Nucleotide sequence and genomic organization of apple chlorotic leaf spot closterovirus

Application of Biotechniques for In Vitro Virus and Viroid Elimination in Pome Fruit Crops

Sustainable production of pome fruit crops is dependent upon having virus-free planting materials. The production and distribution of plants derived from virus- and viroid-negative sources is necessary not only to control pome fruit viral diseases but also for sustainable breeding activities, as well as the safe movement of plant materials across borders. With variable success rates, different in vitro-based techniques, including shoot tip culture, micrografting, thermotherapy, chemotherapy, and shoot tip cryotherapy, have been employed to eliminate viruses from pome fruits. Higher pathogen eradication efficiencies have been achieved by combining two or more of these techniques. An accurate diagnosis that confirms complete viral elimination is crucial for developing effective management strategies. In recent years, considerable efforts have resulted in new reliable and efficient virus detection methods. This comprehensive review documents the development and recent advances in biotechnological methods that produce healthy pome fruit plants. [Formula: see text] Copyright © 2024 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.

The functions of triple gene block proteins and coat protein of apple stem pitting virus in viral cell-to-cell movement

Apple stem pitting virus is a species in the genus Foveavirus in the family Betaflexiviridae. Apple stem pitting virus (ASPV) commonly infects apple and pear plants grown worldwide. In this study, by integrating bimolecular fluorescence complementation, split-ubiquitin-based membrane yeast two-hybrid, and Agrobacterium-mediated expression assays, the interaction relationships and the subcellular locations of ASPV proteins TGBp1-3 and CP in Nicotiana benthamiana leaf cells were determined. Proteins CP, TGBp1, TGBp2, and TGBp3 were self-interactable, and TGBp2 played a role in the formation of perinuclear viroplasm and enhanced the colocalization of TGBp3 with CP and TGBp1. We found that the plant microfilament and endoplasmic reticulum structures were involved in the production of TGBp3 and TGBp2 vesicles, and their disruption decreased the virus accumulation level in the systemic leaves. The TGBp3 motile vesicles functioned in delivering the viral ribonucleoprotein complexes to the plasma membrane. Two cysteine residues at sites 35 and 49 of the TGBp3 sorting signal were necessary for the diffusion of TGBp3-marked vesicles. Furthermore, our results revealed that TGBp1, TGBp2, and CP could increase plasmodesmal permeability and move to the adjacent cells. This study demonstrates an interaction network and a subcellular location map of four ASPV proteins and for the first time provides insight into the functions of these proteins in the movement of a foveavirus.

Peach RNA viromes in six different peach cultivars

Many recent studies have demonstrated that several known and unknown viruses infect many horticultural plants. However, the elucidation of a viral population and the understanding of the genetic complexity of viral genomes in a single plant are rarely reported. Here, we conducted metatranscriptome analyses using six different peach trees representing six individual peach cultivars. We identified six viruses including five viruses in the family Betaflexiviridae and a novel virus belonging to the family Tymoviridae as well as two viroids. The number of identified viruses and viroids in each transcriptome ranged from one to six. We obtained 18 complete or nearly complete genomes for six viruses and two viroids using transcriptome data. Furthermore, we analyzed single nucleotide variations for individual viral genomes. In addition, we analyzed the amount of viral RNA and copy number for identified viruses and viroids. Some viruses or viroids were commonly present in different cultivars; however, the list of infected viruses and viroids in each cultivar was different. Taken together, our study reveals the viral population in a single peach tree and a comprehensive overview for the diversities of viral communities in different peach cultivars.

Generation of an Infectious Clone of a New Korean Isolate of Apple chlorotic leaf spot virus Driven by Dual 35S and T7 Promoters in a Versatile Binary Vector

The full-length sequence of a new isolate of Apple chlorotic leaf spot virus (ACLSV) from Korea was divergent, but most closely related to the Japanese isolate A4, at 84% nucleotide identity. The full-length cDNA of the Korean isolate of ACLSV was cloned into a binary vector downstream of the bacteriophage T7 RNA promoter and the Cauliflower mosaic virus 35S promoter. Chenopodium quinoa was successfully infected using in vitro transcripts synthesized using the T7 promoter, detected at 20 days post inoculation (dpi), but did not produce obvious symptoms. Nicotiana occidentalis and C. quinoa were inoculated through agroinfiltration. At 32 dpi the infection rate was evaluated; no C. quinoa plants were infected by agroinfiltration, but infection of N. occidentalis was obtained.

