First Report of Apricot latent virus and Plum bark necrosis stem pitting-associated virus in Apricot from Spain

Representing 2% of world production, 20,000 ha of apricot (Prunus armeniaca L.), are cultivated in Spain, primarily in the southeast. A survey was conducted during the spring of 2008 in orchards in the region of Murcia to assess the incidence of several stone fruit viruses. Leaf and fruit samples from 160 trees from 40 orchards were collected randomly for reverse transcription (RT)-PCR analysis. Total RNA extracted (3) from leaves and fruits was tested by a multiplex one-step RT-PCR protocol with a mix of primers that detect eight distinct viruses (4). Amplicons of 250 bp expected for Plum bark necrosis stem pitting-associated virus (PBNSPaV), corresponding to part of the heat shock 70 protein gene, were obtained from four trees and amplicons of 700 bp expected for Apricot latent virus (ApLV), corresponding to part of the coat protein (CP) gene, were obtained from two trees. In all cases, amplicons were obtained using RNA extracted from leaf and fruit tissues. RT-PCR results were confirmed by uniplex RT-PCR with primers specific for each virus and dot-blot hybridization with virus-specific digoxygenin-labeled RNA probes (2). To further characterize the new viruses, we designed primers to amplify specifically the CP gene of ApLV (5'-CCCGACCATGGCTACAAGC-3' and 5'-TTGCCGTCCCGATTAGGTTG-3') and the minor CP gene of PBNSPaV (5'-GAACAAACTACAGCAGCACC-3' and 5'-CAAGGGTAGGACGGGTAACGC-3'). Amplicons of 1,500 and 950 bp corresponding to the ApLV and PBNSPaV CP genes, respectively, were purified from agarose gels and cloned in the pTZ57R plasmid (Fermentas, Burlington, Ontario, Canada). Blastp analysis of the full-length ApLV CP sequence from one infected tree (GenBank Accession No. GQ919051) revealed 86% amino acid (aa) similarity to the single full-length ApLV CP sequence available (No. AAC16234) and 79 and 66.9% similarity to Peach sooty ringspot virus (No. AAG48314) and Apple stem pitting virus (No. NP604468), respectively. Identity/similarity analysis of the full-length PBNSPaV minor CP genes using the Matrix Global Alignment Tool software, version 2.02 (1), revealed 98.8 to 99.6% aa similarity between the Spanish PBNSPaV isolates (Nos. GQ919047, GQ919048, GQ919049, and GQ919050) and 97.1 to 97.4% with the PBNSPaV isolate from the United States (No. EF546442). None of the six infected trees were associated with any particular field symptoms. Five infected trees were cv. Búlida and one was native cv. Murciana, which was infected with ApLV. All infected trees were located in geographically separated orchards. The incidence of ApLV and PBNSPaV was 1.25 and 2.5%, respectively. The low incidence of both viruses together with the scattered geographic distribution could be due to the recent introduction of virus-contaminated plants, although we cannot exclude that it is a consequence of a low dissemination rate. Even though no symptoms were observed, we cannot discard that the infection could affect fruit production or flowering or even cause a synergistic effect in mixed infection with other stone fruit viruses, a risk especially relevant considering the total area of cultivated apricot. To our knowledge, this is the first report of ApLV and PBNSPaV in Spain. References: (1) J. J. Campanella et al. BMC Bioinformatics 4:29, 2003. (2) M. C. Herranz et al. J. Virol. Methods 124:49, 2005. (3) D. J. Mackenzie et al. Plant Dis. 81:222, 1997. (4) J. A. Sánchez-Navarro et al. Eur. J. Plant Pathol. 111:77, 2005.

