Coat protein of potyviruses. 6. Amino acid sequences suggest watermelon mosaic virus 2 and soybean mosaic virus-N are strains of the same potyvirus

Potyviruses and the digital revolution

The potyviruses are one of the two most speciose taxa of plant viruses. Our expanded knowledge of the breadth and depth of their diversity and its origins has depended greatly on the use of computing and the Internet in biological research and is reviewed here. We report a fully supported phylogeny based on gene sequence data for approximately half the named species. The phylogeny shows that the genus probably originated from a virus of monocotyledonous plants and that it first diverged approximately 7250 years ago in Southwest Eurasia or North Africa. The use of computer programs to better understand the structure and evolutionary trajectory of potyvirus populations is illustrated. The review concludes with recommendations for improving potyvirus nomenclature and the databasing of potyvirus information.

Determination of the taxonomic position and characterization of yam mosaic virus isolates based on sequence data of the 5'-terminal part of the coat protein cistron

The sequences of the N-terminal part of the coat protein cistron from six isolates of yam mosaic virus (YMV-TOG, YMV-COT, YMV-12, YMV-CAR, YMV-BU1 and YMV-BU2) were determined. The analysis of the deduced amino acid sequences revealed the presence of consensus motifs characteristic of the potyvirus genus supporting the classification of YMV as a potyvirus member. The alignment of the N-terminal part of the coat protein of YMV-TOG, YMV-COT, YMV-12 and YMV-CAR showed that they were identical in size (152 aa) while YMV-BU1 and YMV-BU2 were shorter (140 aa) due to a deletion of 12 aa. These amino acid sequences exhibit an overall sequence identity ranging from 70.4% to 97.4% while the identity level with the other potyviruses sequenced in the considered region is below 50%, confirming that YMV is a distinct member of the potyvirus genus. The detailed analysis of the amino acid sequence alignment and of the identity levels observed between the N-terminal part of the coat protein of the six YMV isolates lead us to suggest that they have to be considered as distantly related strains of YMV rather than closely related but distinct viruses.

Variability in the length of the amino terminal sequence contributes to the capsid protein diversity among dasheen mosaic potyvirus isolates

Western blot analysis of several dasheen mosaic virus isolates revealed molecular weight differences among their capsid proteins (CPs). Sequence analysis of the CP gene showed that the CP of isolate TEN was 15 amino acids shorter than that of isolate LA due to a 57-base deletion and a 12-base insertion into the 5' end of the TEN CP gene. Our data suggest that frequent deletions and insertions are responsible for the CP size diversity among DMV isolates.

Inheritance of resistance to potyviruses in Phaseolus vulgaris L. II. Linkage relations and utility of a dominant gene for lethal systemic necrosis to soybean mosaic virus

A single dominant factor, Hss, that conditions a rapid lethal necrotic response to soybean mosaic virus (SMV) has been identified in Phaseolus vulgaris L. cv. 'Black Turtle Soup', line BT-1. Inoculated plants carrying this factor developed pinpoint necrotic lesions on inoculated tissue followed by systemic vascular necrosis and plant death within about 7 days, regardless of ambient temperature. BT-1 also carries dominant resistance to potyviruses attributed to the tightly linked or identical factors, I, Bcm, Cam, and Hsw, so linkage with Hss was evaluated. No recombinants were identified among 381 F3 families segregating for potyvirus susceptibility, thus if Hss is a distinct factor, it is tightly linked to I, Bcm, Cam, and Hsw. BT-1 was also crossed reciprocally with the line 'Great Northern 1140' ('GN 1140') in which the dominant gene, Smv, for systemic resistance to SMV was first identified. Smv and Hss segregated independently and are co-dominant. The ('GN 1140' x BT-1) F1 populations showed a seasonal shift of the codominant phenotype. Evaluation of the ('GN 1140' x BT-1) F2 population under conditions where Smv is partially dominant allowed additional phenotypic classes to be distinguished. Pathotype specificity has not been demonstrated for either Smv or Hss. Genotypes that are homozygous for both dominant alleles are systemically resistant to the virus and in addition show undetectable local viral replication or and no seed transmission. This work demonstrates that a gene which conditions a systemic lethal response to a pathogen may be combined with additional gene(s) to create an improved resistant phenotype.

