mosaic virus 35S promoter and polyadenylation signal. Although the 35S in vivo transcripts should have contained up to forty 5' and several hundred 3' nonviral nucleotides, the progeny viral RNAs had the same sizes as in naturally infected sugarbeets. The progeny RNAs did not hybridize with the nonviral sequences indicating that they were apparently not replicated. Deletion and insertion mutants of RNA 3 cDNA clones were also biologically active in plants but a plasmid which contained the cDNA of RNA 3 in antisense orientation was not. The biological activity of plasmid DNAs compared with the corresponding synthetic transcripts is discussed.

Multiplication of beet necrotic yellow vein virus RNA 3 lacking a 3' poly(A) tail is accompanied by reappearance of the poly(A) tail and a novel short U-rich tract preceding it

Beet necrotic yellow vein virus RNAs 1 and 2 but not RNAs 3 and 4 are required for viral multiplication in Chenopodium quinoa leaves. Elimination of the 3' poly(A) tail from RNA 3 transcripts markedly attenuated their ability to be amplified when co-inoculated with RNAs 1 and 2 to this host. Successful multiplication of the tailless RNA 3 was accompanied by the reappearance of new 3' poly(A) tails on the progeny. The evidence suggests that the newly acquired poly(A) sequence results from the action of a poly(A) polymerase rather than recombination with the homologous 3' terminal domains of RNAs 1 or 2. An unexpected feature of these progeny RNA 3 molecules was the presence of a novel short heterogenous U-rich tract separating the poly(A) tail from the 3' end of the heteropolymeric RNA 3 sequence proper.

Mapping sequences required for productive replication of beet necrotic yellow vein virus RNA 3

Of the four genome components of beet necrotic yellow vein virus only RNAs 1 and 2 are essential for viral replication in leaves. We have mapped cis-regulatory elements on RNA 3 by introducing deletions into expressible cDNA clones and inoculating leaves with the altered transcripts along with RNAs 1 and 2. Transcripts carrying internal deletions extending to within 69 residues of the 3' poly(A) tail or to within about 300 residues of the 5' terminus were efficiently amplified and encapsidated in vivo. The 3' terminal cis-essential domain can be folded into a secondary structure which is conserved among all four genomic RNAs and which probably contains the minus-strand promoter. RNA 3 transcripts with 75% of the central core of the sequence deleted or replaced by the beta-glucuronidase (GUS) gene were also viable. GUS activity was detected in infected tissue in the latter case.