First Report of Avocado sunblotch viroid in Avocado from Michoacán, México

The State of Michoacán, México cultivates approximately 100,000 ha of avocados (Persea americana M.) (4). During a survey from 2006 to 2007 in cv. Hass avocado groves in Tingambato County, in the State of Michoacán, deep yellow spots and streaks, which sometimes became necrotic or reddish, were observed on the skin of fruits and the pulp of the fruit also showed big yellow spots. Some young shoots developed fine, yellow streaks, and leaves of symptomatic trees sometimes showed irregular, white-to-yellow spots. These symptoms were similar to those recorded for Avocado sunblotch viroid (ASBVd) (3). To determine if ABSVd was associated with these symptoms, total RNA extracted (1) from the skin and pulp of symptomatic and asymptomatic fruits and also from leaves and bark of shoots from five trees collected in a commercial plot in Tingambato County was tested by a one-step reverse transcription (RT)-PCR protocol using one primer pair to amplify specifically the complete ASBVd genome sequence (3). All 30 samples of skin and pulp of fruits, leaves, and cortex of shoots from symptomatic trees yielded two PCR fragments with estimated sizes of 250 and 500 base pairs (bp) corresponding to the putative monomeric and dimeric forms of ASBVd, respectively. The 500-bp RT-PCR fragments obtained from the different samples were purified from an agarose gel and cloned. The 249-bp nucleotide sequence of the ASBVd genomic monomer was determined using the clones from the fruit skin from sample Arb No. 3 (GenBank Accession No. EU888588), pulp from sample Arb No. 5 (GenBank Accession No. EU888590), leaves from samples Arb No. 15 (GenBank Accession No. EU888589) and Arb No. 8 (GenBank Accession Nos. EU888591 and EU888592), and cortex of shoots from sample Arb No. 16 (GenBank Accession Nos. EU888593, EU888594, EU888595, EU888596, and EU888597). BLAST analysis of the ASBVd sequences showed a range of 98 to 100% nucleotide identity to ASBVd sequences (GenBank Accession Nos. AF404064, AF404051, or AF229821). A clone of the Michoacán ASBVd (GenBank Accession No. EU888593) was used to synthesize a Dig-High Prime-UTP-T7 (Roche, Mannheim, Germany) fluorescent riboprobe complementary to the ASBVd plus strand to perform a dot-blot analysis as described previously (2). All ASBVd samples positive by RT-PCR gave a strong signal in the dot-blot analysis. This riboprobe will be used to index the ASBVd in other commercial avocado groves in Michoacán. To our knowledge, this is the first report of ASBVd in Michoacán, México. References: (1) D. J. Mackenzie et al. Plant Dis. 81:222, 1997. (2) J. A. Sánchez-Navarro et al. Plant Pathol. 47:780, 1998. (3) R. J. Schnell et al. Plant Dis. 81:1023, 1997. (4) D. Téliz and A. Mora. El aguacate y su Manejo Integrado. Mundiprensa, Mexico City, 2007.

A peptide derived from a single-modified viroid-RNA can be used as an "in vivo" nucleolar marker

Viroids are small, single-stranded, circular, non-coding pathogenic RNAs. Hop stunt viroid (HSVd) is characterized by possesses rod-like structure and replicate in the host nuclei. Green fluorescent protein (GFP) fusions with transit sequences or entire proteins can be used for deliberate labelling of particular cell compartments. Different GFP-fusions have been obtained to selectively illuminate different organelles and membranes in many cell types. However, as far as we know, examples for established efficient markers for nucleoli are scarce. In this work, a viroid-RNA was made translatable by inserting an ATG at position 1 and fused to the GFP. The results showed that the resultant fusion can be used as an efficient "in vivo" nucleolar marker in "real time" cellular observations. Thus, this construct can be a very useful tool to study processes related with nucleolus functions.

Mature monomeric forms of Hop stunt viroid resist RNA silencing in transgenic plants

Viroids, small non-coding pathogenic RNAs, are able to induce RNA silencing, a phenomenon that has been associated with the pathogenesis and evolution of these small RNAs. It has been recently suggested that viroids may resist this plant defense mechanism. However, the simultaneous degradation of non-replicating full-length viroid RNA, and the resistance of mature forms of viroids to RNA silencing, have not been experimentally demonstrated. Transgenic Nicotiana benthamiana plants expressing a dimeric form of Hop stunt viroid (HSVd) that have the capability to cleave and circularize this viroid RNA were used to address this question. A reporter construct, consisting of a full-length HSVd RNA fused to GFP-mRNA, was agroinfiltrated in these plants and its expression was suppressed. Interestingly, both circular and linear HSVd molecules were stable and able to traffic through grafts in these restrictive conditions, indicating that the mature forms of HSVd are able, in some way, to resist the RNA-silencing mechanism. The observation that a full-length HSVd RNA fused to GFP-mRNA, but not circular and/or linear viroid forms, was fully susceptible to RNA degradation strongly suggests that structures adopted by the free mature monomer protect the pathogenesis-associated forms of the viroid from RNA silencing.

RNA-binding properties and membrane insertion of Melon necrotic spot virus (MNSV) double gene block movement proteins

Advances in structural and biochemical properties of carmovirus movement proteins (MPs) have only been obtained in p7 and p9 from Carnation mottle virus (CarMV). Alignment of carmovirus MPs revealed a low conservation of amino acid identity but interestingly, similarity was elevated in regions associated with the functional secondary structure elements reported for CarMV which were conserved in all studied proteins. Nevertheless, some differential features in relation with CarMV MPs were identified in those from Melon necrotic virus (MNSV) (p7A and p7B). p7A was a soluble non-sequence specific RNA-binding protein, but unlike CarMV p7, its central region alone could not account for the RNA-binding properties of the entire protein. In fact, a 22-amino acid synthetic peptide whose sequence corresponds to this central region rendered an apparent dissociation constant (K(d)) significantly higher than that of the corresponding entire protein (9 mM vs. 0.83-25.7 microM). This p7A-derived peptide could be induced to fold into an alpha-helical structure as demonstrated for other carmovirus p7-like proteins. Additionally, in vitro fractionation of p7B transcription/translation mixtures in the presence of ER-derived microsomal membranes strongly suggested that p7B is an integral membrane protein. Both characteristics of these two small MPs forming the double gene block (DGB) of MNSV are discussed in the context of the intra- and intercellular movement of carmovirus.