Movement protein of Apple chlorotic leaf spot virus is genetically unstable and negatively regulated by Ribonuclease E in E. coli

Movement protein (MP) of Apple chlorotic leaf spot virus (ACLSV) belongs to “30 K” superfamily of proteins and members of this family are known to show a wide array of functions. In the present study this gene was found to be genetically unstable in E. coli when transformed DH5α cells were grown at 28 °C and 37 °C. However, genetic instability was not encountered at 20 °C. Heterologous over expression failed despite the use of different transcriptional promoters and translational fusion constructs. Total cell lysate when subjected to western blotting using anti-ACLSV MP antibodies, showed degradation/cleavage of the expressed full-length protein. This degradation pointed at severe proteolysis or instability of the corresponding mRNA. Predicted secondary structure analysis of the transcript revealed a potential cleavage site for an endoribonuclease (RNase E) of E. coli. The negating effect of RNase E on transcript stability and expression was confirmed by northern blotting and quantitative RT-PCR of the RNA extracted from RNase E temperature sensitive mutant (strain N3431). The five fold accumulation of transcripts at non-permissive temperature (43 °C) suggests the direct role of RNase E in regulating the expression of ACLSV MP in E. coli.

Genome Sequences of Three Apple chlorotic leaf spot virus Isolates from Hawthorns in China

The genome sequences of Apple chlorotic leaf spot virus (ACLSV) isolates from three accessions of hawthorns (Crataegus pinnatifida) grown at Shenyang Agricultural University were determined using Illumina RNA-seq. To confirm the assembly data from the de novo sequencing, two ACLSV genomic sequences (SY01 and SY02) were sequenced using the Sanger method. The SY01 and SY02 sequences obtained with the Sanger method showed 99.5% and 99.7% nucleotide identity with the transcriptome data, respectively. The genome sequences of the hawthorn isolates SY01, SY02 and SY03 (GenBank accession nos. KM207212, KU870524 and KU870525, respectively) consisted of 7,543, 7,561 and 7,545 nucleotides, respectively, excluding poly-adenylated tails. Sequence analysis revealed that these hawthorn isolates shared an overall nucleotide identity of 82.8–92.1% and showed the highest identity of 90.3% for isolate YH (GenBank accession no. KC935955) from pear and the lowest identity of 67.7% for isolate TaTao5 (GenBank accession no. EU223295) from peach. Hawthorn isolate sequences were similar to those of ‘B6 type’ ACLSV. The relationship between ACLSV isolates largely depends upon the host species. This represents the first comparative study of the genome sequences of ACLSV isolates from hawthorns.

Molecular characterization of a novel mycovirus of the family Tymoviridae isolated from the plant pathogenic fungus Fusarium graminearum

We isolated a novel mycovirus, Fusarium graminearum mycotymovirus 1 (FgMTV1/SX64), which is related to members of the family Tymoviridae, from the plant pathogenic fungus F. graminearum strain SX64. The complete 7863 nucleotide sequence of FgMTV1/SX64, excluding the poly (A) tail, was determined. The genome of FgMTV1/SX64 is predicted to contain four open reading frames (ORFs). The largest ORF1 is 6723 nucleotides (nt) in length and encodes a putative polyprotein of 2242 amino acids (aa), which contains four conserved domains, a methyltransferase (Mtr), tymovirus endopeptidase (Pro), viral RNA helicase (Hel), and RNA-dependent RNA polymerase (RdRp), of the replication-associated proteins (RPs) of the positive-strand RNA viruses. ORFs 2-4 putatively encode three putative small hypothetical proteins, but their functions are still unknown. Sequence alignments and phylogenetic analyses based on the putative RP protein and the three conserved domains (Mtr, Hel and RdRp) showed that FgMTV1/SX64 is most closely related to, but distinctly branched from, the viruses from the family Tymoviridae. Although FgMTV1/SX64 infection caused mild or no effect on conidia production, biomass and virulence of its host F. graminearum strain SX64, its infection had significant effects on the growth rate, colony diameter and deoxynivalenol (DON) production. This is the first molecular characterization of a tymo-like mycovirus isolated from a plant pathogenic fungus. It is proposed that the mycovirus FgMTV1/SX64 is a representative member of new proposed lineage Mycotymovirus in the family Tymoviridae.

