Nucleotide sequence of the coat protein gene of pea seed-borne mosaic potyvirus

Sequence of the 3'-terminal region of a Zimbabwe isolate of cowpea aphid-borne mosaic virus (CABMV)

The 3'-terminal 1221 nucleotides of a Zimbabwe isolate of cowpea aphid-borne mosaic potyvirus (CABMV) genome have been sequenced. The sequence comprises an open reading frame (ORF) of 990 nucleotides and a 3' non-coding-region of 231 nucleotides followed by a poly-A. The ORF has high similarity to NIb and coat proteins (CP) of potyviruses. A potential CP Q/S cleavage site was identified, yielding a CP of 30.5 kDa containing 275 amino acids. The CABMV sequence is closely related to that of South African passiflora virus (SAPV) which should therefore be regarded as a strain of CABMV.

Cloning and sequence analysis of the coat protein genes of an Australian strain of peanut mottle and an Indonesian 'blotch' strain of peanut stripe potyviruses

We have analysed the coat protein gene sequences of two potyviruses infecting peanut. The 3' terminal 1247 nucleotides (nt) of an Australian strain of peanut mottle virus (PeMoV-AU) and the 3' terminal 1388 nt of an Indonesian 'blotch' strain of peanut stripe virus (PStV-Ib) were cloned and sequenced. Those regions included the 861 and 864 nt encoding the respective putative coat proteins as well as the 285 and 253 nt, respectively of 3' non-coding sequences. Comparison of the nucleotide sequences of PeMoV-AU and PStV-Ib revealed a sequence similarity of 64.4% for the coat protein gene and 34.6% for the 3' non-coding region. The deduced amino acid sequences of PeMoV-AU and PStV-Ib coat proteins are 66.7% identical. These results provide further evidence that PeMoV and PStV are distinct viruses. Comparisons of the 3' terminal sequences of PeMoV-AU and PStV-Ib with those of the genomic RNA of other strains of PeMoV and PStV and with other potyviruses are discussed.

Cloning of the capsid protein gene from a blotch isolate of peanut stripe virus

The 3' terminal 1,367 nucleotides (nts) of a blotch isolate of the potyvirus, peanut stripe virus (PStV), were cloned and sequenced. This region included the 861 nts (287 amino acids) of the PStV capsid protein (CP). The amino acid sequence of the predicted proteinase cleavage site was identified. This region shared limited homology with other potyvirus proteinase cleavage sites. The viral CP gene sequence was followed by 254 nucleotides of 3' nontranslated sequence and a poly-A tail. Based on computer modeling, the 3' nontranslated region could form two lengthy stem-loop structures and two pseudoknot structures. Subclones containing the coding sequences of the CP (amino acids 1-287, 17-287, 17-113 and 106-287) were constructed and expressed in Escherichia coli. These polypeptides were detected using polyclonal antibodies in Western blots.

Cloning and sequence analysis of the coat protein gene of barley mild mosaic virus

The sequence of the 3' 1462nts of RNA-1 of a UK isolate of the fungal-transmitted virus barley mild mosaic (BaMMV) has been determined. An open reading frame encoding the coat protein gene was identified within this region using amino acid sequence information obtained by cyanogen bromide cleavage of virus particles. The amino acid sequence of the full-length coat protein was deduced from the nucleotide sequence. Amino acid sequence comparisons revealed highest homology to the coat protein of barley yellow mosaic virus. In addition, a significant, but limited, number of the amino acid residues that are conserved between aphid-transmitted potyviruses were also conserved between BaMMV and potyviruses.

Detection of pea seedborne mosaic potyvirus by sequence specific enzymatic amplification

The polymerase chain reaction (PCR) was used to detect pea seedborne mosaic potyvirus (PSbMV) pathotype P1 RNA after reverse transcription of total nucleic acid preparations from pea (Pisum sativum) tissues. Tissues assayed for PSbMV included leaves, roots, petals, seed parts, and pollen. Three oligonucleotide primers in appropriate combination yielded two products of the predicted size: 730 and 1200 bp. The described methodology allows for rapid pathotype-specific PSbMV detection with utmost sensitivity and wide applicability.

