Point mutations in helper component protease of clover yellow vein virus are associated with the attenuation of RNA-silencing suppression activity and symptom expression in broad bean

Helper component protease (HC-Pro) is a potyvirus-encoded multifunctional protein and a major determinant of symptom expression in a susceptible plant. Here, we show the involvement of clover yellow vein virus (ClYVV) HC-Pro in necrotic symptom expression in broad bean (Vicia faba cv. Wase). In this host, lethal necrosis was induced by ClYVV no. 30, from which a spontaneous, mosaic-inducing mutant (MM) was obtained. Mapping with chimeric viruses between ClYVV no. 30 and MM attributed the symptom attenuation to two mutations at the HC-Pro positions 27 (threonine to isoleucine) and 193 (aspartic acid to tyrosine). Although neither mutant with the single amino acid substitution at position 27 or 193 (ClYVV/T27I or D193Y) induced the lethal necrosis, ClYVV/T27I still retained the ability to induce necrotic symptoms, but ClYVV/D193Y scarcely did so. The virus accumulation of ClYVV/D193Y was also lower than that of ClYVV no. 30. The mutations, T27I and D193Y, are located in a putative zinc finger domain and in one (N-terminal) of the two RNA binding domains, respectively, of HC-Pro. RNA-silencing suppression (RSS) activity of P1/HC-Pro in Nicotiana benthamiana was weakened by both mutations. Our results suggest a correlation between viral virulence and RSS function and the importance of the two domains in HC-Pro.

3C-like protease encoded by Rice tungro spherical virus is autocatalytically processed

The 3C-protease of Rice tungro spherical virus (RTSV) was previously identified as a cis- and trans-acting protease. In vitro translation of the protease resulted in several protein products, demonstrating that the protease is cleaved by itself. The protease was then produced in Escherichia coli as a fusion protein with maltose-binding protein (MBP). Two forms of the protease were purified after MBP affinity chromatography in the column buffer. After analyses of the purified proteins, we speculated that a major internal cleavage site was in the C-terminal half. A point mutation was introduced at a potential major self-cleavage site (C(2763)). The mutation abolished the catalytic activity, suggesting that the mutation site is important for the recognition of the protease.

Adaptation of Cucumber mosaic virus soybean strains (SSVs) to cultivated and wild soybeans

Cucumber mosaic virus soybean strains formerly called soybean stunt virus (SSV) were inoculated onto 23 wild soybeans collected from four Asian countries to investigate their infectivity in order to improve understanding of the co-evolution of SSVs and soybean. SSV inoculation resulted in systemic infection in most of the wild soybeans used. However, an SSV strain (SSV-In), which was isolated in Indonesia, did not result in systemic infection of many of the wild soybeans distributed in southern Japan. This exceptional infectivity of SSV-In may be due to its specific adaptation to the local soybean population(s) of Indonesia, which has rarely been affected by gene flows from wild soybean. In the present study, the nucleotide sequences of the 3a and CP genes of SSV were determined, and the data were used to classify seven SSV isolates among known Cucumber mosaic virus (CMV) strains. The phylogenetic analysis showed that the seven SSVs formed a distinct cluster separated from the other CMV strains despite their different geographical origins; SSV-In was the most divergent of the seven isolates. Comparison of the rates of synonymous and nonsynonymous substitutions revealed that the SSV group had evolved faster than subgroup IA. The implications of the findings are discussed in relation to the so-called Red Queen hypothesis.

The 3' terminal region is strictly required for clover yellow vein virus genome replication

To identify the cis-element in the 3' terminal region of infectious cDNA required for replication of clover yellow vein virus (ClYVV), a series of mutants with duplications or deletions of the 3' terminal non-coding region (3'-NCR) of the genome that did not affect the ORFs in the genome was constructed. These were tested for infectivity, and the 3' terminal regions of their progeny RNAs were sequenced. Deletion mutants that lacked portions of the 3'-NCR were not infectious. Various mutants with duplicated 3' terminal sequences were infective only when the authentic 3' terminal sequence was restored, probably by recombination, and none of the constructs retained the original sequence in progeny viral RNA. When a coat protein gene sequence of bean yellow mosaic virus (BYMV) followed by a termination codon was introduced between the nuclear inclusion b and coat protein genes, infective progeny were generated. Sequence analyses of the progeny viruses showed that the coat protein gene was a chimera of the BYMV N-terminal and CIYVV C-terminal portions. These results suggest that the 3'-NCR of ClYVV contains cis-acting elements and is strictly required for genome replication.

