The complete nucleotide sequence of prune dwarf ilarvirus RNA 3: implications for coat protein activation of genome replication in ilarviruses.

The complete nucleotide sequence of prune dwarf ilarvirus (PDV) RNA 3 has been determined from cloned viral cDNAs. The PDV RNA 3 is 2129 nucleotides and contains two large open reading frames (ORFs) separated by an intergenic region of 72 nucleotides. The 5' proximal ORF (ORF-1) is 882 nucleotides, encoding a gene product which shares homology with putative cell-to-cell movement proteins of related viruses, including tobacco streak virus (TSV) and alfalfa mosaic virus (AIMV). The downstream ORF (ORF-2) is 657 nucleotides and encodes a gene product which shares primary sequence homology and structural features with AIMV coat protein. Furthermore, when expressed in bacteria, this ORF produces a polypeptide which comigrates with authentic PDV coat protein and reacts with PDV coat protein antiserum. Hybridization data suggest that the genomic organization of PDV RNAs 3 and 4 is similar to that of TSV, the only other ilarvirus for which sequence information is published. The 3' untranslated region (UTR) of PDV RNA 3 is similar to that of TSV and AIMV, containing a potential stem-loop structure followed by the sequence AUGC, a structure which may signal binding of coat protein and activation of genome replication. However, a striking feature of the deduced PDV coat protein sequence is the absence of a "zinc-finger" motif thought to function in binding of the coat protein to the 3'-UTR in ilarviruses and AIMV. This result suggests that the zinc-finger motif is not a required aspect of coat protein activation of replication in ilarviruses.