Simultaneous detection and differentiation of three viruses in pear plants by a multiplex RT-PCR

A multiplex RT-PCR (mRT-PCR) assay was developed for detection and differentiation of the Apple stem pitting virus (ASPV), Apple stem grooving virus (ASGV) and Apple chlorotic leaf spot virus (ACLSV), which are viruses frequently occurring in pear trees. Different combinations of mixed primer pairs were tested for their specificity and sensitivity for the simultaneous detection of the three viruses. Three primer pairs were used to amplify their fragments of 247bp, 358bp and 500bp, respectively. The primer pair for ASPV was designed in this work, while the primer pairs for ACLSV and ASGV were from previous reports. The sensitivity and specificity of the mRT-PCR assay for the three viruses were comparable to that of each uniplex RT-PCR. The mRT-PCR was applied successfully for the detection of three viruses in leaves of pear and apple plants, but was unreliable in the detection of ASGV in dormant barks. In conclusion, this mRT-PCR provides a useful tool for the routine and rapid detection and the differentiation of three pear viruses.

Strategies to facilitate the development of uncloned or cloned infectious full-length viral cDNAs: Apple chlorotic leaf spot virus as a case study

BACKGROUND

Approaches to simplify and streamline the construction of full-length infectious cDNA clones (FL-cDNAs) are needed. Among desirable improvements are the ability to use total nucleic acids (TNA) extracts from infected hosts (to bypass viral purification limitations) for the direct one-step amplification of large FL-cDNAs, the possibility to inoculate plants with uncloned FL-cDNAs and the simplified cloning of these large molecules.

RESULTS

Using the 7.55 kb genome of Apple chlorotic leaf spot trichovirus (ACLSV) approaches allowing the rapid generation from TNA extracts of FL-cDNAs under the control of the T7 promoter and the successful inoculation of plants using in vitro transcripts obtained from these uncloned amplification products have been developed. We also show that the yeast homologous recombination system permits efficient cloning of FL-cDNAs and the simultaneous one-step tailoring of a ternary Yeast-Escherichia coli-Agrobacterium tumefaciens shuttle vector allowing efficient inoculation of both herbaceous and woody host plants by agroinfiltration.

CONCLUSIONS

The fast and efficient strategies described here should have broad applications, in particular for the study of "difficult" plant viruses, such as those infecting woody hosts, and potentially for other, non plant-infecting viral agents.

Complete nucleotide sequence of cherry virus A (CVA) infecting sweet cherry in India

Cherry virus A (CVA) is a graft-transmissible member of the genus Capillovirus that infects different stone fruits. Sweet cherry (Prunus avium L; family Rosaceae) is an important deciduous temperate fruit crop in the Western Himalayan region of India. In order to determine the health status of cherry plantations and the incidence of the virus in India, cherry orchards in the states of Jammu and Kashmir (J&K) and Himachal Pradesh (H.P.) were surveyed during the months of May and September 2009. The incidence of CVA was found to be 28 and 13% from J&K and H.P., respectively, by RT-PCR. In order to characterize the virus at the molecular level, the complete genome was amplified by RT-PCR using specific primers. The amplicon of about 7.4 kb was sequenced and was found to be 7,379 bp long, with sequence specificity to CVA. The genome organization was similar to that of isolates characterized earlier, coding for two ORFs, in which ORF 2 is nested in ORF1. The complete sequence was 81 and 84% similar to that of the type isolate at the nucleotide and amino acid level, respectively, with 5' and 3' UTRs of 54 and 299 nucleotides, respectively. This is the first report of the complete nucleotide sequence of cherry virus A infecting sweet cherry in India.

