Nucleotide sequence of rice black-streaked dwarf virus genome segment 10.

Abstract

Plant reoviruses have segmented genomes consisting of 10-12 dsRNAs. They have been classified into subgroups 1, 2 and 3 based on vector species, particle morphology, and number of segmented genome. 7) Genome structure of wound tumor virus (WTV) genome segments 4-12 and rice dwarf virus (RDV) genome segments 9 and 10 have been determined.'~-4).s~,15).1`f2') From these studies, RDV and wTV, both belong to the same subgroup 1, have been shown to have some structural features in common. For example, both RDV and wTV have the same conserved tetranucleotides at both 5' and 3' termini and have the segment-specific inverted repeat at the terminal regions.1 19>,21) Furthermore, the comparable genes encoded by the genome segments of RDV and WTV were found to have a significant amino acid sequence homology.2'~.s~ These results indicated comparative analyses of the genome structure would elucidate some insight on function of the genes and thus on mechanisms involved in transcription, replication, and gene expression of the plant reoviruses. Rice black-streaked dwarf virus (RBSDV), a member of the subgroup 2, has a distinct double-shelled particle and 10 genome segments."'~ This is the largest subgroup among three subgroups consisting of 9 viruses. 7 However, none is known about the genome structure of the viruses in the subgroup 2. Since we are interested in whether the genes encoded by the RBSDV have some structural features common to other plant reoviruses, we have sequenced the genome segment 10 and a deduced amino acid sequence is presented. This is the first report on the genome structure of the plant reovirus subgroup 2. Materials and methods. RNA extraction. RBSDV was purified from the infected maize leaves and sheeth as previously described.The genome dsRNAs were extracted from the purified virus by phenol-SDS after proteinase-K treatment as previously described.' ~~ ssRNA contaminants were removed by 2M LiCI fractionation.1 (DNA synthesis and molecular cloning. The cDNAs were synthesized from the denatured genome dsRNAs as described elsewhere.>> The cDNAs were inserted into bacterial plasmid pBR 322 at Pst I site after homopolymeric tailing. And E. toll strain HB101 was transformed with the recombinant DNAs according to CaCl method described by Maniatis et al.13? Sequence analyses. cDNA was subeloned into M-13 phage mp18 and mp19" and sequenced by dideoxy chain termination methods 7 using a DEAZA sequencing kit (Takara Shuzou). Direct RNA sequence was done by reverse transcription and dideoxy chain termination method using viral transcripts or genomic RNA as a template.J~ 2 ' Results and discussion. A clone pRB C3 had a insert of about 1800 nucleotides. This clone reacted specifically with the genome segment 10 by a

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

“…1). These data showed that the 5' and 3' termini of the plus strands of all segments are adenine and cytidine, respectively, because the 3' termini of the plus strand of genome segments S 10 Uyeda et al, 1990), $8 and $7 (data not shown) were identified as cytidine by cDNA analysis. The nucleotide sequences of terminal regions of the genome were analysed by the wandering spot method (de Wachter & Fiers, 1972;Rensing & Schoenmarkers, 1973) after partial alkaline hydrolysis of 32p-labelled dsRNA in 100 mM-NaHCO3 for 1 h at 100 °C (Nomoto & Imura, 1979;Kudo et al, 1991).…”

Molecular characterization of Fiji disease fijivirus genome segment 9.

“…Other fijiviruses include maize rough dwarf (MRDV), rice black-streaked dwarf (RBSDV), pangola stunt (all belonging to serogroup 2), and oat sterile dwarf (serogroup 3). The nucleotide sequences of several genome segments from different fijiviruses belonging to serogroups 2 and 3 have been published (Uyeda et al, 1990 ;Marzachi et al, 1991 ;Azuhata et al, 1993). However, sequence data on FDV have been limited to primer sequences for use in PCR-based diagnostics (Smith et al, 1992).…”

Nucleotide sequence of Nilaparvata lugens reovirus genome segment S8 coding for the major outer capsid protein

“…For example, the amino acid sequence identities between the major outer capsid proteins (MOCPs) range from 48 to 56 % (Omura et al, 1989;Xu et al, 1989;Noda et al, 1991 b). In the Fijivirus genus, the nucleotide sequences of MRDV genome segment 6 ($6) (Marzachi et al, 1991) and RBSDV S10 (Uyeda et al, 1990), $8 and $7 (Azuhata et al, 1993) have been reported, but those of their MOCPs are unknown. We previously reported the nucleotide sequence ofNLRV S10 (Noda et al, 1994).…”

“…3. Comparison of the amino acid sequences of the predicted proteins encoded by NLRV $8 and RBSDV S10 (Uyeda et al, 1990). The sequences were aligned by the LFASTA program (Pearson, 1990) from the amino acid residues 7 to 522.…”

“…The conserved terminal sequences of the plus strand of NLRV are also similar to those of members of the Fijivirus genus. Fijiviruses have six uridine residues in the 5'-terminal region of the plus strand, and $3, $4, $8 and $9 segments of NLRV have Short communication NLRV $8 and RBSDV S10 (Uyeda et al, 1990). They were generated by the software GENETYX using the program of Kyte & Doolittle (1982) with a sliding window of 15 residues.…”