Towards a system for the identification and classification of potyviruses. I. Serology and amino acid composition of six distinct viruses

Complete genome sequencing and construction of full-length infectious cDNA clone of papaya ringspot virus-HYD isolate and its efficient in planta expression

Papaya ringspot virus (PRSV) is a devastating Potyvirus that causes papaya ringspot disease in Carica papaya plantations globally. In this study, the complete genome sequence of a PRSV isolate from Shankarpalli, Telangana, India, was reported and designated as PRSV-HYD (KP743981.1). The genome is a single-stranded positive-sense RNA comprising 10,341 nucleotides. Phylogenetic analysis revealed that PRSV-HYD is closely related to PRSV Pune (Aundh) isolate with 92 and 95% nucleotide and amino acid sequence identity, respectively. To develop infectious cDNA (icDNA), the complete nucleotide sequence of PRSV-HYD was cloned between the right and left borders in the binary vector pCB301 using BglII and XmaI restriction sites. Cauliflower mosaic virus (CaMV) double promoter (35S) was fused at the 5'-end and Avocado sunblotch viroid (ASBVd) ribozyme (RZ) sequence was fused to the 3' end to generate an authentic 3' viral end in the transcribed mRNAs. The icDNA generated was mobilized into the Agrobacterium tumefaciens EHA 105, and the agrobacterial cultures were infiltrated into the natural host C. papaya and a non-host Nicotiana benthamiana plants; both did not show any symptoms. In RT-PCR analysis of RNAs isolated from N. benthamiana, we could detect viral genes as early as 3 days and continued up to 28 days post infiltration. Alternatively, virion particles were purified from agroinfiltrated N. benthamiana plants and introduced into C. papaya by mechanical inoculation as well as by pinprick method. In both cases, we could see visible systemic symptoms similar to that of wild type by 40 days. Additionally, we studied the expression patterns of the genes related to plant defense, transcription factors (TFs), and developmental aspects from both C. papaya and N. benthamiana.

Potyviral coat protein and genomic RNA: A striking partnership leading virion assembly and more

Potyvirus genus clusters a significant and expanding number of widely distributed plant viruses, responsible for large losses impacting most crops of economic interest. The potyviral genome is a single-stranded, linear, positive-sense RNA of around 10kb that is encapsidated in flexuous rod-shaped filaments, mostly made up of a helically arranged coat protein (CP). Beyond its structural role of protecting the viral genome, the potyviral CP is a multitasking protein intervening in practically all steps of the virus life cycle. In particular, interactions between the CP and the viral RNA must be tightly controlled to allow the correct assignment of the RNA to each of its functions through the infection process. This review attempts to bring together the most relevant available information regarding the architecture and modus operandi of potyviral CP and virus particles, highlighting significant discoveries, but also substantial gaps in the existing knowledge on mechanisms orchestrating virion assembly and disassembly. Biotechnological applications based on potyvirus nanoparticles is another important topic addressed here.

Bean Common Mosaic Virus and Bean Common Mosaic Necrosis Virus: Relationships, Biology, and Prospects for Control

The closely related potyviruses Bean common mosaic virus (BCMV) and Bean common mosaic necrosis virus (BCMNV) are major constraints on common bean (Phaseolus vulgaris) production. Crop losses caused by BCMV and BCMNV impact severely not only on commercial scale cultivation of this high-value crop but also on production by smallholder farmers in the developing world, where bean serves as a key source of dietary protein and mineral nutrition. In many parts of the world, progress has been made in combating BCMV through breeding bean varieties possessing the I gene, a dominant gene conferring resistance to most BCMV strains. However, in Africa, and in particular in Central and East Africa, BCMNV is endemic and this presents a serious problem for deployment of the I gene because this virus triggers systemic necrosis (black root disease) in plants possessing this resistance gene. Information on these two important viruses is scattered throughout the literature from 1917 onward, and although reviews on resistance to BCMV and BCMNV exist, there is currently no comprehensive review on the biology and taxonomy of BCMV and BCMNV. In this chapter, we discuss the current state of our knowledge of these two potyviruses including fundamental aspects of classification and phylogeny, molecular biology, host interactions, transmission through seed and by aphid vectors, geographic distribution, as well as current and future prospects for the control of these important viruses.