Functional analysis of the five melon necrotic spot virus genome-encoded proteins

Function of the melon necrotic spot virus (MNSV) genome-encoded proteins (p29, p89, p7A, p7B and p42) has been studied. Protein-expression mutants of an infectious, full-length cDNA clone of a Spanish MNSV-Al isolate and a recombinant green fluorescent protein (GFP)-expressing virus were used in infection bioassays on melon plants. Results revealed that p29 and p89 are both essential for virus replication, whereas small proteins p7A and p7B are sufficient to support viral movement between adjacent cells operating in trans. It is also demonstrated that, in addition to its structural role as coat protein, p42 is an important factor controlling symptoms and is required for systemic transport. Moreover, both p42 and p7B, among all of the MNSV-encoded proteins, were able to delay RNA silencing in transient-expression assays on GFP-transgenic Nicotiana benthamiana plants. Finally, the presence of p42 also produced an enhancing effect on local spread similar to that of potyviral helper component proteinase (HC-Pro), probably due to its RNA silencing-suppression ability.

Identification of translocatable RNA-binding phloem proteins from melon, potential components of the long-distance RNA transport system

Phloem proteins (P-proteins) are an enigmatic group of proteins present in most angiosperm species. The best characterized P-proteins (PP1 and PP2) are synthesized in companion cells, transported into sieve elements via pore plasmodesmata and translocated through the plant. Characteristics such as long-distance translocation, RNA-binding activity and capacity of increasing plasmodesmata exclusion size suggest that certain phloem proteins could be involved in RNA transport within the plant, forming translocatable ribonucleoprotein complexes with endogenous or pathogenic RNAs. Long-distance movement of RNA through the phloem is a process known to occur, but both the mechanisms involved and the components constituting this potential information network remain unclear. Here, we demonstrate that several melon phloem proteins have a wide RNA-binding activity. Serological assays strongly suggest that one of these proteins is the melon phloem protein 2 (CmmPP2). Mass spectrometry analysis undoubtedly identifies another one as the recently characterized melon phloem lectin (CmmLec17). Grafting experiments demonstrate that the CmmLec17 is a translocatable phloem protein, able to move through intergeneric grafts from melon to pumpkin. Translocatability and RNA-binding activity was also demonstrated for an uncharacterized protein of approximately 14 kDa. In light of these results the possible involvement of these phloem proteins in the long-distance transport of melon RNAs is discussed.

First Record of Hop stunt viroid in Canada

"Tissue-printing" hybridization (3) for Peach latent mosaic viroid (PLMVd) and Hop stunt viroid (HSVd) was used to assess the sanitary status of stone fruit accessions in the Canadian Clonal Genebank (CCG) located in Harrow (Ontario). The Prunus spp. accessions in the CCG are primarily of Canadian origin; other countries of origin include the United States, the United Kingdom, Hungary, the Czech Republic, the Former Soviet Union, Spain, New Zealand, and Italy. All Prunus spp. accessions were donated to the Genebank from Canadian or American sources. Leaves were harvested in November 2003 from 336 trees (116 peach and nectarine, 84 sweet and sour cherries, 54 plum, 44 apricot, and 38 of other cherries) representing 267 accessions. No visible symptoms were observed during the collection of the accessions to be evaluated. The petioles were excised at the base and imprinted on a nylon membrane in triplicate for each sample. The membranes were air dried and submitted by mail to the laboratory. The digoxigenin-labeled riboprobes used for hybridization were obtained by T7 RNA polymerase transcription of the linearized plasmids pHSVd (1) and pPLMVd (2). Thirty stone fruit samples were infected by viroids. PLMVd occurred in 28 peach and nectarine samples, representing the following cultivars and selections: Harblaze Hardired, Harko, Earlyvee, Harbelle, Harken, Harland, Harrow Beauty, Harrow Rubirose, HW264, Redhaven, Silver Gold, Suncling, V68101, Vanity, Veeglo, Velvet, Vesper, Villa Doria, and Vulcan. PLMVd-infected samples represented 24.1% of the tested peaches and nectarines. PLMVd finding confirms previous reports of the viroid in Canada from British Columbia and Ontario. Two CCG apricot accessions, 'Bulida' and 'Velkopavlovicka', were found to be infected with only HSVd, representing 4.5% of tested apricot samples. These samples, determined to be positive by tissue-printing hybridization, were also positive by reverse transcription-polymerase chain reaction (RT-PCR) (1). In addition, nucleotide sequences of the PCR products were obtained. The 'Bulida' isolate showed 100% homology to a Spanish isolate, apr9, while the 'Velkopavlovicka' isolate showed 99% homology to an Italian isolate. Since HSVd has not been previously reported in Canada (4), to our knowledge, this report documents its first detection in the country. This report may prompt the inclusion of regular testing for HSVd in existing Prunus spp. virus testing programs in Canada. References: (1) N. Astruc et al. Eur. J. Plant Pathol. 102:837, 1996. (2) M. Badenes et al. Acta Hortic. 472:565, 2001. (3) V. Pallás et al. Page 135 in: Virus and Virus-Like Diseases of Stone Fruits, with Particular Reference to the Mediterranean Region. A. Myrta et al., eds. CIHEAM-IAMB, 2003. (4) R. Singh et al. Page 255 in: Viroids. A. Hadidi et al., eds. CSIRO Publishing, Australia, 2003.