Inhibition of long-distance movement of RNA silencing signals in Nicotiana benthamiana by Apple chlorotic leaf spot virus 50 kDa movement protein

Apple chlorotic leaf spot virus 50 kDa movement protein (P50) acts as a suppressor of systemic silencing in Nicotiana benthamiana. Here, we investigate the mode of action of P50 suppressor. An agroinfiltration assay in GFP-expressing N. benthamiana line16c (GFP-plant) showed that P50 could not prevent the short-distance spread of silencing. In grafting experiments, the systemic silencing was inhibited in GFP-plants (scion) grafted on P50-expressing N. benthamiana (P50-plant; rootstock) when GFP silencing was induced in rootstock. In double-grafted plants, GFP-plant (scion)/P50-plant (interstock)/GFP-plant (rootstock), the systemic silencing in scion was inhibited when GFP silencing was induced in rootstock. Analysis of P50 deletion mutants indicated that the N-terminal region (amino acids 1-284) is important for its suppressor activity. In gel mobility shift assay, P50 lacks binding ability with siRNAs. These results indicated that P50 has a unique suppressor activity that specifically inhibits the long-distance movement of silencing signals.

Combinations of two amino acids (Ala40 and Phe75 or Ser40 and Tyr75) in the coat protein of apple chlorotic leaf spot virus are crucial for infectivity

Amino acid sequences of apple chlorotic leaf spot virus (ACLSV) coat protein (CP) were compared between 12 isolates from apple, plum and cherry, and 109 cDNA clones that were amplified directly from infected apple tissues. Phylogenetic analysis based on the amino acid sequences of CP showed that the isolates and cDNA clones were separated into two major clusters in which the combinations of the five amino acids at positions 40, 59, 75, 130 and 184 (Ala(40)-Val(59)-Phe(75)-Ser(130)-Met(184) or Ser(40)-Leu(59)-Tyr(75)-Thr(130)-Leu(184)) were highly conserved within each cluster. Site-directed mutagenesis using an infectious cDNA clone of ACLSV indicated that the combinations of two amino acids (Ala(40) and Phe(75) or Ser(40) and Tyr(75)) are necessary for infectivity to Chenopodium quinoa plants by mechanical inoculation. Moreover, an agroinoculation assay indicated that the substitution of a single amino acid (Ala(40) to Ser(40) or Phe(75) to Tyr(75)) resulted in extreme reduction in the accumulation of viral genomic RNA, double-stranded RNAs and viral proteins (movement protein and CP) in infiltrated tissues, suggesting that the combinations of the two amino acids at positions 40 and 75 are important for effective replication in host plant cells.

Apple chlorotic leaf spot virus 50 kDa movement protein acts as a suppressor of systemic silencing without interfering with local silencing in Nicotiana benthamiana

Apple chlorotic leaf spot virus (ACLSV) is the type species of the genus Trichovirus and its single-stranded, plus-sense RNA genome encodes a 216 kDa protein (P216) involved in replication, a 50 kDa movement protein (P50) and a 21 kDa coat protein (CP). In this study, it was investigated whether these proteins might have RNA silencing-suppressor activities by Agrobacterium-mediated transient assay in the green fluorescent protein-expressing Nicotiana benthamiana line 16c. The results indicated that none of these proteins could suppress local silencing in infiltrated leaves. However, systemic silencing in upper leaves induced by both single- and double-stranded RNA could be suppressed by P50, but not by a frame-shift mutant of P50, P216 or CP. Moreover, when P50 was expressed separately from where silencing signals were generated in a leaf, systemic silencing in upper leaves was inhibited. Collectively, our data indicate that P50 acts as a suppressor of systemic silencing without interfering with local silencing, probably by inhibiting the movement of silencing signals.

