Nucleotide sequence analysis and genomic organization of the NY-RPV isolate of barley yellow dwarf virus

Abstract

cDNA clones representing the ssRNA genome of the NY-RPV isolate of barley yellow dwarf luteovirus (BYDV) were sequenced and 5600 nucleotides of the genome were determined. The deduced genome organization has limited similarity to that of another BYDV isolate, Vic-PAV, but is identical to that of beet western yellows (BWYV) and potato leafroll (PLRV) luteoviruses. NY-RPV has six major positive-sense open reading frames (ORFs) and, by comparison with RNA-dependent RNA polymerase and nucleic acid helicase consensus sequence motifs, it is postulated that NY-RPV ORF2 and ORF3 encode the viral replicase, which is expressed by a translational frameshift mechanism. The region of the NY-RPV genome containing the 22K coat protein ORF, the apparently associated internal apparent VPg ORF and the ORF immediately 3'-proximal (ORF6) to the coat protein ORF are organized as reported for other luteoviruses. Evidence is presented showing that ORF6 is expressed by readthrough of the coat protein gene termination codon, and that this protein is associated with the intact virus as a 65K protein. Although NY-RPV infects graminaceous rather than dicotyledonous plants, the taxonomic relationships between BYDV isolates and other luteoviruses deduced from the genome organization and sequence data strongly suggest that NY-RPV is distinct from the PAV-like isolates of BYDV and is more closely related to BWYV and PLRV.

The chimeric nature of the genome of pea enation mosaic virus: the independent replication of RNA 2

“…4;Hodgman, 1988;Habili & Symons, 1989;Koonin, 1991). Based on the occurrence and arrangement of these motifs, it has been proposed that this group of viruses constitutes a separate taxonomic entity, different from the PLRV-BWYV subgroup of the tuteoviruses which also contains the NY-RPV isolate of BYDV and RNA 1 of PEMV (Habili & Symons, 1989;Koonin, 1991;Vincent et al, 1991). Consistent with this model is the observation that this 65K product does not display homology with the polymerase cassette of PEMV RNA 1, nor with its allied luteoviruses.…”

Nucleotide sequence analysis of the genomes of the MAV-PS1 and P-PAV isolates of barley yellow dwarf virus

“…The product encoded by the MAV-PS10RF6 is 4.3K and that of P-PAV ORF6 is 6.5K. The genome organization of these BYDV isolates is similar to that described for Vic-PAV (Miller et al, 1988), yet different from that of BYDV (NY-RPV) (Vincent et aL, 1991). As such, for MAV-PS1, P-PAV and Vic-PAV, ORFs l and 2 are proposed to encode the viral replicase, ORF3 the coat protein and, based on the identification of a 17K genome-linked small protein (VPg) from a BYDV (RPV) isolate (Murphy et al, 1989), ORF4 putatively encodes the VPg.…”

“…In fact, the transcriptional start site of a 2.6 kb subgenomic RNA from PLRV has recently been mapped to 34 nucleotides 5' of the coat protein translation initiation codon (Tacke et al, 1990) and corresponds to a conserved region identified in all other published luteovirus sequences (Vincent et al, 1991). Between MAV-PS1 and P-PAV there is 91~ sequence identity for the coat protein leader sequences; for P-PAV and Vic-PAV this region has 99~ identity.…”

“…Virus purification, viral genomic RNA extraction, cDNA library construction and mapping procedures were as previously described (Barbara et al, 1987;Vincent et al, 1990). cDNA clones representing the genome of each viral isolate were sequenced by the dideoxynucleotide chain termination method (Sanger et al, 1977) with a modified T7 polymerase (Sequenase, US Biochemical) utilizing the same strategies described for NY-RPV (Vincent et al, 1991). Sequence analyses were performed with software by Devereux et al (1984) and Microgenie (Beckman Instruments).…”

“…In recent years nucleotide sequences of several luteovirus genomes have been described, including an Australian PAV serotype (Miller et al, 1988), hereafter referred to as Vic-PAV, the NY-RPV isolate of BYDV (Vincent et al, 1991), BWYV (Veidt et al, 1988) and PLRV (Keese et al, 1990;Mayo et al, 1989). The close relationship between MAV and PAV serotypes has prompted us to compare an MAV and a PAV serotype (MAV-PS1 and P-PAV, see below) with the aim of Short communication …”