Nucleotide sequence of the coat protein gene of a necrotic strain of potato virus Y from New Zealand

Molecular characterization of coat protein genes of serologically distinct isolates of potato virus Y necrotic strain

The cost protein (CP) genes of two potato virus Y necrotic isolates (N27 and a mutant strain N27-92), which differed in their reactivity to a monoclonal antibody (mab), were characterized. Both isolates could be detected by mab 4E7, but mab VN295.5 selectively reacted to N27 and not to N27-92. The CP genes of both isolates coded for 267 amino acids with approximately 99.0% identity at both the nucleotide and the amino acid levels. nucleotide sequence comparison indicated five substitutions in N27-92 compared with N27. Three of these changes resulted in substitution of amino acids. Two transitions (A-->G) in N27-92 changed threonine to alanine and lysine to arginine at positions 7 and 55, respectively, whereas a A-->T transversion changed asparagine to isoleucine at positions 27. The surface probability curves of both the isolates could almost be superimposed, except at amino acid positions 7 and 27. Since amino acid substitution at position 55 is conservative, changes from polar to hydrophobic amino acids (threonine-->alanine and asparagine-->isoleucine) at positions 7 and 27 might have changed the epitope(s) of N27-92, abolishing its detection by mab VN295.5.

A strain-type clustering of potato virus Y based on the genetic distance between isolates calculated by RFLP analysis of the amplified coat protein gene

Potato virus Y (PVY) isolates have been classified into genetic strains by a host-independent criterion using a molecular typing method. The method used extracts from infected tissue, and included immunocapture-RT-PCR-RFLP analysis using 5 different restriction endonucleases (Dde I, Eco RV, Hinf I, Rsa I and Taq I). Genetic distances between the different PVY "restrictotypes" were calculated and used to define the PVY genetic strains. Three main clusters were found: PVYO, PVYN, and non-potato PVY (PVYNP), in good agreement with classical PVY strain definitions that combine different biological criteria. Our approach was incomparably quicker and more reliable and reproducible than biotyping. The potential of this approach for very quick, simple and automatable molecular epidemiological studies is discussed.

Molecular cloning and nucleotide sequencing of the 3'-terminal region of a South African isolate of ryegrass mosaic virus RNA and in vitro expression of the coat protein gene

The 2094 nucleotides at the 3'-terminus of a South African isolate of ryegrass mosaic virus (RGMV) was cloned and sequenced. Two putative polyprotein cleavage sites were found: Q/L and E/A, both of which are novel in the Potyviridae. The RGMV-SA cDNA was cloned into an expression vector, pUEX, and a fusion protein of 185 kDa was obtained which reacted strongly to anti-RGMV-SA antiserum. Alignment of the predicted amino acid sequence of RGMV-SA with those of other Potyviridae members showed limited identity, indicating that RGMV-SA is a definite and distinct virus.

Cloning and sequence analysis of RNA-2 of a mechanically transmitted UK isolate of barley mild mosaic bymovirus (BaMMV)

A mutant of the 'Streatley' isolate of barley mild mosaic bymovirus was selected from the original field isolate by repeated mechanical inoculation. Unlike the wild-type barley mild mosaic virus, which is transmitted by the soilborne fungus Polymyxa graminis, the mutant could not be transmitted by this vector. RNA-2 of the mutant virus was shorter than that of the wild-type virus suggesting that a deletion of part of the genome segment had occurred. The nucleotide sequence of the mutant RNA-2 was determined and revealed a high degree of homology with the RNA-2 of a German BaMMV field isolate. The deletion comprises 1092 nucleotides and is located in the 3'-terminal part of the coding region. The 34-kDa truncated form of the C-terminal protein is less than half the size of the corresponding protein of full-length BaMMV RNA-2. Taken together, the sequence data and results of biological experiments suggest an essential role of the C-terminal protein for fungus transmission of BaMMV.