Nucleotide sequence, serology and symptomatology suggest that vanilla necrosis potyvirus is a strain of watermelon mosaic virus II

Vanilla necrosis potyvirus (VNV) is the cause of significant losses to the South Pacific islands vanilla crop. The gene for the coat protein of VNV has been cloned and sequenced. Comparison of this gene with other potyviral coat protein sequences revealed 97% nucleotide sequence homology (98% amino acid homology) to a US isolate of watermelon mosaic virus II (WMV-II), 93% nucleotide sequence homology (96% amino acid homology) to an Australian isolate of WMV-II and 81% nucleotide sequence homology (88% amino acid homology) to soybean mosaic virus-N (SMV-N). Serological analysis, by Western blot and ELISA, confirmed the close relationship between VNV and WMV-II. Furthermore, a limited host range determination found VNV and WMV-II able to infect the same series of test plants. However, symptoms differed significantly on three test species demonstrating that VNV and WMV-II are not identical in biological properties. We suggest that VNV be renamed WMV-II (Tonga).

Watermelon mosaic virus-Morocco is a distinct potyvirus

The relationship of the Morocco isolate of watermelon mosaic virus (WMV) to WMV2, soybean mosaic virus (a virus closely related to WMV2) and the W strain of papaya ringspot virus (PRSV-W), formerly WMV1, was examined by comparing tryptic peptide profiles using high performance liquid chromatography. The profiles indicated that the coat protein sequence of WMV-Morocco differed substantially from those of the other potyviruses. This conclusion was supported by sequence data from five tryptic peptides from the coat protein of WMV-Morocco, which showed only 61-68% identity to equivalent sequences in PRSV-W, WMV2 and zucchini yellow mosaic, another potyvirus infecting cucurbits. Based on the above data, and on known correlations between coat protein sequence similarities and potyvirus relationship, it is concluded that WMV-Morocco should be regarded as a distinct potyvirus.

Detection of potyviruses with antisera to synthetic peptides

Eight peptides corresponding to conserved regions of the coat protein of potyviruses were synthesized. All the peptides were recognized by anti-virus or anti-core-virus. Antisera raised to the synthetic peptides were tested with purified viruses and viral antigens present in plant sap. In many cases, the extent of cross-reactivity between different potyviruses was not correlated with the degree of sequence homology between the peptide used for immunization and the corresponding region in the coat protein of the potyvirus tested. An antiserum raised to a peptide of 18 residues containing a highly conserved region was found to react with all seven potyviruses tested.

Cross-reactive potential of monoclonal antibodies raised against proteolysed tobacco etch virus

Monoclonal antibodies (mAb) capable of reacting with different potyviruses were obtained by immunizing mice with proteolysed tobacco etch virus. The mAb were not equally effective in all ELISA formats and some were specific for different conformational states of the viral coat protein. The mAb also detected antigenic differences between purified virus particles and viral antigen in infected plant sap. In an ELISA format using antigen-coated plates, 5 different potyviruses (out of 7 viruses tested) could be detected in plant sap by one mAb. Different combinations of mAb and polyclonal antiserum could also be used for detecting several potyviruses 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.

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.

Differentiation of potyviruses and their strains by hybridization with the 3' non-coding region of the viral genome

Nucleic acid hybridization with the 3' non-coding region of the potyvirus genome as the probe was shown to be a relatively simple means of distinguishing between distinct potyviruses and their strains. Comparisons of the nucleotide sequences of potyvirus genomes (ignoring gaps) showed that the degree of identity between equivalent genes of strains was greater than 96%, while between distinct potyviruses the identity ranged from 42% to 65%, suggesting that any extended sequence could be considered representative of the whole genome and be suitable as a diagnostic probe. The comparisons however, also revealed that some parts of the genome, but not the 3' non-coding region, had local regions of high sequence identity that could lead to cross-hybridization between distinct potyviruses. For this reason, and because its location immediately upstream of the poly(A) tail makes it the most accessible region for the purpose of cloning and sequencing, the 3' non-coding sequence should be most suitable for use as a diagnostic probe. Successful hybridizations (using radiolabeled, polymerase chain reaction-amplified 3' non-coding sequences) have been achieved by probing recombinant clones, purified potyviral RNA, partially purified total RNA from infected plants, and a crude extract of infected plant tissue. The method has been used to support the proposals that watermelon mosaic virus 2 and soybean mosaic virus-N are both strains of the same virus, and to discriminate between several isolates previously believed to be strains of sugarcane mosaic virus. The method should have wide application as a means of differentiating distinct potyviruses from strains.