Molecular characterization of Hop mosaic virus: its serological and molecular relationships to Hop latent virus

The 3'-terminal sequence of hop mosaic virus (HpMV) genomic RNA was determined. A cDNA of approximately 1.8 kbp was amplified from the HpMV genome by 3' RACE using a degenerate primer, which was designed to anneal to the overlapping region of open reading frames (ORFs) 2 and 3 of eight carlavirus genomes. The sequence contained three ORFs, encoding proteins of 7-, 34-, and 11-kDa, which corresponded to ORFs 4, 5, and 6 of the carlavirus genome, respectively. The amino acid sequence of ORF 5, encoding the coat protein (CP) of HpMV, shows the highest identity (67%) to that of Hop latent virus (HpLV). The HpMV CP N-terminal sequence differs from that of HpLV, but the central and C-terminal sequences of the CP of both viruses are similar. The sequence similarity possibly causes the cross-reaction of heterologous antibodies of HpMV and HpLV. Phylogenetic analyses based on the CP amino acid and 3' non-coding region sequences indicate close relationships among HpMV, HpLV, and Potato virus M. We report here the first molecular characterization of HpMV genomic RNA.

Molecular characterization of Hop latent virus and phylogenetic relationships among viruses closely related to carlaviruses

The complete nucleotide sequence of the hop latent virus (HpLV) genome was determined. The viral RNA genome is 8,612 nucleotides long, excluding the poly(A) tail, and contains six open reading frames (ORFs), which encode putative proteins of 224-kDa (ORF 1), 25-kDa (ORF 2), 11-kDa (ORF 3), 7-kDa (ORF 4), 34-kDa (ORF 5), and 12-kDa (ORF 6). ORF 5 encodes the coat protein as demonstrated by N-terminal sequencing of three proteolytic peptides derived from the virus particle. The genome organization of HpLV is similar to that of other species in the genus Carlavirus, and the overall sequence of HpLV is more similar to that of Potato virus M than to sequences of other carlaviruses reported to date. The amino acid sequences of the putative methyltransferase, RNA helicase, and RNA-dependent RNA polymerase encoded in ORF 1 and an 'accessory' helicase encoded in ORF 2 of the HpLV genome were compared with those of viruses in the 'tymo' lineage: the genera Carlavirus, Potexvirus, Allexivirus, Foveavirus, Trichovirus, Capillovirus, Vitivirus, and Tymovirus. The phylogenetic relationships among the viruses in these genera are discussed. This is the first molecular characterization of a carlavirus infecting hop plants.

Development of clover yellow vein virus as an efficient, stable gene-expression system for legume species

A highly infectious cDNA clone of clover yellow vein virus (pClYVV) was tested as a viral vector, especially for legume species. The genes for green fluorescent protein (GFP) and soybean glutamine synthetase (GS) were inserted between the genes for P1 and HC-Pro on pClYVV to create three recombinant plasmids: pClYVV-GFP, pClYVV-GFP-GS, and pClYVV-GFP:GS. In the former two constructs all the junctions between the inserted proteins contained the sequences of protease cleavage recognition sites, whereas the third construct expressed a fusion of GFP and GS. Western blot analyses showed that GFP and GS appeared to have been precisely excised from the viral polyprotein with the viral proteases (P1 and NIa). Under UV irradiation, green fluorescence was detected in infected broad bean, kidney bean, and soybean plants. The stability of the constructs in the symptomatic tissues was confirmed by RT-PCR and Western blot analyses. The plants expressing GS together with GFP became tolerant to the herbicide glufosinate, and flowered early. As the GS gene, one of the nodulin genes for nitrogen fixation, is expressed in legume species, this system will be useful for examining the function of genes important to legume plants.