Potato virus Y HCPro localization at distinct, dynamically related and environment-influenced structures in the cell cytoplasm

Potyvirus HCPro is a multifunctional protein that, among other functions, interferes with antiviral defenses in plants and mediates viral transmission by aphid vectors. We have visualized in vivo the subcellular distribution and dynamics of HCPro from Potato virus Y and its homodimers, using green, yellow, and red fluorescent protein tags or their split parts, while assessing their biological activities. Confocal microscopy revealed a pattern of even distribution of fluorescence throughout the cytoplasm, common to all these modified HCPros, when transiently expressed in Nicotiana benthamiana epidermal cells in virus-free systems. However, in some cells, distinct additional patterns, specific to some constructs and influenced by environmental conditions, were observed: i) a small number of large, amorphous cytoplasm inclusions that contained α-tubulin; ii) a pattern of numerous small, similarly sized, dot-like inclusions distributing regularly throughout the cytoplasm and associated or anchored to the cortical endoplasmic reticulum and the microtubule (MT) cytoskeleton; and iii) a pattern that smoothly coated the MT. Furthermore, mixed and intermediate forms from the last two patterns were observed, suggesting dynamic transports between them. HCPro did not colocalize with actin filaments or the Golgi apparatus. Despite its association with MT, this network integrity was required neither for HCPro suppression of silencing in agropatch assays nor for its mediation of virus transmission by aphids.

Virus diseases in lettuce in the Mediterranean basin

Lettuce is frequently attacked by several viruses causing disease epidemics and considerable yield losses along the Mediterranean basin. Aphids are key pests and the major vectors of plant viruses in lettuce fields. Lettuce mosaic virus (LMV) is probably the most important because it is seed-transmitted in addition to be transmissible by many aphid species that alight on the crop. Tomato spotted wilt virus (TSWV) is another virus that causes severe damage since the introduction of its major vector, the thrips Frankliniella occidentalis. In regions with heavy and humid soils, Lettuce Mirafiori big-vein virus (LMBVV) can also produce major yield losses.

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.

Estimation of the number of virus particles transmitted by an insect vector

Plant viruses are submitted to narrow population bottlenecks both during infection of their hosts and during horizontal transmission between host individuals. The size of bottlenecks exerted on virus populations during plant invasion has been estimated in a few pathosystems but is not addressed yet for horizontal transmission. Using competition for aphid transmission between two Potato virus Y variants, one of them being noninfectious but equally transmissible, we obtained estimates of the size of bottlenecks exerted on an insect-borne virus during its horizontal transmission. We found that an aphid transmitted on average 0.5-3.2 virus particles, which is extremely low compared with the census viral population into a plant. Such narrow bottlenecks emphasize the strength of stochastic events acting on virus populations, and we illustrate, in modeling virus emergence, why estimating this parameter is important.