First Report of Peach latent mosaic viroid on Peach in Uruguay

Peach latent mosaic viroid (PLMVd) (2) is widely distributed and causes yellow, chlorotic mosaics and delayed foliation, flowering, and ripening. Infected fruits display a cracked suture and are often dented, misshapen, frequently flattened, and discolored. In the greenhouse, PLMVd natural isolates are divided into severe or latent strains depending on whether they induce leaf symptoms on seedlings of the peach indicator GF-305. PLMVd was detected in 2001 during a survey in three locations in the Canelones Department, the main peach producing area in Uruguay. Fifty samples were tested for the presence of five viruses: Prunus necrotic ringspot virus (PNRSV), Prune dwarf virus (PDV), American plum line pattern virus (APLPV), Plum pox virus (PPV) and Apple chlorotic leaf spot virus (ACLSV); samples were also tested for the viroids affecting stone fruits, Hop stunt viroid (HSVd) and PLMVd. The analyses were completed with molecular hybridization using specific nonisotopic riboprobes for each virus (4). PLMVd, undescribed in Uruguay, was detected in 9 of 50 samples in three peach cultivars, Scarlet Pearl, EarliGrande, and Barcelo. The PLMVd-positive sample for 'Scarlet Pearl' showed mild mosaic symptoms on leaves whereas the two PLMVd-positives of 'EarliGrande' showed clear calico type symptoms. The remaining PLMVd-positive samples belonged to 'Barcelo' and showed no symptoms or mild chlorosis. The first two cultivars were imported from the United States, a source with a high percentage of PLMVd infections in peach germ plasm (1). In five of nine PLMVd-positive samples, the viroid occurred with PNRSV and in one with PDV and PNRSV. PLMVd has previously been reported in Brazil (3), but to our knowledge, this is the first report of PLMVd in Uruguay. These results reveal the importance of following strict sanitary practices with plant material used for propagation. Molecular tools are available to prescreen scion and rootstock sources for PLMVd. References: (1) M. L. Badenes and G. Llácer. Acta Hortic. 309:565, 1998. (2) R. Flores et al. Res. Virol. 141:109, 1990. (3) A. Hadidi et al. Plant Dis. 81:154, 1997. (4) V. Pallás et al. Detection of plant RNA viruses by non-isotopic dot-blot hybridization. Pages 461-468 in: Plant Virus Protocols: From Virus Isolation to Transgenic Resistance. G. Foster and S. Taylor, eds. Humana Press, Totowa, NJ. 1998.

Molecular variability of twenty-one geographically distinct isolates of Carnation mottle virus (CarMV) and phylogenetic relationships within the Tombusviridae family

The complete nucleotide sequence of a Spanish isolate of Carnation mottle carmovirus (CarMV) has been determined. Phylogenetic analyses were carried out with the replicase, coat protein (CP) and the putative movement proteins (p7 and p9) of CarMV with the homologous proteins of representative members of the different genera included within the family Tombusviridae. These analyses revealed that phylogenetic trees obtained depended on the protein analyzed, and that the best correlation with taxonomy grouping was observed with the replicase and, to a lesser extent, with CP phylogenies. This result indicates that speciation has evolved as a consequence of different selection pressures to different genomic regions. In addition, the CP, p7 and p9 coding sequences of twenty-one CarMV isolates from nine different countries have been determined. Comparative analyses revealed that CarMV isolates separated in time and space show a very high genetic stability. A division in three protein motifs is proposed for the p7 movement protein, based on the homology data presented here and on our previous identification of RNA binding sequences and structural characterization of the protein. Interestingly, a remarkable covariation in the amino acid sequence was found for the CP between Pro164 (located at the S domain) and Lys331 (within the P domain), by which a change Pro164 --> Ala correlated with a change Lys331 --> Asn, strongly suggesting the existence of tertiary interactions between these two regions of the protein. In addition, this perfect covariation allows to segregate the 23 CarMV isolates characterised so far into two main groups that we propose to name as group PK and group AN for further studies.

Identification of an in vitro ribonucleoprotein complex between a viroid RNA and a phloem protein from cucumber plants

We used the interaction of Hop stunt viroid (HSVd) and cucumber plants to investigate the involvement of phloem proteins in the systemic transport of RNA molecules. A ribonucleoprotein complex, stable even at high salt and temperature conditions, was detected in vitro between HSVd-RNA and the phloem exudate obtained from sectioned internodes from cucumber plants. The phloem protein 2 was recovered from this ribonucleoprotein complex and its RNA-binding properties as demonstrated by gel retardation analysis. The involvement of this protein in the movement of RNAs in cucumber is discussed.