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.

Systematic fractionation of serum antibodies using multiple antigen homologous peptides as affinity ligands

The fractionation of polyclonal antibodies on multiple peptide ligands is described. The method is an application of a procedure for the synthesis of large numbers of peptides on individual polyethylene pins (Geysen et al., 1987). In this application, each pin-bound peptide is used as an affinity support. Antibodies bound to the peptides are then eluted, using buffers of either high or low pH. Each eluted antibody is then tested for specific binding to peptides or proteins, using ELISA procedures. A rabbit antiserum raised to gonococcal pilin was fractionated on a complete set of octapeptides homologous with the sequence of the pilin protein. Antibodies eluted from some of the peptides bound to pilin in solution. In a second example three hyperimmune sera raised to three different potyviruses were fractionated on their respective homologous peptide sequences. Testing the eluted antibodies on the three virus coat proteins revealed peptides which bound cross-reacting antibodies. Thus the method can be used to confirm direct peptide binding evidence for sequential epitopes. These peptides can then be used in affinity chromatography to increase the specificity of polyclonal sera. This can be achieved either by elution of the specific antibody from the peptide or by removal of cross-reacting antibodies from the whole serum by absorption on peptide.

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.

Nucleotide sequence of the 3' terminal region of lettuce mosaic potyvirus RNA shows a Gln/Val dipeptide at the cleavage site between the polymerase and the coat protein

DNA complementary to the 3' terminal 1651 nucleotides of the genome of the common strain of lettuce mosaic virus (LMV-O) has been cloned and sequenced. Microsequencing of the N-terminus enabled localization of the coat protein gene in this sequence. It showed also that the LMV coat protein coding region is at the 3' end of the genome, and that the coat protein is processed from a larger protein by cleavage at an unusual Q/V dipeptide between the polymerase and the coat protein. This is the first report of such a site for cleavage of a potyvirus polyprotein, where only Q/A, Q/S, and Q/G cleavage sites have been reported. The LMV coat protein gene encodes a 278 amino acid polypeptide with a calculated Mr of 31,171 and is flanked by a region which has a high degree of homology with the putative polymerase and a 3' untranslated region of 211 nucleotides in length. Percentage of homology with the coat protein of other potyviruses confirms that LMV is a distinct member of this group. Moreover, amino acid homologies noticed with the coat protein of potexvirus, bymovirus, and carlavirus elongated plant viruses suggest a functional significance for the conserved domains.

Identification and classification of potyviruses on the basis of coat protein sequence data and serology. Brief review

The identification and classification of potyviruses has been in a very unsatisfactory state due to the large size of the group, the apparent vast variation among the members and the lack satisfactory taxonomic parameters that will distinguish distinct viruses from strains. In the past, use of classical methods, such as host range and symptomatology, cross-protection, morphology of cytoplasmic inclusions and conventional serology, revealed a "continuum" implying that the "species" and "strain" concepts cannot be applied to potyviruses. In contrast nucleic acid and amino acid sequence data of coat proteins has clearly demonstrated that potyviruses can be divided into distinct members and strains. This sequence data in combination with information of the structure of the potyvirus particle has been used to develop simple techniques such as HPLC peptide profiling, serology (using polyclonal antibody probes obtained by cross-adsorption with core protein from trypsin treated particles) and cDNA hybridization. These findings, along with immunochemical analyses of overlapping synthetic peptides have established the molecular basis for potyvirus serology; explained many of the problems associated with the application of conventional serology; and provided a sound basis for the identification and classification of potyviruses. As a result, the virus/strain status of some potyviruses has been redefined, requiring a change in the potyvirus nomenclature. These new developments necessitate a re-evaluation of the earlier literature on symptomatology, cross-protection, cytoplasmic inclusion body morphology and serology.