Small-scale field tests with transgenic potato, cv. Bintje, to test resistance to primary and secondary infections with potato virus y

The coat protein (CP) gene of the potato virus Y (PVY) strain N605 has been cloned into a plant binary expression vector and introduced into the potato variety Bintje. The transformed lines, Bt6, that contained two copies of the CP gene showed complete resistance to the homologous strain PVY-N605 and a good resistance to the related strain PVY-O803 in the greenhouse. The good resistance of Bt6 to primary and secondary infections by PVY was confirmed in two successive field tests where the virus was transmitted by its natural aphid vector.

Taxonomic relationships between distinct potato virus Y isolates based on detailed comparisons of the viral coat proteins and 3'-nontranslated regions

Detailed comparisons were made of the sequences of the coat protein (CP) cistrons and 3'-nontranslated regions (3'-NTR) of 21 (geographically) distinct isolates of potato virus Y (PVY) and a virus isolate initially described as pepper mottle virus (PepMoV). Multiple sequence alignments and phylogenetic relationships based on these alignments resulted into a subgrouping of virus isolates which largely corresponded with the historical strain differentiation based on biological criteria as host range, symptomatology and serology. Virus isolates belonging to the same subgroup shared a number of characteristic CP amino acid and 3'-NTR nucleotide residues indicating that, by using sequences from the 3'-terminal region of the potyvirus genome, a distinction could be made between different isolates of one virus species as well as between different virus species. RNA secondary structure analysis of the 3'-NTR of twelve PVY isolates revealed four major stem-loop structures of which, surprisingly, the loop sequences gave a similar clustering of isolates as resulting from the overall comparisons of CP and 3'-NTR sequences. This implies a biological significance of these structural elements.

Cloning and sequencing of potato virus Y (Hungarian isolate) genomic RNA

A sequence of 9703 nucleotides (nt) is reported for the genomic RNA of potato virus Y (Hungarian isolate, PVY-H), which causes necrotic rings around the buds on the tubers and mottling of leaves. The sequence contains one large open reading frame of 3061 amino acids (aa), a noncoding region of 189 nt at the 5' end and a 330-nt 3' nontranslated region. The nt sequence and the predicted aa sequence of the polyprotein of PVY-H were analysed pairwise with the only available complete sequence of PVY strain N (PVYn) and with the partial sequences of different PVY strains, as well as with other potyviruses and potyvirus-related plant viruses. The overall relationship between PVY-H and PVYn shows a nt sequence identity of 88.5% and an aa sequence identity of 94.2%. The lowest degree of homology was detected at the 5' terminus of the genome, including the 5' noncoding region (70.3%) and the 275-aa P1 protein (78%). A fivefold sequence repeat block of 5'-UUUCA was found in the 5' noncoding region of PVY-H, which seems to be characteristic of PVY strains.

Efficient pathogen-derived resistance induced by integrated potato virus Y coat protein gene in tobacco

The coat protein (CP) gene from potato virus Y (Hungarian isolate, PVY-H) was engineered into Agrobacterium tumefaciens binary vector for expression in different tobacco lines. Three different Nicotiana tabacum breeding lines were transformed and the integration of the CP gene was confirmed by PCR technique using genomic DNA preparations. The transcription and expression of the integrated CP gene was detected by Northern and Western blots. Pathogen-derived resistance was demonstrated by inoculation of the R1 progeny of the transformed lines with purified PVY-H. The efficiency of protection varied between different transgenic plants ranging from almost complete to no protection. Five CP expressing tobacco lines were resistant to challenge infection with PVY-H as indicated by attenuation or absence of symptom development associated with reduction or lack of detectable virus accumulation. Data from Western blots showed that there is no correlation between the level of the expressed CP and the extent of protection. This suggests that the mechanism of the observed resistance is independent of the level of CP accumulation in the transgenic tobacco plants.