Recognition of cis-acting sequences in RNA 3 of Prunus necrotic ringspot virus by the replicase of Alfalfa mosaic virus

Alfalfa mosaic virus (AMV) and Prunus necrotic ringspot virus (PNRSV) belong to the genera ALFAMOVIRUS: and ILARVIRUS:, respectively, of the family BROMOVIRIDAE: Initiation of infection by AMV and PNRSV requires binding of a few molecules of coat protein (CP) to the 3' termini of the inoculum RNAs and the CPs of the two viruses are interchangeable in this early step of the replication cycle. CIS:-acting sequences in PNRSV RNA 3 that are recognized by the AMV replicase were studied in in vitro replicase assays and by inoculation of AMV-PNRSV RNA 3 chimeras to tobacco plants and protoplasts transformed with the AMV replicase genes (P12 plants). The results showed that the AMV replicase recognized the promoter for minus-strand RNA synthesis in PNRSV RNA 3 but not the promoter for plus-strand RNA synthesis. A chimeric RNA with PNRSV movement protein and CP genes accumulated in tobacco, which is a non-host for PNRSV.

Simultaneous detection of the three ilarviruses affecting stone fruit trees by nonisotopic molecular hybridization and multiplex reverse-transcription polymerase chain reaction

ABSTRACT The three most economically damaging ilarviruses affecting stone fruit trees on a worldwide scale are the related Prunus necrotic ringspot virus (PNRSV), Prune dwarf virus (PDV), and Apple mosaic virus (ApMV). Nonisotopic molecular hybridization and multiplex reverse-transcription polymerase chain reaction (RT-PCR) methodologies were developed that could detect all these viruses simultaneously. The latter technique was advantageous because it was discriminatory. For RT-PCR, a degenerate antisense primer was designed which was used in conjunction with three virus-specific sense primers. The amplification efficiencies for the detection of the three viruses in the multiplex RT-PCR reaction were identical to those obtained in the single RT-PCR reactions for individual viruses. This cocktail of primers was able to amplify sequences from all of the PNRSV, ApMV, and PDV isolates tested in five Prunus spp. hosts (almond, apricot, cherry, peach, and plum) occurring naturally in single or multiple infections. For ApMV isolates, differences in the electrophoretic mobilities of the PCR products were observed. The nucleotide sequence of the amplified products of two representative ApMV isolates was determined, and comparative analysis revealed the existence of a 28-nucleotide deletion in the sequence of isolates showing the faster electrophoretic mobility. To our knowledge, this is the first report on the simultaneous detection of three plant viruses by multiplex RT-PCR in woody hosts. This multiplex RT-PCR could be a useful time and cost saving method for indexing these three ilarviruses, which damage stone fruit tree yields, and for the analysis of mother plants in certification programs.

Subcellular localisation of cherry leaf roll virus coat protein and genomic RNAs in tobacco leaves

The in vivo subcellular location of the coat protein and RNAs of cherry leaf roll nepovirus (CLRV) was studied in infected tobacco plants by two different approaches and it was correlated with the cytopathic structures induced by the virus. Subcellular fractions were obtained by differential centrifugation, visualised by electron microscopy and analysed for their viral RNA and coat protein content by Northern blot and Western blot analysis, respectively. Results indicate that viral RNAs accumulated preferentially at the microsomal fraction. Immunocytochemical studies revealed a clear association of the coat protein of CLRV with the virus-induced cytopathological structures. In situ hybridisation studies confirmed the cytoplasmic location of the virus and allowed one to elucidate the distribution of the CLRV genomic RNAs in the different cell types of infected tissue.

Molecular Variability Among Isolates of Prunus Necrotic Ringspot Virus from Different Prunus spp

ABSTRACT Viral sequences amplified by polymerase chain reaction from 25 isolates of Prunus necrotic ringspot virus (PNRSV), varying in the symptomatology they cause in six different Prunus spp., were analyzed for restriction fragment polymorphisms. Most of the isolates could be discriminated by using a combination of three different restriction enzymes. The nucleotide sequences of the RNA 4 of 15 of these isolates were determined. Sequence comparisons and phylogenetic analyses of the RNA 4 and coat proteins (CPs) revealed that all of the isolates clustered into three different groups, represented by three previously sequenced PNRSV isolates: PV32, PE5, and PV96. The PE5-type group was characterized by a 5' untranslated region that was clearly different from that of the other two groups. The PV32-type group was characterized by an extra hexanucleotide consisting of a duplication of the six immediately preceding nucleotides. Although most of the variability was observed in the first third of the CP, the amino acid residues in this region, which were previously thought to be functionally important in the replication cycle of the virus, were strictly conserved. No clear correlation with the type of symptom or host specificity could be observed. The validity of this grouping was confirmed when other isolates recently characterized by other authors were included in these analyses.