Complete nucleotide sequence of the rice tungro spherical virus genome of the highly virulent strain Vt6

The complete nucleotide sequence of rice tungro spherical virus (RTSV) strain Vt6, originally from Mindanao, the Philippines, with higher virulence to resistant rice cultivars, was determined and compared with the published sequence for the Philippine-type strain A (RTSV-A-Shen). It was reported that RTSV-A was not able to infect a rice resistant cultivar TKM 6 (10). RTSV-Vt6 and RTSV-A-Shen share 90% and 95% homology at nucleotide and amino-acid levels, respectively. The N-terminal leader sequence of RTSV-Vt6 contained a 39-amino acids-region (positions 65 to 103) which was totally different from that of RTSV-A-Shen; the difference resulted from frame shifting by nucleotide insertions and deletions. To confirm the amino-acid sequence differences of the leader polypeptide, the same region was cloned and sequenced using a newly obtained variant of RTSV-type 6, which had been collected in the field of IRRI, and seven field isolates from Mindanao, the Philippines. Since all the sequences of the target region are identical to that of the Vt6 leader polypeptide, the sequence difference in the leader region seems not to correlate with the virulence of Vt6.

Restoration of the 3' end of potyvirus RNA derived from Poly(A)-deficient infectious cDNA clones

Poly(A)-deficient full-length cDNA clones of clover yellow vein virus (ClYVV), a member of the genus Potyvirus, were found to be infectious when expressed from the CaMV 35S promoter. The poly(A) tail was replaced with different short sequences and the infectivities of the cDNA constructs were examined. Although the infectivity of the plasmid varied depending on the sequences introduced, all the constructs were infectious. In all cases, progeny viral RNAs from the cDNA clones had an authentic viral sequence at their 3' regions with poly(A) tails and the downstream nonviral sequences were completely lost. However, two minor mutations, a two-nucleotide deletion at the 3' end and a single-nucleotide addition at the second nucleotide position downstream of the poly(A) site, were also observed. The clones of the viral (-) strand RNAs had poly(U) tracts at their 5' ends, suggesting that their synthesis is primed by the poly(U) sequence. It furthermore suggests that the mutations were introduced during or after primary transcription from the cDNA and were maintained during authentic viral replication. Although the mechanism involved is not known, recovery of the poly(A) tail is an essential step for maintaining the infectivity of the viral cDNAs.

The C-terminal region of the P3 structural protein of rice dwarf phytoreovirus is important for P3-P3 interaction

Using a random peptide library designed for the yeast two-hybrid system, we identified a peptide that binds strongly to the P3 structural protein of rice dwarf phytoreovirus (RDV). The amino acid sequence of the peptide showed a high homology to the C-terminal region of P3. C-terminally truncated P3 lost its ability to interact with authentic P3. Our observations suggest that the C-terminal region of P3 is important for the P3-P3 interaction, which forms the core shell structure of RDV.

A simple, rapid method of nucleic acid extraction without tissue homogenization for detecting viroids by hybridization and RT-PCR

A simple, rapid method of nucleic acid extraction on a microcentrifuge tube scale for detecting viroids is presented. Five distinct citrus viroids (CVds), chrysanthemum stunt viroid (CSVd), hop stunt viroid (HSVd), hop latent viroid (HLVd) and potato spindle tuber viroid (PSTVd) were detected in their natural host plants by hybridization using cRNA probes and reverse transcription-polymerase chain reaction (RT-PCR). Nucleic acids (NA) were liberated from tissues by incubation in a buffer containing potassium ethyl xanthogenate (PEX) without tissue homogenization, and then precipitated with ethanol (NA-PEX). All the viroids except CVd-IV could be detected clearly in NA-PEX by hybridization. HSVd, HLVd and PSTVd could also be detected in NA-PEX by RT-PCR. Although CVds and CSVd could not be detected in NA-PEX by RT-PCR, they were detected after further purification: differential precipitation with 2-butoxyethanol and HCl treatment followed by ethanol-precipitation. In addition, PCR in the presence of tetramethylammonium chloride specifically amplified the cDNA of all five distinct CVds under the same temperature and cycle conditions. Since all the viroids could be detected in NA liberated by PEX, the amount of NA extracted by the method described here is sufficient for detecting viroids, enabling the processing of a large number of samples.

Evolution of a quadripartite hybrid virus by interspecific exchange and recombination between replicase components of two related tripartite RNA viruses

Cucumber mosaic virus (CMV) and tomato aspermy virus (TAV) belong to the Cucumovirus genus. They have a tripartite genome consisting of single-stranded RNAs, designated 1, 2, and 3. Previous studies have shown that viable pseudorecombinants could be created in vitro by reciprocal exchanges between CMV and TAV RNA 3, but exchanges of RNAs 1 and 2 were replication deficient. When we coinoculated CMV RNAs 2 and 3 along with TAV RNAs 1 and 2 onto Nicotiana benthamiana, a hybrid quadripartite virus appeared that consisted of TAV RNA 1, CMV RNAs 2 and 3, and a distinctive chimeric RNA originating from a recombination between CMV RNA 2 and the 3'-terminal 320 nucleotides of TAV RNA 2. This hybrid arose by means of segment reassortment and RNA recombination to produce an interspecific hybrid with the TAV helicase subunit and the CMV polymerase subunit. To our knowledge, this is the first report demonstrating the evolution of a new plant or animal virus strain containing an interspecific hybrid replicase complex.

