Molecular analysis of coat protein coding region of tobacco stunt virus shows that it is a strain of Lettuce big-vein virus in the genus Varicosavirus.

To evaluate the relationship between tobacco stunt virus (TStV) and Lettuce big-vein virus (LBVV), we determined nucleotide sequences of the coat protein (CP) coding region of five TStV and three LBVV isolates and compared them with those of one Japanese and four Spanish isolates of LBVV. CP coding regions were identical in size and the nucleotide and amino acid sequence identities between TStV and LBVV were 95.6-96.5% and 97.2-98.7%, respectively. Phylogenetic analysis of nucleotide sequences indicated that TStV was very closely related to LBVV and a strain of LBVV rather than a distinct species.

Nucleotide sequence and genome organization of apple latent spherical virus: a new virus classified into the family Comoviridae.

A virus with isometric virus particles (ca. 25 nm) was isolated from an apple tree and named Apple latent spherical virus (ALSV). Virus particles purified from infected Chenopodium quinoa formed two bands with densities of 1.41 and 1.43 g/cm(3) in CsCl equilibrium density-gradient centrifugation, indicating that the virus is composed of two components. The virus had two ssRNA species (RNA1 and RNA2) and three capsid proteins (Vp25, Vp24 and Vp20). The complete nucleotide sequences of RNA1 and RNA2 were determined to be 6815 nt and 3384 nt excluding the 3' poly(A) tail, respectively. RNA1 contains two partially overlapping ORFs encoding polypeptides of molecular mass 23 kDa ('23K'; ORF1) and 235 kDa ('235K'; ORF2); RNA2 has a single ORF encoding a polypeptide of 108 kDa ('108K'). The 235K protein has, in order, consensus motifs of the protease cofactor, the NTP-binding helicase, the cysteine protease and the RNA polymerase, in good agreement with the gene arrangement of viruses in the COMOVIRIDAE: The 108K protein contains an LPL movement protein (MP) motif near the N terminus. Direct sequencing of the N-terminal amino acids of the three capsid proteins showed that Vp25, Vp20 and Vp24 are located in this order in the C-terminal region of the 108K protein. The cleavage sites of the 108K polyprotein were Q/G (MP/Vp25 and Vp25/Vp20) and E/G (Vp20/Vp24). Phylogenetic analysis of the ALSV RNA polymerase domain showed that ALSV falls into a cluster different from the nepo-, como- and fabavirus lineages.

Biological, serological, and molecular variabilities of clover yellow vein virus.

ABSTRACT A comparative study was made on the host reactions, serological properties, and nucleotide sequences of the coat protein (CP) gene of 10 clover yellow vein virus (C1YVV) isolates and one bean yellow mosaic virus (BYMV) isolate collected from different host plant species and locations in Japan. Two strains of C1YVV isolates, grouped on the basis of host reactions on Chenopodium amaranticolor, C. quinoa, Nicotianaclevelandii, N. benthamiana, Vicia faba, and Trifolium repens, corresponded to two serotypes determined by double-antibody sandwich- and triple-antibody sandwich-enzyme-linked immunosorbent assay using three polyclonal and nine monoclonal antibodies. These results were also confirmed by nucleotide sequence analysis of the CP gene. The CP gene of C1YVV isolates of strain 1, including the Australian isolate C1YVV-B, had 93 to 98% nucleotide identities and 97 to 99.6% amino acid identities. The CP of C1YVV isolates of strain 2, including the New Zealand isolate C1YVV-NZ, had 92 to 98% nucleotide identities and 95 to 98% amino acid identities. The nucleotide identities and the amino acid identities between the two C1YVV strains were 82 to 84%, and 90 to 94%, respectively. When compared with the CP sequences of 12 C1YVV isolates, the CP sequence of the BYMV isolate had 71 to 73% nucleotide identity and 73 to 77% amino acid identity. Amino acid sequence differences among C1YVV isolates from strains 1 and 2 were located mostly at the N-terminal regions of the CP. Our results indicated that the C1YVV isolates studied could be separated into two strains on the basis of host reactions, serology, and the nucleotide sequence of the CP gene.

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.

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.

Nucleotide sequence of capsid protein gene of rice tungro bacilliform virus.

The sequence of 5,028 nucleotides, including one open reading frame (ORF), of rice tungro bacilliform virus (RTBV) dsDNA was determined. The predicted translational product comprises 1,675 amino acids and has Mr of 194,134 (p194). The amino acid sequences of three tryptic fragments from the 32 k capsid protein of RTBV (p32) were found in the predicted translational product indicating that the ORF codes for the RTBV capsid protein.

Nucleotide sequence of segment S9 of the genome of rice gall dwarf virus.

DNA complementary to the ninth largest (S9) of the 12 genome segments of rice gall dwarf virus (RGDV) was cloned and its sequence was determined. It is 1202 nucleotides in length and contains one open reading frame which extends for 969 nucleotides from nucleotide 26. It encodes a polypeptide of 323 amino acids with an Mr of 35,560. The dinucleotide sequence at the 5' end and the trinucleotide sequence at the 3' end of the plus strand, 5' GG--GAU 3', which are present in the RNA of both wound tumour virus (WTV) and rice dwarf virus (RDV), were also found in RGDV genome segment S9. The nucleotide sequences in the noncoding region at the 5' terminus and in the 15 nucleotides at the 3' terminus, which form an imperfect inverted repeat of 10 bp together with the 5' terminus, are approximately 70% homologous with those of the WTV genome segment S9, but only 30% and 50% homologous with the respective termini of RDV S9.

Nucleotide sequence and secondary structure of apple scar skin viroid.

The complete nucleotide sequence of apple scar skin viroid(ASSV) has been established, and a probable secondary structure is proposed. A single-stranded circular ASSV RNA consists of 330 nucleotides and can assume the rodlike conformation with extensive base-pairing characteristic of all the known viroids. ASSV shows low sequence homologies with other viroids and lacks the central conserved region. These indicate that ASSV should be allocated to a separate viroid group. However, homologous sequences with potato spindle tuber viroid(PSTV) in ASSV occur in limited and scattered regions of both viroids. These homologous regions fall within the particular domains in the viroid domain model which has been previously proposed by Keese and Symons(Proc. Natl. Acad. Sci. USA. 82, 4582-4586, 1985).