Simultaneous detection of five carnation viruses by non-isotopic molecular hybridization

Several viruses, which in some cases can cause severe losses, affect carnation plants. These viruses include carnation mottle virus, carnation etched ring virus (CERV), carnation vein mottle virus, carnation ringspot virus, carnation Italian ringspot virus and carnation latent virus. A non-isotopic molecular hybridization was developed for the detection of these viruses in host plants and the sensitivity of the technique has been compared with enzyme-linked immunosorbent assay and bioassay methods. A procedure was developed to test simultaneously for the five RNA viruses (except CERV). The conditions established for this simultaneous detection did not include the DNA virus CERV due to the necessity of incorporating an additional step of RNase A treatment in the procedure to eliminate background signals. The sensitivity limits obtained for each virus using this multiple detection assay were identical to those obtained with the individual assays. The relative benefits of using this detection procedure for routine diagnosis of carnation viruses are discussed.

Characterization and in vitro translation analysis of pelargonium flower break virus

Pelargonium flower break virus (PFBV) is one of the common viruses in the glasshouses of Western Europe and has been assigned to the genus Carmovirus. A Spanish isolate obtained from nursery-grown Pelargonium zonale plants (PFBV-m) has been characterized. The molecular weight of genomic RNA and coat protein of PFBV-m were determined to be 1.36 x 10(6) (corresponding to approximately 4 kb) and 36,000, respectively. Only genomic-size RNA was encapsidated in PFBV virions; making necessary to purify double-stranded RNA from infected tissue in order to detect putative PFBV subgenomic RNAs. PFBV RNA directed the synthesis of a major polypeptide of 34 kDa and three other relevant polypeptides of estimated sizes 88-90 kDa, 42 kDa and 35-36 kDa. Antisera specific to PFBV immunoprecipitated the in vitro translated 35-36 kDa polypeptide indicating that this polypeptide is the PFBV coat protein. The PFBV in vitro translation pattern was very similar to that of CarMV although the relative levels of translated coat protein differed dramatically between the two viruses, most probably due to the lack of encapsidation of subgenomic PFBV. In vitro translation studies with a different biological clone obtained from the same PFBV-m isolate revealed a prominent additional polypeptide which is postulated to be a truncation of the 5' proximal ORF.

In vitro evidence for RNA binding properties of the coat protein of prunus necrotic ringspot ilarvirus and their comparison to related and unrelated viruses

The RNA binding properties of the prunus necrotic ringspot virus (PNRSV) coat protein (CP) were demonstrated by northwestern and dot-blot analyses. The capability to bind PNRSV RNA 4 was compared with viruses representing three different interactions prevailing in the assembly and architecture of virions. The results showed that cucumber mosaic virus (CMV) and PNRSV CPs, which stabilise their virions mainly through RNA-protein interactions bound PNRSV RNA 4 even at very high salt concentrations. The CP of cherry leaf roll nepovirus, whose virions are predominantly stabilised by protein-protein interactions did not bind even at the lowest salt concentration tested. Finally the CP of carnation mottle carmovirus, that has an intermediate position in which both RNA-protein and protein-protein interactions are equally important showed a salt-dependent RNA binding.

In vivo detection, RNA-binding properties and characterization of the RNA-binding domain of the p7 putative movement protein from carnation mottle carmovirus (CarMV)

Biochemical and structural characterization studies on the p7 putative movement protein from a Spanish isolate of carnation mottle carmovirus (CarMV) have been conducted. The CarMV p7 gene was fused to a sequence coding for a six-histidine tag and expressed in bacteria, allowing the purification of CarMV p7 and the production of a specific antiserum. This antiserum led to the immunological identification of CarMV p7 in infected leaf tissue from the experimental host Chenopodium quinoa. Putative nucleic acid-binding properties of the CarMV p7 have been explored and demonstrated with both electrophoretic mobility shift and RNA-protein blot in vitro assays using digoxigenin-labeled riboprobes. CarMV p7 did not show preferential binding to any of the different regions of the CarMV genomic RNA tested, suggesting that RNA binding was sequence nonspecific. Quantitative analyses of the data allowed calculation of the apparent dissociation constant of the p7-RNA complex (Kd approximately 0.7 microM) and supported a cooperative type of binding. A small 19-amino-acid synthetic peptide whose sequence corresponds to the putative RNA-binding domain of CarMV p7, at the basic central part of the protein, was synthesized, and it was demonstrated that it binds viral RNA probes. Peptide RNA binding was as stable as p7 binding, although data indicated it was not cooperative, thus suggesting that this cooperative binding requires another motif or motifs within the p7 amino acid sequence. The peptide could be induced to fold into an alpha-helix structure in which amino acids that are conserved among carmovirus p7-like proteins are distributed on one side. This alpha-helix motif could define a new and previously uncharacterized RNA-binding domain for plant virus movement proteins.