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).

Detection and assignment of proteins encoded by rice black streaked dwarf fijivirus S7, S8, S9 and S10

The proteins encoded by rice black streaked dwarf fijivirus (RBSDV) genomic segments 7-10 (S7-S10) were characterized. Open reading frames (ORFs) from these segments were expressed as fusion proteins in Escherichia coli. Antibodies raised against the expressed products were used as probes to determine whether the viral ORFs encode structural proteins. In Western blots, antibodies to the expressed S8 and S10 products reacted with a core capsid (65 kDa) and a major outer capsid (56 kDa) protein, respectively, while none of the antibodies to S7 and S9 products reacted with structural proteins. Antisera to RBSDV S7 ORF1 and S9 ORF1 each detected a single protein of the predicted size in total protein extracts from infected rice plants and viruliferous Laodelphax striatellus. Immunoelectron microscopy revealed that antibodies to RBSDV S7 ORF1 and RBSDV S9 ORF1 reacted with tubular structures and viroplasm, respectively, in sections of both infected maize plants and viruliferous L. striatellus. Antisera to ORF2 of S7 and S9 failed to detect any proteins in the infected tissue using either Western blotting or immuno-electron microscopic techniques.

Direct formation of human interleukin-11 by cis-acting system of plant virus protease in Escherichia coli

To produce a large amount of recombinant proteins in Escherichia coli, we constructed a unique cis-acting expression system using a plant virus protease. This new expression system could directly produce recombinant proteins, that had a biologically active form. A gene of nuclear inclusion-a (NIa), which had a specific amino acid sequence, was fused with a foreign protein gene at the same protein reading frame. One of the NIa-specific cleavage amino acid sequences, Gln-Ala, was also contained at the protein-protein junction. In the case of human interleukin-11 (hIL-11), a 23-kDa specific signal band was obtained from recombinant bacteria. N-terminal sequencing of the 23-kDa protein showed that NIa specifically cleaved the fusion protein at Gln-Ala, producing Ala-hIL-11. Furthermore, we could produce the mature rhIL-11 by extending the culture time. This 23-kDa protein had the same biological activity as hIL-11 in a mouse plasmacytoma, T1165. Combined with fermentation control, we produced mature rhIL-11 in E. coli.

Inosine 5'-triphosphate can dramatically increase the yield of NASBA products targeting GC-rich and intramolecular base-paired viroid RNA

Nucleic acid sequence-based amplification (NASBA) according to the standard protocol failed to amplify cRNA of viroids, probably because of their GC-rich and intramolecular base-paired structure. However, NASBA in the presence of inosine 5'-triphosphate successfully amplified the cRNAs to viroids in total nucleic acid extracts from citrus plants. As sequence specificity of the cRNA to viroids was confirmed by northern analysis, the amplification and fidelity of cRNAs are sufficient for the sensitive and specific detection of viroids.

Hypothesis on particle structure and assembly of rice dwarf phytoreovirus: interactions among multiple structural proteins

To study the morphogenesis and packaging of rice dwarf phytoreovirus (RDV), the interactions among multiple structural proteins were analysed using both the yeast two-hybrid system and far-Western blotting analysis. The following protein-protein interactions were observed. P3 (major core protein) bound to itself as well as to P7 (nucleic acid-binding protein) and P8 (major outer capsid protein). P7 bound to P1 (RNA-dependent RNA polymerase) and P8, in addition to P3. Based on these findings, we hypothesize that the core shell structure is based on P3-P3 interactions and that P7 has the ability to bind to multiple structural proteins as well as to genomic RNAs during viral particle assembly. Based on the observed protein-protein interactions and on computer-aided analysis of the numbers of structural proteins per particle, possible RDV assembly events are proposed.