Characterization of a New Potyvirus Naturally Infecting Chickpea

During the 1999 to 2001 growing seasons, symptoms consisting of mosaic, stunting, yellowing, wilting, shortening of internodes, and phloem discoloration were observed in chickpea (Cicer arietinum) grown in the Department of Chuquisaca in southern Bolivia. In some fields, approximately 10% of the plants exhibited viruslike symptoms and suffered greatly reduced seed yields. Lentil (Lens culinaris) was also observed to be infected but not pea (Pisum sativum) or faba bean (Vicia faba) growing in nearby fields. Infected chickpea tissue reacted positively to the potyvirus group-specific monoclonal antibody (MAb), but there was no serological reaction with antisera to the potyviruses Bean yellow mosaic virus, Clover yellow vein virus, Cowpea aphid-borne mosaic virus, Pea seedborne mosaic virus, Bean common mosaic virus, or Bean common mosaic necrosis virus. Western blots of total protein extracts probed with the potyvirus MAb revealed a single band ca. 32 kDa. Comparative sequence analysis of cDNA clones generated from the putative coat protein gene consisted of 282 amino acids (31.9 kDa) and showed moderate identities of 67, 66, 63, 63, and 61% with the coat proteins of potyviruses Pepper severe mosaic virus, Pepper yellow mosaic virus, Potato virus Y, Plum pox virus, and Pepper mottle virus, respectively. Phylogenetic analysis of the coat protein amino acid sequence revealed that this virus is a unique member of the family Potyviridae and is phylogenetically most closely related to a group of Solanaceae-infecting potyviruses rather than to other legumeinfecting potyviruses. The proposed name for the new causal agent is Chickpea yellow mosaic virus.

Characterization of a monoclonal antibody recognizing a DAG-containing epitope conserved in aphid transmissible potyviruses: evidence that the DAG motif is in a defined conformation

Two viral proteins, the helper component-protease and the coat protein, are required for the non-persistent aphid transmission of potyviruses. In the potyvirus coat protein, the tripeptide aspartate-alanine-glycine (DAG) has often been shown to be involved. A monoclonal antibody, raised against a synthetic decapeptide containing the DAG tripeptide, reacted with the peptide as well as with isolates of soybean mosaic, tobacco etch and tobacco vein mottling potyviruses. Experiments indicate that the monoclonal antibody recognizes a conformational rather than a sequential epitope. The data support the suggestion that the DAG region plays a structural role to determine a coat protein-helper component-protease conformation that influences aphid transmission.

Banana bract mosaic virus: characterisation using potyvirus specific degenerate PCR primers

Banana bract mosaic (BBMV) is a relatively new, non-persistently aphid transmitted disease of bananas in the Philippines. Partially purified preparations from infected plants contained low numbers of flexuous virions, 660 to 760 nm in length, and a 38kDa protein, possibly the coat protein, which reacted with a general potyvirus antiserum in western blots. There were insufficient virions for conventional antiserum production or cDNA synthesis. Therefore, DNA was amplified using potyvirus-specific degenerate primers and reverse transcriptase PCR. The PCR products were cloned, sequenced and analysed and contained a 5' open reading frame of up to 150 amino acids and a 3' untranslated region of up to 190 nucleotides which were clearly related to the C-terminal half of the coat proteins and the 3' untranslated regions, respectively of potyviruses. The BBMV open reading frame amino acid sequence was most similar to the C-terminal half of the maize dwarf mosaic potyvirus coat protein (71.3% similarity) and the BBMV 3' untranslated region was most similar to that of ornithogalum mosaic potyvirus (39.6% similarity). Our results show that BBMV is a distinct potyvirus and also demonstrate the application of virus group specific primers in the characterisation of previously undescribed viruses.

A single amino acid substitution at N-terminal region of coat protein of turnip mosaic virus alters antigenicity and aphid transmissibility

The antigenic activity of the N-terminal region of coat protein of turnip mosaic virus (TuMV) aphid transmissible strain 1 and non-transmissible strain 31 was examined by using a panel of monoclonal antibodies (MAbs) raised against the two virus strains as well as antisera raised against several synthetic peptides from the N-terminal region of the protein. The reactivity of these antibodies was tested in ELISA and in a biosensor system (BIAcore Pharmacia) using virus particles, dissociated coat protein and synthetic peptides as antigens. Substitution of a single amino acid at position 8 in the coat protein of TuMV strain 1 abolished any cross-reactivity between MAbs to strain 1 and the substituted peptide (strain 31) in ELISA although some cross-reactivity was apparent in BIAcore inhibition experiments. In reciprocal tests with MAbs to strain 31 no cross-reactivity with the heterologous peptide was detected in either type of assay. The amino acid residue present at position 8 appears to play a critical role in the binding capacity of MAbs specific for the N-terminal region of TuMV. Antiserum to a synthetic peptide corresponding to residues 1-14 of the protein of TuMV strain 1 was found to react strongly with dissociated coat protein and intact virus particles and was able to inhibit the aphid transmission of the virus. Antiserum to the corresponding peptide of strain 31 did not have this capacity.