Hop stunt viroid (HSVd) sequence variants from Prunus species: evidence for recombination between HSVd isolates

Hop stunt viroid (HSVd) is able to infect a number of herbaceous and woody hosts, such as grapevine, Citrus or Prunus plants. Previous phylogenetic analyses have suggested the existence of three major groups of HSVd isolates (plum-type, hop-type and citrus-type). The fact that these groups often contain isolates from only a limited number of isolation hosts prompted the suggestion that group-discriminating sequence variations could, in fact, represent host-specific sequence determinants which may facilitate or be required for replication in a given host. In an effort to further understand the relationships between HSVd and its different hosts, HSVd variants from eight naturally infected Prunus sources, including apricot, peach and Japanese plum have been cloned and sequenced. In total, ten molecular variants of HSVd have been identified, nine of which have not been described before. A detailed phylogenetic analysis of the existing HSVd sequences, including the new ones from Prunus determined in this work, points towards a redefinition of the grouping of variants of this viroid, since two new groups were identified, one of them composed of sequences described here. A bias for the presence of certain sequences and/or structures in certain hosts was observed, although no conclusive host-determinants were found. Surprisingly, our analysis revealed that a number of HSVd isolates probably derived from recombination events and that the previous hop-type group itself is likely to be the result of a recombination between members of the plum-type and citrus-type groups.

Replication of alfalfa mosaic virus RNA 3 with movement and coat protein genes replaced by corresponding genes of Prunus necrotic ringspot ilarvirus

Alfalfa mosaic virus (AMV) and Prunus necrotic ringspot virus (PNRSV) are tripartite positive-strand RNA plant viruses that encode functionally similar translation products. Although the two viruses are phylogenetically closely related, they infect a very different range of natural hosts. The coat protein (CP) gene, the movement protein (MP) gene or both genes in AMV RNA 3 were replaced by the corresponding genes of PNRSV. The chimeric viruses were tested for heterologous encapsidation, replication in protoplasts from plants transformed with AMV replicase genes P1 and P2 (P12 plants) and for cell-to-cell transport in P12 plants. The chimeric viruses exhibited basic competence for encapsidation and replication in P12 protoplasts and for a low level of cell-to-cell movement in P12 plants. The potential involvement of the MP gene in determining host specificity in ilarviruses is discussed.

Evolutionary relationships in the ilarviruses: nucleotide sequence of prunus necrotic ringspot virus RNA 3

The complete nucleotide sequence of an isolate of prunus necrotic ringspot virus (PNRSV) RNA 3 has been determined. Elucidation of the amino acid sequence of the proteins encoded by the two large open reading frames (ORFs) allowed us to carry out comparative and phylogenetic studies on the movement (MP) and coat (CP) proteins in the ilarvirus group. Amino acid sequence comparison of the MP revealed a highly conserved basic sequence motif with an amphipathic alpha-helical structure preceding the conserved motif of the '30K superfamily' proposed by Mushegian and Koonin [26] for MP's. Within this '30K' motif a strictly conserved transmembrane domain is present in all ilarviruses sequenced so far. At the amino-terminal end, prune dwarf virus (PDV) has an extension not present in other ilarviruses but which is observed in all bromo- and cucumoviruses, suggesting a common ancestor or a recombinational event in the Bromoviridae family. Examination of the N-terminus of the CP's of all ilarviruses revealed a highly basic region, part of which resembles the Arg-rich motif that has been characterized in the RNA-binding protein family. This motif has also been found in the other members of the Bromoviridae family, suggesting its involvement in a structural function. Furthermore this region is required for infectivity in ilarviruses. The similarities found in this Arg-rich motif are discussed in terms of this process known as genome activation. Finally, phylogenetic analysis of both the MP and CP proteins revealed a higher relationship of A1MV to PNRSV, apple mosaic virus (ApMV) and PDV than any other member of the ilarvirus group. In that sense, A1MV should be considered as a true ilarvirus instead of forming a distinct group of viruses.

Long-distance movement of cherry leaf roll virus in infected tobacco plants

The long-distance movement of cherry leaf roll virus (CLRV) in tobacco plants was studied using a tissue printing technique with non-isotopic RNA probes. Time-course analysis revealed that CLRV RNA accumulated in the inoculated leaf at an early stage, such as 20 h post-inoculation. The virus accumulation reached a peak at 8-10 days post-inoculation (d.p.i.) and then progressively decreased. The virus RNA signal was detected before the appearance of symptoms. The virus invaded stem vascular tissues at 3 d.p.i., moving towards the roots before moving to the upper leaves. In systemically infected leaves, the virus appeared first in the basal regions and then moved to the distal parts through the vascular system. The distribution pattern of the virus coat protein in systemically infected leaves was parallel to that observed for the virus RNA, suggesting that CLRV requires the coat protein for long-distance movement. The movement of the virus was influenced by the phyllotactic position of the leaves. The viral symptoms and the virus RNA signal in older systemically infected leaves were asymmetrically distributed, being localized in the side of the lamina closest to the inoculated leaf. Virus distribution in infected plants as well as the susceptibility of the plant to systemic infection were also influenced by the developmental stage of the inoculated leaves. Inoculation of leaves at 95% of their final size resulted in virus replication but no systemic infection. In fully mature leaves the virus did not replicate.