A cDNA clone to clover yellow vein potyvirus genome is highly infectious

We obtained a highly infectious cDNA clone of clover yellow vein virus (CIYVV). The cDNA fragments, from which a full-length cDNA clone was constructed, were sequenced, and the complete nucleotide sequence of C1YVV RNA was determined. The viral genome is 9584 nucleotides (nt) in length excluding the poly(A) tail and contains one open reading frame (ORF) encoding a large polyprotein of 3072 amino acids. The non-coding region preceding the ORF is 190 nt long. The termination codon is followed by a 175-nt sequence. Seven potential protease NIa, one HC-pro and one P1 protease recognition sites were found in the C1YVV polyprotein by searching for cleavage consensus sequences among the potyvirus group. The cleavage dipeptides of C1YVV NIa protease are Q(E)/S(A,G). The F is conserved at the -2 position from the cleavage site except for at the P3/6K1 junction, and the V conserved at the -4 position among many potyviruses is not present at all. The genome organization of C1YVV was determined, and the amino acid sequence was compared with that of other potyviruses. The full-length cDNA clone of C1YVV was constructed by combining cDNA fragments and placed it under the control of the cauliflower mosaic virus 35S promoter. The full-length cDNA was constructed so that no extra nucleotide was present at the transcription initiation site and only 10 adenine residues were present at the 3' end of the C1YVV cDNA clone. Mechanical inoculation of a circular-formed plasmid DNA onto broad bean seedlings led to systemic infection, and the symptoms were similar to those caused by the wild-type virus but rather mild. Plasmid diluted as low as 500 pg/microl was able to induce symptoms, demonstrating that this full-length C1YVV cDNA is more infectious than any other infectious cDNAs so far reported. Filamentous particles reacting with the antiserum to C1YVV were observed in the crude sap of infected plants by immunoelectron microscopy, and genome replication was demonstrated by RT-PCR of 3' non-coding regions of C1YVV genome in total plant RNAs.

Genomic rearrangement in genome segment 12 of rice dwarf phytoreovirus

The genome segment 12 (S12) of rice dwarf phytoreovirus (RDV) isolated from the Philippines (RDV-P) and of a variant (RDV-S-6) of RDV severe strain (RDV-S) migrated abnormally slower during polyacrylamide gel electrophoresis than that of the isolate maintained at Hokkaido University (RDV-H). Nucleotide sequence analysis revealed that rearrangement had occurred in these segments, affecting the open reading frame. A polypeptide encoded by S12 (Pns12) of RDV-P had a duplication of 28 amino acids while 1/3 of the carboxyl terminus of Pns12 was deleted in RDV-S-6 by premature termination due to a frameshift. RDV-S is always present in plants infected with the RDV-S-6 variant, suggesting that Pns12 of RDV-S-6 is defective. On the other hand, Pns12 of RDV-P was expressed and appeared to be functional in infected cells in spite of the duplication, as demonstrated by immunoblot analyses using antibody raised against Pns12 expressed in Escherichia coli.

High resolution genome typing and genomic reassortment events of rice dwarf Phytoreovirus

Genomic reassortment of rice dwarf Phytoreovirus (RDV) was experimentally demonstrated for the first time in plant reoviruses. Combinations of two genomic variants, most of the genomic segments of which could be distinguished by a high resolution polyacrylamide gel electrophoresis, were used to produce genomic reassortants. After artificial mixed injection of two of three isolates (RDV-S, RDV-AI, and RDV-AN) into the insect vector Nephotettix cincticeps, rice seedlings were sequentially inoculated and the genomic origin of the viruses present in the infected plants was examined by electrophoresis. The progeny virus population contained either one or both of the respective genomic segments from the parents. Genomic segments reassorted randomly except for genome segment 1 (S1) and S9. S9 of RDV-S was mostly excluded in the reassortants in both the insects and the infected plants when it was mixed with RDV-AI or RDV-AN. On the other hand, S9 reassorted randomly in most of the virus populations in infected plants when RDV-AI and RDV-AN were co-injected into insects. When RDV-S and RDV-AI were mixed, S1 from RDV-S was present more frequently in the infected plants although both parental S1's were present in equimolar amounts in insects.