Nucleotide sequence of the 3'-terminal region of the genome confirms that pea mosaic virus is a strain of bean yellow mosaic potyvirus

The 1,035 nucleotides at the 3'end of the I strain of pea mosaic potyvirus (PMV-I) genomic RNA, encoding the coat protein, have been cloned and sequenced. A comparison of the derived coat protein sequence with those of the bean yellow mosaic virus (BYMV) strains, CS, S, D and GDD, indicates that PMV-I is a strain of BYMV. Sequence comparisons and hybridisation studies using the 3'-noncoding region support this classification. The nucleotide and protein sequence data also suggest that PMV-I and BYMV-CS form one subset of BYMV strains while the other three strains form another.

Evolutionary relationships among bean common mosaic virus strains and closely related potyviruses

Bean common mosaic virus (BCMV) consists of a large number of strains with complex and controversial relationships among them and with other potyviruses that infect legumes. In order to elucidate the BCMV taxonomic pattern and its evolutionary implications, a phylogenetic analysis has been carried out. The analysis of the coat protein gene and 3' non-coding region (NCR) sequences recently obtained by us and other currently available potyviral sequences confirms the clustering of viruses comprised in BCMV strains with other closely related potyviruses and reveals the great informative content of 3' NCR, suggesting a more relevant role for this region in phylogenetic analysis.

In vitro destabilization of plant viruses and cDNA synthesis

DNA copies of a wide range of RNA viruses can be made by the direct addition of appropriately treated, purified virus particles to a reverse transcription reaction. Therefore, many problems associated with RNA isolation can be circumvented. Virus particles can be sufficiently destabilized by adjustments of salt content, buffer, pH or by the use of physical force supplied by a freeze/thaw cycle so that RNA in sufficient quantity and physical condition is available for the synthesis of in some cases, full length cDNAs. cDNAs have been made of viruses in the bromo-, poty-, carla-, ilar-, potex-, tobra and tobamovirus groups. Reported here are experiments with cowpea chlorotic mottle virus and bean common mosaic virus.

Characterization of epitopes recognized by monoclonal antibodies to aphid transmissible and non-transmissible strains of turnip mosaic virus

Fourteen monoclonal antibodies (MAbs) were prepared against two strains of turnip mosaic virus (TuMV) differing in aphid transmissibility. Serological specificity of fourteen MAbs against the two strains was tested by indirect ELISA. Three MAbs were able to distinguish aphid transmissible TuMV strain 1 from non-aphid transmissible strain 31 while four MAbs reacted only with strain 31. No cross-reactivity between the two strains was found using these specific MAbs. Based upon the ability of Mab to inhibit the reaction of other MAbs, antibody competition test indicated that fourteen MAbs recognized six different epitopes on the virus particle; MAbs specific to strain 1 recognized two epitopes while MAbs specific to strain 31 also recognized two epitopes. The remaining two epitopes are common. Since the six amino acid differences between the coat proteins of the two strains were found at the N-terminal regions, MAbs specific to strain 1 or 31 bound to the different epitopes on the N-terminal regions in coat proteins of the two strains.