Non-isotopic tissue-printing hybridization: a new technique to study long-distance plant virus movement

A non-isotopic tissue-print hybridization technique was developed to study long-distance plant virus movement. By using digoxigenin-labeled RNA probes the distribution pattern of the viral RNA was observed in leaf, stem and petiole tissues. In leaf tissue viral RNA was confined preferentially to symptoms and veins, and in stem and petiole sections, the hybridization signal was observed in vascular tissue. Both chemiluminescent and colorigenic detection methods were used. The colorigenic method, though less sensitive, is advantageous in that it gives some anatomical information on the signal distribution. This non-isotopic tissue-print hybridization technique can provide considerable information about the spatial and temporal virus expression with regard to its symptoms.

Nucleotide sequence of apple mosaic ilarvirus RNA 4

The complete nucleotide sequence of apple mosaic ilavirus RNA 4 was obtained from cloned cDNAs and direct sequencing of the 5'-terminal RNA region. The sequence is 891 nucleotides long and can encode a protein of 226 amino acids (M(r) 25,171) that, by analogy to alfalfa mosaic virus (AlMV) and tobacco streak virus (TSV), should correspond to the coat protein (CP). Database comparisons showed that no significant similarity to other proteins was apparent. Analysis of the CP sequence revealed a putative 'zinc finger' domain and a region rich in basic residues at the amino-terminal portion of the protein, similar to that of TSV. The secondary structure proposed for the 3'-terminal region of RNA 4 shows the presence of three hairpin structures flanked by the tetranucleotide AUGC that are highly similar to those previously described in the RNA 4 species from AlMV and TSV. These results support the idea that both features (metal-binding domain and highly conserved hairpin structures) are characteristics of ilarviruses and are probably involved in the peculiar 'genome activation' phenomenon described in these viruses.

Chemiluminescent and colorigenic detection of cherry leaf roll virus with digoxigenin-labeled RNA probes

Digoxigenin-labeled RNA probes were used to detect cherry leaf roll virus in infected plants. A dot-blot hybridization immunoenzymatic assay in both crude sap extracts and partially purified tissue with a colorigenic and chemiluminescent detection was developed. The use of the new AMPPD substrate was found to be effective in clarified sap extracts in conditions were the colorigenic detection method failed. Both detection assays were effective when using unfractionated nucleic acid preparations, the chemiluminescent being five times more sensitive than the colorigenic. The chemiluminescent hybridization assay makes it possible to detect the virus at the picogram level. The non-radioactive dot-blot hybridization techniques described here turned out to be very suitable for plant virus diagnosis. The sensitivity of this method and those obtained by ELISA or radioactive dot-blot described previously is compared.

Interactions between citrus exocortis and potato spindle tuber viroids in plants of Gynura aurantiaca and Lycopersicon esculentum

Plants of Gynura aurantiaca and tomato (Lycopersicon esculentum) were inoculated with severe strains of citrus exocortis viroid (CEV) and potato spindle tuber viroid (PSTV). The progeny of both viroids was analyzed by two systems of PAGE which allowed discrimination between CEV and PSTV on the basis of their different sizes. When inoculated separately to G. aurantiaca CEV and PSTV induced severe and very mild symptoms, respectively, with CEV accumulating to a higher level than PSTV, whereas when tomato was the host, each viroid induced severe symptoms (although the reaction caused by PSTV was more intense) with PSTV reaching a higher steady-state concentration than CEV. The simultaneous inoculation of both viroids induced in G. aurantiaca the characteristic symptomatology of CEV, which was the only viroid that could be detected, whereas the response observed in tomato was that typical of PSTV, and only this viroid could be recovered. On the other hand, when G. aurantiaca plants were first inoculated with PSTV and later challenged with CEV, part of the plants displayed the characteristic severe reaction of CEV and both viroids were present in the corresponding extracts, but the other part showed the mild symptomatology induced by PSTV, and only this viroid could be isolated. However, when the protected plants were topped the new shoots exhibited severe symptoms and only CEV could be detected. These results suggest that CEV and PSTV compete for a limiting host factor needed for their replication, transport or accumulation, with CEV and PSTV having the highest affinity for the G. aurantiaca and tomato factors, respectively.

The sequence of a viroid from grapevine closely related to severe isolates of citrus exocortis viroid

The primary structure of a grapevine viroid (GVs) isolated in Spain was determined. The sequence consisted of 369 nucleotide residues forming a circular molecule. GVs presented extensive homology with viroids of the potato spindle tuber viroid (PSTV) group, that was specially high in the case of citrus exocortis viroid (CEV) both with variants found in isolates inducing severe (92% with CEV-A) and mild (89% with CEV-DE26) symptoms on tomato. The secondary structure proposed for GVs showed that the changes in the sequence in relation to CEV-A generated modifications of the secondary structure particularly important in the left terminal (Tl), variable (V) and pathogenesis (P) viroid domains that have been postulated. Nevertheless it was noted in GVs a central core in the P domain that is conserved in the class A sequence variants characteristic of severe isolates, but not in the class B ones found in mild isolates of CEV. These observations indicate that GVs should be considered as a severe isolate of CEV from grapevine (CEV-g), a suggestion that correlates with the biological properties of CEV-g both in tomato and in Gynura aurantiaca. The presence of this central core in the P domain seems to characterize all the variants of CEV inducing severe symptoms in tomato.