Heterogeneity of rice ragged stunt oryzavirus genome segment 9 and its segregation by insect vector transmission

Genomic heterogeneity of genome segment 9 (S9) of rice ragged stunt virus (RRSV) was investigated and a point mutation was found to be responsible for an electrophoretic mobility shift of S9 on polyacrylamide gel electrophoresis (PAGE). A new form of S9 (S9L) which migrated slightly faster than natural S9 (S9U) had the same length with A-->C transversion at nt 843. Synthetic S9 with a C:G pair at nt 843 migrated slightly faster than that with an A:U pair. Therefore, we conclude that the single point mutation shifts the electrophoretic mobility. Using polymerase chain reaction-single strand conformation polymorphism (PCR-SSCP), we could detect S9U and S9L alone or mixture in insect vectors after acquisition as well as in infected rice plants.

Rice ragged stunt Oryzavirus genome segment 9 encodes a 38 600 Mr structural protein

The complete nucleotide sequence of rice ragged stunt virus genome segment 9 (S9) was determined. The S9 segment is 1132 nucleotides long and has a long open reading frame starting from the first AUG codon at nucleotide position 14-16 and terminating at a UAG codon located at 1028-1030, which could encode a polypeptide with an Mr of 38 600 (P9). The encoded polypeptide has no sequence homology to polypeptides of any other plant reoviruses published previously. An immunological study demonstrated that P9 was the smallest of the structural proteins. The P9 polypeptide was expressed as a fusion protein with maltose binding protein in Escherichia coli. Antisera to purified virions and to the fusion protein reacted with both the bacterially expressed polypeptide and the smallest polypeptide of the purified virus in immunoblotting analyses.

Genomic heterogeneity of rice dwarf phytoreovirus field isolates and nucleotide sequences of variants of genome segment 12

Electrophoretic profiles of the dsRNAs of field isolates of rice dwarf virus (RDV) were compared with those of an isolate maintained at Hokkaido University (RDV-H). Unexpectedly, the genomic dsRNAs of most of the field isolates showed distinct electrophoretic mobility profiles. This was the case even among isolates from the same region. Genome segment 12 (S12) from some variants migrated faster than S12 from RDV-H. These RNAs were converted to full-length cDNAs and sequenced. S12 from all the variants had the same length of 1066 nucleotides with nucleotide sequence identities of 96 to 99%. Three open reading frames previously reported were present in all the variants, and the sequence identities were 95 to 99% for P12, 98 to 100% for P12OPa, and nearly 100% for P12OPb. A comparison of the nucleotide and amino acid sequences of the variants with sequences of the RDV-H and Akita isolate showed that there are two genomic types, one represented by RDV-H and the other by the Akita isolate.

Nucleotide sequence of rice dwarf phytoreovirus genome segment 2: completion of sequence analyses of rice dwarf virus

The complete nucleotide sequence of rice dwarf phytoreovirus genome segment 2 (S2) was determined to be 3,512 nucleotides long with one open reading frame initiating at nucleotide 15 and terminating at nucleotide 3363. The encoded polypeptide was predicted to have 1,116 residues with a relative molecular weight of 123 kD. Comparison of S2 of two isolates showed they had identical lengths and 97 and 98.3% nucleotide and amino acid sequence identities, respectively. A search of the Swiss-Prot data base (R 22.0) failed to find any proteins with significant homology to the S2-encoded protein. Determination of the nucleotide sequence of the S2 has completed the sequence determination of the genome of rice dwarf virus. Homology searches made for proteins encoded by each of the genomic segments showed that the polypeptide encoded by S11 has similarity to histone H1 protein and VP6 of blue tongue virus, indicating it might possess nucleic acid binding properties.

Close similarity between genome structures of rice black-streaked dwarf and maize rough dwarf viruses

The complete nucleotide sequences of rice black-streaked dwarf virus (RBSDV) genome segments 8 (S8) and 7 (S7) were determined, and were found to have high sequence identities to the corresponding maize rough dwarf virus (MRDV) genome segments. RBSDV S8 and S7 consisted of 1927 and 2193 nucleotides, respectively. RBSDV S8 had a single long open reading frame (ORF) encoding 591 amino acids. RBSDV S7 had two nonoverlapping ORFs encoding 362 (ORF1) and 309 (ORF2) amino acids. The two ORFs of RBSDV S7 were inserted separately into an Escherichia coli expression vector (pKK223-3). When they were expressed in E. coli cells, the products of both ORFs migrated identically at an apparent M(r) of 40K. High nucleotide sequence identity was observed between RBSDV S7 and MRDV S6 (85%), and between the terminal regions of RBSDV S8 and MRDV S7. In addition, RBSDV S7 and MRDV S6 showed 91% (ORF1 product) and 85% (ORF2 product) amino acid sequence identities.