Characterisation and epitope analysis of monoclonal antibodies to virions of clover yellow vein and Johnsongrass mosaic potyviruses

Mouse monoclonal antibodies (MAbs) against the Australian B strain of clover yellow vein (ClYVV-B) and the JG strain of Johnsongrass mosaic (JGMV) potyviruses were produced, characterised and the epitopes with which they reacted were deduced. Using intact particles of ClYVV a total of ten MAbs were obtained which reacted strongly with ClYVV-B in an enzyme-linked immunosorbent assay and Western blots. Four of these MAbs (1, 2, 4, and 13) were found to be ClYVV-specific, as they reacted with all five ClYVV strains from Australia and the U.S.A. but not with 11 strains of bean yellow mosaic (BYMV), pea mosaic (PMV), and white lupin mosaic (WLMV) viruses which, together with ClYVV, form the BYMV subgroup of potyvirses. These MAbs failed to react with eight other potyvirus species, including six which infect legumes like the viruses in the BYMV subgroup. The ClYVV MAb 10 was found to be BYMV subgroup-specific. It reacted strongly with 15 of the 16 strains of viruses in the subgroup and gave no reaction with eight other potyviruses. The other five ClYVV MAbs reacted with varying degrees of specificity with the BYMV subgroup viruses and also with other potyviruses. Eight of the ClYVV MAbs (1, 2, 4, 5, 13, 17, 21, and 22) reacted with the intact coat proteins only and not with the truncated (minus amino terminus) coat protein of ClYVV suggesting that the epitopes for these MAbs are located in the surface-exposed, amino-terminal region of the ClYVV coat protein. Comparison of published coat protein sequences of BYMV and ClYVV isolates indicated that the epitopes for the four ClYVV-specific MAbs may be in the amino-terminal region spanning amino acid residues 18 to 30, whereas those for the other four MAbs may be located in the first 17 amino-terminal amino acid residue region. The epitopes that reacted with BYMV subgroup-specific MAb 10 and MAb 30 which reacted with 20 of the 24 potyvirus isolates, are probably located in the core region of ClYVV coat protein as these MAbs reacted with the intact as well as truncated coat protein of ClYVV. Analysis, in Western blot immunoassay, of 17 MAbs raised against virions of JGMV revealed that only two MAbs (1-25 and 4-30) were JGMV-specific, whereas others displayed varying degrees of specificity to different potyviruses.(ABSTRACT TRUNCATED AT 400 WORDS)

The coat protein genes of squash mosaic virus: cloning, sequence analysis, and expression in tobacco protoplasts

Complementary DNA of the middle-component RNA of the melon strain of squash mosaic comovirus (SqMV) was cloned. Clones containing the coat protein genes were identified by hybridization with a degenerate oligonucleotide synthesized according to the amino acid sequence of a purified peptide fragment of the SqMV large coat protein. A clone containing of 2.5 kbp cDNA insert of SqMV M-RNA was sequenced. The total insert sequence of 2510 bp included a 2373 bp open reading frame (ORF) (encoding 791 amino acids), a 123 bp 3'-untranslated region, and a poly(A) region. This ORF is capable of encoding both the 42 and 22 k SqMV coat proteins. Direct N-terminal sequence analysis of the 22 k coat protein revealed its presence at the 3' end of this ORF and the position of the proteolytic cleavage site (Q/S) used to separate the large and small coat proteins from each other. A putative location of the N-terminal proteolytic cleavage site of the 42 k coat protein (Q/N) was predicted by comparisons with the corresponding coat proteins of cowpea mosaic virus, red clover mottle virus, and bean-pod mottle virus. Although the available nucleotide sequences of these viruses revealed little similarity, their encoded coat proteins shared about 47% identity. The identity of the encoded 42 k and 22 k peptides was confirmed by engineering the respective gene regions for expression followed by transfer into tobacco protoplasts using the polyethylene glycol method. Both SqMV coat proteins were expressed in vivo as determined by their reactivity to SqMV coat protein specific antibodies.