Interference of Long-Distance Movement of Grapevine berry inner necrosis virus in Transgenic Plants Expressing a Defective Movement Protein of Apple chlorotic leaf spot virus

ABSTRACT Transgenic Nicotiana occidentalis plants expressing a movement protein (P50) and partially functional deletion mutants (DeltaA and DeltaC) of the Apple chlorotic leaf spot virus (ACLSV) showed resistance to Grapevine berry inner necrosis virus (GINV). The resistance is highly effective and GINV was below the level of detection in both inoculated and uninoculated upper leaves. In contrast, GINV accumulated in inoculated and uninoculated leaves of nontransgenic (NT) plants and transgenic plants expressing a dysfunctional mutant (DeltaG). On the other hand, in some plants of a transgenic plant line expressing a deletion mutant (DeltaA', deletion of the C-terminal 42 amino acids), GINV could spread in inoculated leaves, but not move into uninoculated leaves. In a tissue blot hybridization analysis of DeltaA'-plants inoculated with GINV, virus could be detected in leaf blade, midribs, and petiole of inoculated leaves, but neither in stems immediately above inoculated leaves nor in any tissues of uninoculated leaves. Immunohistochemical analysis of GINV-inoculated leaves of DeltaA'-plants showed that GINV could invade into phloem parenchyma cells through bundle sheath of minor veins, suggesting that the long-distance transport of GINV might be inhibited between the phloem cells and sieve element (and/or within sieve element) rather than bundle sheath-phloem interfaces. Immunogold electron microscopy using an anti-P50 antiserum showed that P50 accumulated on the parietal layer of sieve elements and on sieve plates. The results suggested that resistance in P50-transgenic plants to GINV is due to the interference of both long-distance and cell-to-cell movement of the virus.

Molecular Characterization, Phylogenetic Relationships, and Specific Detection of Peach mosaic virus

ABSTRACT Peach mosaic virus (PcMV) and Cherry mottle leaf virus (CMLV) are serologically related viruses that cause distinct diseases, have a different host range, and are vectored by different eriophyid mites. Sequence analysis of the genome of PcMV indicates that it is closely related genetically to CMLV but distinct, with similar genome organization and a member of the genus Trichovirus. The genome of PcMV consists of 7,988 nucleotides, excluding a poly(A) tail at the 3' end of the genome. Four putative open reading frames (ORF1 to 4) were identified coding for proteins of 216.3, 47.2, 21.7, and 15.7 kDa, respectively. Also, three noncoding regions were identified, including an intergenic region separating ORF3 and ORF4. The complete nucleotide sequence of PcMV shares 73% identity with CMLV. The CP amino acid sequence identity between isolates of PcMV ranged from 97 to 99% versus 83% identity when compared with the CP of CMLV. In vitro expression and subsequent western blot analysis confirmed ORF3 as encoding the CP gene of PcMV. Phylogenetic analysis supports classification of PcMV and CMLV as members of the genus Trichovirus. They are unique members of this genus with an extra ORF (ORF4). PcMV ORF4 appears to code for a putative nucleic acid-binding (NB) protein which has identity with the NB protein of CMLV and members of the genera Allexivirus, Carlavirus, and Vitivirus. PcMV and CMLV appear to be the products of recombination between members of the genus Trichovirus and a virus group containing the putative NB protein. Alternatively, PcMV and CMLV may represent the intact genome, with a deletion event producing members that lack ORF4. A reverse transcription-polymerase chain reaction procedure was developed for reliable and specific detection of PcMV. This will be an asset for stone fruit virus certification.