Nucleotide sequence of the coat protein gene of a strain of clover yellow vein virus from New Zealand: conservation of a stem-loop structure in the 3' region of potyviruses

The sequence of the 3'-terminal 1492 nucleotides of the genome of a New Zealand isolate of clover yellow vein potyvirus (CYVV) has been determined. This sequence encodes a large open reading frame of 1314 nucleotides, the start of which was not identified, but which encodes a putative 272 amino acid coat protein. Downstream of the coat protein coding region is a 177 nucleotide untranslated sequence terminated by a polyadenylate tract. Comparison of the deduced CYVV-NZ coat protein amino acid sequence with two other strains of CYVV showed 86-93% similarity, suggesting CYVV-NZ should be regarded as a separate CYVV strain. CYVV-NZ shares with other CYVV strains a direct repeat of 14-16 nucleotides that is capable of forming a stem-loop structure. Examination of 35 strains of 15 other potyviruses showed a similar stem-loop structure conserved in all cases. A possible role in replication is hypothesized for the structure.

Procedures for the efficient purification of pea seed-borne mosaic virus and its genomic RNA

An efficient protocol for the purification of pea seed-borne mosaic potyvirus (PSbMV) particles was developed. This led to the purification of 10 PSbMV isolates by a single procedure. Virus aggregation during purification did not occur and consequently, high virus yield was consistently obtained. The virus thus purified was suitable for preparing viral genomic RNA, although conventional methods for RNA extraction resulted in RNA degradation. An alternative method was adopted which yielded reproducibly full length and infectious RNA. This was applied to three isolates of PSbMV and the RNA used to direct complementary DNA synthesis which in turn yielded nearly full length cDNA products.

Coat protein phylogeny and systematics of potyviruses

The feasibility of applying molecular phylogenetic methods of analysis to aligned coat-protein sequences and other molecular data derived from coat proteins or genomic sequences of members of the proposed taxonomic family of Potyviridae, is discussed. We show that comparative sequence analysis of whole coat-protein sequences may be used reliably to differentiate between sequences of closely related strains, and to show groupings of more distantly related viruses; that coat proteins of putative Potyviridae cluster according to the proposed generic divisions, and, even if some are only very distantly related, the members of the family form a cluster distinct from coat proteins of other filamentous and rod-shaped viruses. Taxonomic revisions based on perceived evolutionary relationships, and the lack of feasibility of erecting higher taxa for these viruses, are discussed.

Potyvirus serology, sequences and biology

Amino acid sequences of the cytoplasmic cylindrical inclusion protein (CIP), large nuclear inclusion protein (NIb), and coat protein (CP) of potyviruses were re-examined in light of reported serological relationships, and correlated with known and deduced biological functions. No obvious correlations were observed between either amino acid sequences or epitopes recognized by monoclonal antibodies and the natural host ranges of the potyviruses examined. Whereas the identified sequence motifs of the RNA helicase (CIP) and replicase (NIb) are predicted to be antigenic, most of the conserved sequences and epitopes in the CIP, NIb and CP were presumed to be maintained for structural rather than functional reasons. Three possible potyvirus clusters are proposed on the basis of the length and composition of the virion surface-exposed amino terminal extension of the CP; these clusters do not correlate with overall CP sequence homology, host range, or vectors, but are of potential evolutionary significance and hence of possible taxonomic value.

Nucleotide sequence of pea seed-borne mosaic potyvirus coat protein gene

cDNA of pea seed-borne mosaic potyvirus (PSbMV) RNA was synthesized and cloned in E. coli. Four overlapping clones that cover the complete PSbMV genome, except the extreme 5' terminus, were identified by restriction enzyme mapping, hybridization analysis, and partial sequencing. Overlapping cDNA clones covering 1386 nucleotides of the 3' terminus were sequenced. The nucleotide sequence contains one open reading frame (ORF), followed by an untranslated region of 163 nucleotides and a poly(A)-tract. The deduced amino acid sequence was found to include the C-terminus of the predicted RNA-dependent RNA polymerase and the coat protein. A glutamine-alanine dipeptide was identified as a putative 49-kD proteinase cleavage site at the N-terminus of the coat protein.

Coat protein of potyviruses. 7. Amino acid sequence of peanut stripe virus

The amino acid sequence of the 287-residue coat protein of peanut stripe virus (PStV) was determined from the sequences of overlapping peptide fragments. Results indicated that the amino terminus was blocked by an acetyl group, as has previously been found for the coat protein of Johnsongrass mosaic potyvirus. Comparison of the PStV sequence with coat proteins of 20 distinct potyviruses gave sequence identities of 47-57%, except for zucchini yellow mosaic virus (ZYMV), passionfruit woodiness virus (PWV), and the related strains watermelon mosaic virus 2 (WMV 2) and soybean mosaic virus-N, which showed sequence identities of 70-76%. Several amino acid residues which were common to the core sequences of these coat proteins were at positions previously found to be invariant among potyvirus coat proteins. The degree of these similarities suggests that although PStV, WMV 2, ZYMV, and PWV are distinct potyviruses, they share a common ancestor in their evolutionary development.