Bean yellow mosaic, clover yellow vein, and pea mosaic are distinct potyviruses: evidence from coat protein gene sequences and molecular hybridization involving the 3' non-coding regions

The sequences of the 3' 1019 nucleotides of the genome of an atypical strain of bean yellow mosaic virus (BYMV-S) and of the 3' 1018 nucleotides of the clover yellow vein virus (CYVV-B) genome have been determined. These sequences contain the complete coding region of the viral coat protein followed by a 3' non-coding region of 173 and 178 nucleotides for BYMV-S and CYVV-B, respectively. When the deduced amino acid sequences of the coat protein coding regions were compared, a sequence identity of 77% was found between the two viruses, and optimal alignment of the 3' untranslated regions of BYMV-S and CYVV-B gave a 65% identity. However, the degree of homology of the amino acid sequences of coat proteins of BYMV-S with the published sequences for three other strains of BYMV ranged from 88% to 94%, while the sequence homology of the 3' untranslated regions between the four strains of BYMV ranged between 86% and 95%. Amplified DNA probes corresponding to the 3' non-coding regions of BYMV-S and CYVV-B showed strong hybridization only with the strains of their respective viruses and not with strains of other potyviruses, including pea mosaic virus (PMV). The relatively low sequence identities between the BYMV-S and CYVV-B coat proteins and their 3' non-coding regions, together with the hybridization results, indicate that BYMV, CYVV, and PMV are distinct potyviruses.

Untranslatable transcripts of the tobacco etch virus coat protein gene sequence can interfere with tobacco etch virus replication in transgenic plants and protoplasts

Transgenic tobacco plants which express untranslatable sense or antisense forms of the tobacco etch virus potyvirus (TEV) coat protein (CP) gene sequence have been generated. One of seven transgenic plant lines expressing a CP gene antisense transcript showed an attenuation of symptoms when inoculated with TEV. Three of ten transgenic plant lines expressing untranslatable sense transcripts did not develop symptoms when inoculated with TEV. These lines were resistant to either aphid or mechanically transmitted TEV. In contrast to CP-mediated resistance reported for other viruses, resistance was (1) mediated by an RNA molecule; (2) TEV-specific (i.e., "broad-spectrum resistance" was not observed); (3) independent of inoculum levels; (4) not dependent on plant size and; (5) due to decreased levels of virus replication. Protoplast experiments were used to demonstrate that resistant plant lines did not support the production of virus protein and progeny virus at wild-type levels.

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.

The nucleotide sequence of the coat protein gene and 3' untranslated region of papaya ringspot virus type W (Aust)

The nucleotide sequence of the 3' terminal region of the Australian isolate of papaya ringspot virus type W [PRSV-W (Aust)] was determined. An open reading frame (864 bp), encoding the putative coat protein gene, occurs upstream of the putative 3' untranslated region (206 bp) and poly(A) tail. A 23 amino acid sequence was obtained from N-terminal analysis of the coat protein from purified virions. This sequence has 100% homology with a region of the amino acid sequence inferred from the nucleic acid sequence of the coat protein gene. However, this region is 13 amino acids downstream from the N terminus predicted for two American isolates of PRSV. The coat protein gene of PRSV-W (Aust) was shown to have 96.8% and 96.4% nucleotide sequence similarity with American isolates of PRSV-W and PRSV-P, respectively.

Protection against detrimental effects of potyvirus infection in transgenic tobacco plants expressing the papaya ringspot virus coat protein gene

We obtained transgenic tobacco plants expressing the papaya ringspot virus (PRV) coat protein (CP) gene by transformation via Agrobacterium tumefaciens. Expression was effectively monitored by enzyme-linked immunosorbent assays (ELISA) of crude tissue extracts. Subcloned plants derived from eight original Ro transformants were inoculated with potyviruses: tobacco etch (TEV), potato virus Y (PVY), and pepper mottle (PeMV). Plants that accumulated detectable levels of the PRV CP showed significant delay in symptom development and the symptoms were attenuated. Similar results were obtained with inoculated R1 plants. We conclude that the expression of the PRV CP-gene imparts protection against infection by a broad spectrum of potyviruses.