Molecular analysis of rice dwarf phytoreovirus segment S1: interviral homology of the putative RNA-dependent RNA polymerase between plant- and animal-infecting reoviruses

We have determined the complete nucleotide sequence of the largest segment S1 of rice dwarf phytoreovirus (RDV), a member of the family Reoviridae. S1 is 4423 nucleotides long with a segment-specific inverted repeat located adjacent to the conserved termini (5'GGCAAA---UGAU3'). A major open reading frame (bases 36 to 4367) on the S1 plus strand, which is preceded by a minicistron (bases 6 to 29), encodes the polypeptide (P1) consisting of 1444 amino acids with a M(r) of 164, 142. The sense-strand transcript derived from the full-length S1 cDNA, the minicistron of which was abolished, directed the synthesis of a polypeptide of 170 kDa in addition to smaller polypeptides in wheat germ extracts, and the 170-kDa product comigrated with the minor core protein in SDS-polyacrylamide gel. Thus, P1 is assumed to be localized in the viral core particle. The consensus sequence element conserved in RNA-dependent RNA polymerase is observed in the P1 amino acid sequence predicted from the nucleotide sequence. Based on the dendrogram established from the sequence alignment around the polymerase module region, and sequence identity within the alignment, P1 of plant-infecting RDV was evolutionarily compared with VP1, lambda 3, and VP1 of three other animal-infecting members of the family, rota-, reo-, and bluetongue viruses. Consequently, RDV S1 was shown to be more closely related to the rotavirus gene segment 1, in terms of molecular evolution, than the animal-infecting members are to one another.

Conserved terminal nucleotide sequences in the genome of rice black streaked dwarf virus

The terminal regions of the dsRNA genome segments of rice black streaked dwarf virus (RBSDV) were sequenced. The individual dsRNAs, which were 32P-labelled at their 3' termini by incubation with [32P]pCp and T4RNA ligase, were separated by 5% PAGE, and the 10 dsRNA segments were sequenced by two-dimensional electrophoresis. The common 3'-terminal sequences ---GUC 3' and ---AAAAACUU 3' were found in the plus and minus strands, respectively. The strictly conserved terminal sequences (5' AAGUUUUU ... GUC 3') of the genome segments of RBSDV differ from those of the phytoreoviruses and rice ragged stunt virus.

Conserved terminal sequences of rice ragged stunt virus genomic RNA

The 5'- and 3'-terminal nucleotide sequences of the dsRNA genome segments of rice ragged stunt virus (RRSV), a member of the plant Reoviridae, were determined and compared with those published for other viruses in this family. The 5'- and 3'-terminal regions of the RRSV plus strand RNA from all genome segments were found to have the same conserved hexanucleotide (5' GAUAAA---) and tetranucleotide (---GUGC 3') sequences, respectively. These conserved terminal sequences were different from those found in viruses in the Phytoreovirus and Fijivirus genera. This result confirms that, as already suggested, RRSV should be placed in a third genus.

Bean yellow mosaic virus subgroup; search for the group specific sequences in the 3' terminal region of the genome

In order to examine relationships among viruses of the bean yellow mosaic subgroup of the Potyvirus genus, several isolates of bean yellow mosaic virus (BYMV) and clover yellow vein virus (C1YVV) were compared by amino acid sequence of the coat protein and nucleotide sequence of the 3' terminal non-coding region. The sequence comparisons showed that BYMV and C1YVV were distinct viruses but had close affinity to each other (85-95% homology among isolates of a virus but 70-77% homology between viruses), justifying establishment of the BYMV subgroup. There was an oligonucleotide consensus sequence present in the 3' terminal non-coding region of all potyviruses examined. This consensus sequence divided the potyviruses into three groups whose significance is not clear.

Viruses in the phytoreovirus genus of the Reoviridae family have the same conserved terminal sequences

The 5'- and 3'-terminal nucleotide sequences of the dsRNA genome segments of rice dwarf virus (RDV) and rice gall dwarf virus (RGDV), members of the Phytoreovirus genus of the Reoviridae family, were determined and compared with those of wound tumour virus (WTV). The 3' tetranucleotides of the plus strand of all genome segments of RDV and RGDV were found to be the same (---UGAU 3'), except for segment 9 of RDV which had the 3'-terminal sequence---CGAU 3'. The conserved 3'-terminal sequence (---UGAU 3') was the same as that found in the genome segments of WTV, another member of the Phytoreovirus genus. On the other hand, the 5' termini of the plus strands of RDV and RGDV were found to have two or three types of common sequence. RDV had either 5' GGCAAA--- or 5' GGUAAA---, whereas RGDV had 5' GGCAUUUU---, 5' GGUAUUUU--- or 5' GGUAAUUU---. These conserved sequences were similar to the conserved 5'-terminal sequence of WTV (5' GGUAUU---). Although the three viruses differ in plant host range, tissue specificity, vector specificity and disease symptom expression, these results suggest that they have a common ancestral origin.