Polyvalent degenerate oligonucleotides reverse transcription-polymerase chain reaction: a polyvalent detection and characterization tool for trichoviruses, capilloviruses, and foveaviruses

ABSTRACT A polyvalent nested reverse transcription-polymerase chain reaction (RT-PCR) test using degenerate primers containing inosine (polyvalent degenerate oligonucleotides [PDO]) was developed for filamentous fruit tree viruses belonging to the genera Trichovirus, Capillovirus, and Foveavirus. The 362-bp product was amplified from nucleic acid extracts obtained from Prunus and Malus leaf samples. All the viruses targeted were detected, demonstrating the polyvalence of the test. The variability of a collection of Apple chlorotic leaf spot virus isolates was analyzed using the sequence of the PDO RT-PCR amplified cDNAs. The technique was also used to screen stone fruit materials infected with known agents or with virus-like graft-transmissible diseases of unknown etiology. The results obtained further validated the broad specificity of the assay, with positive amplification obtained for uncharacterized or partially characterized viruses associated with cherry and peach disorders. Sequencing the amplified PCR products either directly or after cloning allowed the identification of variants of known agents and the tentative identification of two new agents, a Trichovirus and a Foveavirus. In addition, sequence comparisons demonstrated that the sequence of the targeted region is phylogenetically informative and of predictive taxonomic value.

Characterization of Apricot pseudo-chlorotic leaf spot virus, A Novel Trichovirus Isolated from Stone Fruit Trees

ABSTRACT A trichovirus closely related to Apple chlorotic leaf spot virus (ACLSV) was detected in symptomatic apricot and Japanese plum from Italy. The Sus2 isolate of this agent cross-reacted with anti-ACLSV polyclonal reagents but was not detected by broad-specificity anti- ACLSV monoclonal antibodies. It had particles with typical trichovirus morphology but, contrary to ACLSV, was unable to infect Chenopodium quinoa and C. amaranticolor. The sequence of its genome (7,494 nucleotides [nt], missing only approximately 30 to 40 nt of the 5' terminal sequence) and the partial sequence of another isolate were determined. The new virus has a genomic organization similar to that of ACLSV, with three open reading frames coding for a replication-associated protein (RNA-dependent RNA polymerase), a movement protein, and a capsid protein, respectively. However, it had only approximately 65 to 67% nucleotide identity with sequenced isolates of ACLSV. The differences in serology, host range, genome sequence, and phylogenetic reconstructions for all viral proteins support the idea that this agent should be considered a new virus, for which the name Apricot pseudo-chlorotic leaf spot virus (APCLSV) is proposed. APCLSV shows substantial sequence variability and has been recovered from various Prunus sources coming from seven countries, an indication that it is likely to have a wide geographical distribution.

Two classes of subgenomic RNA of grapevine virus A produced by internal controller elements

Grapevine virus A (GVA), a species of the recently established genus Vitivirus, consists of an approximately 7.3-kb single-stranded RNA genome of positive polarity, organized into five open reading frames (ORFs). The virus, which is closely associated with the grapevine rugose wood disease complex, has been poorly investigated genetically. We explored the production of viral RNAs in a GVA-infected Nicotiana benthamiana herbaceous host and characterized one nested set of three 5'-terminal sgRNAs of 5.1, 5.5, and 6.0 kb, and another, of three 3'-terminal sgRNAs of 2.2, 1.8, and 1.0 kb that could serve for expression of ORFs 2-3, respectively. Neither 3'- nor 5'-terminal sgRNAs, which would correspond to ORF5, was detected, suggesting that expression of this ORF occurs via a bi- or polycistronic mRNA. The 5'-terminal sgRNAs were abundant in dsRNA-enriched extracts. Cloning and sequence analysis of the 3' end of 5.5-kb 5'-terminal sgRNA and the 5' end of the 1.8-kb 3'-terminal sgRNA suggested that a mechanism other than specific cleavage was involved in production of these sgRNAs. Apparently, the production of the 5'- and 3'-terminal sgRNAs was controlled by sequences upstream of the 5'-terminus of each of ORFs 2-4. Detection of both plus and minus strands of the 5'- and 3'-terminal sgRNAs, though in different levels of accumulation, suggested that each of these cis-acting elements is involved in production of four RNAs: a 3'-terminal plus-strand sgRNA which could act as an mRNA, the corresponding 3'-terminal minus-strand RNA, a 5'-terminal plus-strand sgRNA, and the corresponding 5'-terminal minus-strand RNA.