A polymerase chain reaction method adapted for selective amplification and cloning of 3' sequences of potyviral genomes: application to dasheen mosaic virus

'Universal' degenerate oligonucleotide primers were used to amplify cDNA sequences containing the 3' untranslated region (3' UTR) and a portion of the coat protein gene sequence of dasheen mosaic potyvirus (DMV). These primers were based on the conserved WCIEN and QMKAAA 'boxes' of the potyviral coat protein and the poly-A tail found at the 3' end of the genome. The forward genome-sense primers were designed taking into consideration the codon degeneracy of the WCIEN and QMKAAA residues for several potyviruses. The anti-sense reverse primer has 21 T residues followed by either A, C or G at the 3' end to ensure specific priming at the end of the 3' UTR and beginning of the poly-A tail. The specificity of amplification was verified using the known potyviruses (watermelon mosaic 2 and soybean mosaic viruses). To demonstrate the applicability of this method, the 3' UTR of the unsequenced DMV was amplified, cloned and sequenced. Sequence comparisons with other potyviral 3' UTRs revealed DMV to be quite distinct: nucleotide sequence similarities of only 34% to 44% were found with sequenced viruses indicating no close affinities with any other potyvirus. The potyvirus 3' sequence amplification procedure is simple and rapid, is potentially useful in developing virus specific probes and may be used to differentiate strains and species of potyviruses on the basis of the 3' UTR sequences.

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.

Production and characteristics of strain common antibodies against a synthetic polypeptide corresponding to the C-terminal region of potato virus Y coat protein

Comparing the predicted amino acid sequence between two Japanese potato virus Y (PVY) strains, necrotic strain and ordinary strain, it was found that the C-terminal regions (H2N-HTTEDVSPSMHTLLGVKNM-COOH) of the coat proteins in the two strains were completely conserved. The conserved amino acid sequence was also found in the C-terminal region coat protein of PVY-36, a strain which did not react with monoclonal antibodies specific to the necrotic and the ordinary strain respectively. Antibodies were produced against a synthetic polypeptide PVY-C19 consisting of 19 amino acids, which correspond to the C-terminal region of the coat protein, using 4 coupling combinations of polypeptide PVY-C19 to protein carriers. Carrier-free polypeptides and those coupled to ovalbumin with ECDI (ethyl-dimethylaminopropyl carbodiimide) produced high titer of antibodies and detected PVY strains from PVY-infected plants by Western blot analysis and by ELISA.

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.

A comparison of pepper mottle virus with potato virus Y and evidence for their distinction

Pepper mottle virus (PepMOV) was identified as a distinct potyvirus infecting peppers in Arizona and Florida in the 1970's. The distinction of PepMoV from potato virus Y (PVY) has recently been challenged on the basis of sequence comparisons of the coat proteins and of the 3' nontranslated regions of the viral RNAs. We summarize the biological, cytological, serological, and in vitro translational studies which compare the apparent differences, and also similarities, between PepMoV and PVY. We conclude that although PepMoV may be more closely related to PVY than to other known potyvirus, PepMoV should be maintained as a separate virus on the basis of its distinctive characteristics.

Is pepper mottle virus a strain of potato virus Y?

On the basis of serological properties and host plant reactions pepper mottle virus (PepMoV) has been classified as a potyvirus related to, but distinct from, other pepper-infecting potyviruses, potato virus Y (PVY) and tobacco etch virus (TEV). Recent amino acid and nucleotide sequence data show that PepMoV is more closely related to PVY than previously assumed. PepMoV shows a high degree of homology to various PVY strains in both the coat protein and the 3' non-translated sequences, while unrelated potyviruses are generally less homologous in these regions. Detailed coat-protein amino acid sequence and 3' non-translated region (3' NTR) nucleotide sequence comparisons described in this paper confirm the close relationship between PepMoV and PVY and it is concluded that the isolate sequenced indeed represents a strain of PVY. Sequence data for several strains of PVY gave two groups with closer relationships among strains in a group than between groups.