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.

Purification of plant viruses and virus coat proteins by high performance liquid chromatography

High performance liquid chromatography (HPLC) gel filtration has been successfully applied in the purification of elongated and isometric plant viruses. Two different approaches have been tested. In one approach, semi-purified virus particles were dissociated with lithium chloride and the released coat proteins purified by HPLC gel filtration. The purified coat protein was highly immunogenic and gave rise to very specific antisera reacting with intact virus particles as well as with SDS-denatured coat protein monomers. This method is generally applicable only for elongated viruses since many isometric viruses are not dissociated by the lithium chloride treatment. The second approach consisted in gel filtration of native, undissociated virus particles and could be used both with elongated and isometric viruses. Both methods were fast and simple to perform and removed all or most of the contaminating plant proteins as judged by sodium dodecylsulphate gel electrophoresis followed by silver staining or by immunoblotting with antiserum against healthy plant extracts. With both methods the recovery of virus coat protein was about 30% on average.

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.

A general method for the detection of potyviral gene products in plant protoplasts and tissue

A rapid immunostaining procedure for detecting potyviral antigens in individual protoplasts, isolated mesophyll cells, and epidermal strips of Nicotiana tabacum is described. Although all specific antibodies tested detected potyviral antigens in electroporated protoplasts, those against cytoplasmic inclusion (CI) protein provided the most useful results. The number of protoplasts reacting with anti-CI increased with time after inoculation, roughly in parallel with the accumulation of capsid protein, which was measured independently by enzyme-linked immunosorbent assay. Potyviral gene products were also detected in epidermal strips and mesophyll cells separated from systemically infected leaves, indicating that the immunostaining method is generally applicable and that it may prove useful for studying the movement of potyviruses from cell to cell in intact plants.

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

The sequence of the 3'-terminal 1,134 nucleotides of the genome of a New Zealand isolate of a necrotic strain of potato virus Y (PVYN) has been determined. This sequence contains one large open reading frame of 796 nucleotides, the start of which was not identified, which is capable of encoding a protein of 264 amino acid residues with a molecular weight of 29,631. Comparison of the amino acid sequence with a published coat protein sequence of another strain, PVY-D, and with the amino acid sequence deduced from PeMV cDNA sequence data, confirms that the 3' cistron encodes the viral coat protein in PVYN. Adjacent to the 3' end of the coding region there is an untranslatable sequence of 326 nucleotides terminating in a polyadenylate tract. An alignment of the PVYN amino acid sequence with the coat protein sequences of six other potyviruses revealed significant sequence similarities in the internal and carboxy terminal regions. Much amino acid sequence similarity was found between PVYN, PVY-D, and PeMV (91-93%), suggesting that PeMV should be regarded as a PVY strain. An analysis of the 3'-untranslated region of the six potyviruse revealed PVYN and PeMV as the only viruses displaying sequence similarity in this region. The 3'-untranslated sequences of PVYN and PeMV were further examined for secondary structure.

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

The amino acid sequence of the coat protein of watermelon mosaic virus 2 (WMV 2) was determined by a combination of peptide and nucleic acid sequencing. The coat protein of WMV 2 contained 281 amino acid residues including a single cysteine at position 132 and a blocked amino terminus. Comparison with the coat protein sequences of 20 strains of ten distinct potyviruses showed sequence homologies ranging from 43% to 69% except for the N strain of soybean mosaic virus (SMV-N), where the sequence homology with WMV 2 was 83%. This degree of homology and the location of sequence differences between WMV 2 and SMV-N is much closer to that observed between strains of the same virus than that found between distinct potyviruses. These data suggest that WMV 2 and SMV-N may be strains of the same virus.