Relatedness of the nucleotide sequence of the 3'-terminal region of clover yellow vein potyvirus RNA to bean yellow mosaic potyvirus RNA

The sequence of the 3'-terminal 1,357 nucleotides of clover yellow vein potyvirus RNA was determined. A coat protein gene was identified and its predicted amino acid sequence deduced. It had 273 residues with a molecular weight of 31,019. The amino acid and nucleotide sequences of the virus were compared with those of five other potyviruses. The homology between these viruses indicated that clover yellow vein virus was a distinct virus, but had a closer affinity to bean yellow mosaic virus than to the four other potyviruses.

Nucleotide sequence of rice dwarf virus genome segment 4

The complete nucleotide sequence of rice dwarf virus (RDV) genome segment 4 was determined. Genome segment 4 was 2468 nucleotides long and had a long open reading frame initiating at nucleotides 64 to 66 and terminating at 2245 to 2247. The deduced polypeptide contained 727 amino acid residues with an Mr of 79.8K. Amino acid sequences similar to a 'zinc-finger' and purine NTP-binding motifs were present in the deduced polypeptide. Considerable amino acid sequence homology was detected between genome segment 4 of RDV and wound tumor virus (WTV). One of the sequences similar to the 'zinc-finger' motif was present in a conserved region of the polypeptide of both viruses. However, the sequence similar to the purine NTP-binding motif was not present in the polypeptide encoded by genome segment 4 of WTV.

Nucleotide sequence of rice dwarf virus genome segment 9

The complete nucleotide sequence of the phytoreovirus rice dwarf virus (RDV) genome segment 9 is presented. It consisted of 1305 nucleotides and had an open reading frame that codes for a putative polypeptide of 351 amino acids. Mr of the protein was calculated to be 38,598. The terminal nucleotides 5' GGUAAA--GAU 3' were the same as those of RDV genome segment 10. The fourth nucleotide from the 3' end of an expected conserved sequence was a C rather than the U found in the previously sequenced genome segment 10. A structure similar to the segment-specific inverted repeat of wound tumour virus was also found in the terminal region of segment 9.

Characterization of RNA polymerase associated with rice ragged stunt virus

The RNA polymerase associated with rice ragged stunt virus (RRSV) was characterized. Activity was optimum at 35-40 degrees in 0.1 MTris-HC1 (pH 8.5) and 6-8 mMMgCl2. S-Adenosyl-L-methionine stimulated the activity about 5- to 6-fold. It was also stimulated in the presence of chymotrypsin (200 micrograms/ml). The molecular weights of RNAs synthesized in vitro were calculated to be about half those of the respective genome segments. The synthesized RNAs hybridized to the genome RNAs, and the hybrids migrated identically to the genome RNAs in PAGE. These results indicate that RRSV particles transcribe full-length copies of the genome RNAs. The characteristics of the polymerase are discussed in relation to those of other members of the Reoviridae.

Nucleotide sequence of cucumber pale fruit viroid: homology to hop stunt viroid

Double stranded cDNA of cucumber pale fruit viroid ( CPFV ) has been cloned by the method of Okayama and Berg (Mol.Cell.Biol.2,161-170 (1982] and the complete nucleotide sequence was established. The covalently closed circular molecules of single-stranded CPFV RNA consists of 303 nucleotides. The nucleotide sequence of CPFV was compared with the previously established sequence of hop stunt viroid (HSV), which consists of 297 nucleotides ( Ohno et al. Nucleic Acid Res.11,6185-6197 (1983]. CPFV differs from HSV in the nucleotide sequence at 16 positions which include 8 exchanges, 7 insertions and 1 deletion. Both viroids share about 95% sequence homology. Considering the pathogenic properties of both viroids together, it is concluded that CPFV is a cucumber isolate of HSV.