Coat protein of potyviruses. 5. Symptomatology, serology, and coat protein sequences of three strains of passionfruit woodiness virus

Three strains of passionfruit woodiness virus, Tip Blight (PWV-TB), Severe (PWV-S) and Mild (PWV-M), were compared on the basis of their biological, serological and coat protein structural properties. Each of the strains could be distinguished on the basis of their reactions on selected test plant species but no differences were observed in the serological properties of the three PWV strains. Molecular weight estimates on SDS-PAGE suggest the PWV coat protein contains 275 amino acid residues and sequence data for 269 of these residues is presented. The amino terminal peptide is blocked and has not been sequenced. The coat proteins of PWV-TB and PWV-S, which cause severe symptoms in infected plants, showed only three sequence differences compared to the eleven or twelve sequence changes between their coat proteins and that of the mild strain. The high sequence homology (96-99%) between the three PWV strains is similar to that previously reported for two strains of tobacco etch virus and three strains of sugarcane mosaic virus. Sequence homology between the three strains of PWV and published sequences for the coat proteins of eight distinct potyviruses ranged from 43-71% (average 57%).

An improved purification procedure for preparing potyviruses and cytoplasmic inclusions from the same tissue

Twelve different potyviruses and cytoplasmic inclusion proteins were purified from a range of plant species utilizing a single purification protocol. Highly purified preparations have been obtained with yields that reflect the relative concentrations in the starting material; virus yields of up to 15 mg per 100 g of tissue were obtained. In some cases aggregation resulted in losses of significant amounts of virus to the inclusion fraction; this varied among preparations of the same virus. Preparations obtained from cesium gradients were typically unaggregated and essentially free of host materials. Purified virus was suitable for the production of antisera with high specific titers and low titers against healthy plant antigens. Both purified virus and RNA prepared from the virus retained infectivity. Purified RNA was free of detectable host plant nucleic acids, as complementary DNA preparations synthesized using virion RNA as template were highly virus-specific.

A beneficial effect of trypsin on the purification of turnip mosaic virus (TuMV) and other potyviruses

The effects of treatment with trypsin during the purification of turnip mosaic virus (TuMV), on virus yield, infectivity and integrity of virus coat protein were examined. Trypsin increased yield markedly, and at a low concentration, increased infectivity. These effects were probably due to reduced aggregation of virus particles. At higher concentrations of trypsin, there was some degradation of virus coat protein, and infectivity was reduced. Treatment with trypsin at the optimum concentration can significantly improve purification of TuMV; more limited experiments suggest that it can also be applied to other potyviruses.

Detection of picogram quantities of potyviruses using a dot blot immunobinding assay

Highly sensitive direct visual detection of potyviruses was achieved using a dot blot immunobinding assay (DBIA). The small sample volumes required permit the detection of as little as 0.5 pg virus in purified preparations. The binding of rabbit antibodies could be visualized using goat anti-rabbit IgG (GAR) conjugated to alkaline phosphatase, beta-D-galactosidase, glucose oxidase, or horseradish peroxidase and histochemical substrates. The avidin-biotin system was also useful, but somewhat less sensitive than GAR-enzyme conjugates. Detection of potyviruses in an aphid vector was also attempted, but without success due to endogenous aphid enzymes.

Electro-blot radioimmunoassay of virus-infected plant sap - a powerful new technique for detecting plant viruses

A new technique for detecting viruses in plant sap is described. It consists of sodium dodecyl sulphate-polyacrylamide gel electrophoresis of the infected plant sap, electrophoretic transfer of protein bands to activated paper by the Electro-Blot technique, the subsequent probing of the viral coat protein band by specific antiserum (prepared against intact virus), and detection of immune complex with 125 I-labelled protein A. The technique successfully detected tobacco mosaic virus at a sap dilution of 1 : 10,000, four strains of sugarcane mosaic virus (a potyvirus) in their perennial hosts infected for about 4 years, and five different isolated of potato leaf roll virus (a luteovirus). The latter virus occurs in extremely low concentration and is difficult to detect by the other known methods.