The 50-kDa protein of Apple chlorotic leaf spot virus interferes with intracellular and intercellular targeting and tubule-inducing activity of the 39-kDa protein of Grapevine berry inner necrosis virus

To understand why transgenic Nicotiana occidentalis plants expressing a functional movement protein (MP) of Apple chlorotic leaf spot virus (ACLSV) show specific resistance to Grapevine berry inner necrosis virus (GINV), the MPs of ACLSV (50KP) and GINV (39KP) were fused to green, yellow, or cyan fluorescent proteins (GFP, YFP, or CFP). These fusion proteins were transiently expressed in leaf cells of both transgenic (50KP) and nontransgenic (NT) plants, and the intracellular and intercellular trafficking and tubule-inducing activity of these proteins were compared. The results indicate that in epidermal cells and protoplasts from 50KP plant leaves, the trafficking and tubule-inducing activities of GINV-39KP were specifically blocked while those of ACLSV-50KP and Apple stem grooving virus MP (36KP) were not affected. Additionally, when 39KP-YFP and 50KP-CFP were coexpressed in the leaf epidermis of NT plants, the fluorescence of both proteins was confined to single cells, indicating that 50KP-CFP interferes with the cell-to-cell trafficking of 39KP-YFP and vice versa. Mutational analyses of 50KP showed that the deletion mutants that retained the activities described above still blocked cell-to-cell trafficking of 39KP, but the dysfunctional 50KP mutants could no longer impede cell-to-cell movement of 39KP. Transgenic plants expressing the functional 50KP deletion mutants showed specific resistance against GINV. In contrast, transgenic plants expressing the dysfunctional 50KP mutants did not show any resistance to the virus. From these results, we conclude that the specific resistance of 50KP plants to GINV is due to the ability of the 50KP to block intracellular and intercellular trafficking of GINV 39KP.

Detection of apple chlorotic leaf spot virus using a 5' nuclease assay with a fluorescent 3' minor groove binder-DNA probe

The development of a real-time 5' nuclease RT-PCR assay for the detection of apple chlorotic leaf spot virus (ACLSV) from infected plant material is described. A short fluorogenic 3' minor groove binder-DNA hydrolysis probe was used to circumvent genome variability between isolates and target a short conserved sequence. The covalent attachment of the minor groove binder moiety at the 3' end of the probe increased the probe/target duplex stability and raised the melting temperature to a range suitable for real-time analysis. The method is rapid, sensitive and takes place within a single tube without post-PCR handling of the amplification products.

The nucleotide sequence and genomic organization of Citrus leaf blotch virus: candidate type species for a new virus genus

The complete nucleotide sequence of Citrus leaf blotch virus (CLBV) was determined. CLBV genomic RNA (gRNA) has 8747 nt, excluding the 3'-terminal poly(A) tail, and contains three open reading frames (ORFs) and untranslated regions (UTR) of 73 and 541 nucleotides at the 5' and 3' termini, respectively. ORF1 potentially encodes a 227.4-kDa polypeptide, which has methyltransferase, papain-like protease, helicase, and RNA-dependent RNA polymerase motifs. ORF2 encodes a 40.2-kDa polypeptide containing a motif characteristic of cell-to-cell movement proteins. The 40.7-kDa polypeptide encoded by ORF3 was identified as the coat protein. The genome organization of CLBV resembles that of viruses in the genus Trichovirus, but they differ in various aspects: (i) in trichoviruses ORF2 overlaps ORFs 1 and 3, whereas in CLBV, ORFs 2 and 3 are separated and ORFs 1 and 2 overlap in one nucleotide; (ii) CLBV gRNA and CP are larger than those of trichoviruses; and (iii) the CLBV 3' UTR is larger than that of trichoviruses. Phylogenetic comparisons based on CP amino acid signatures clearly separates CLBV from trichoviruses. Also contrasting with trichoviruses, CLBV could not be transmitted to Chenopodium quinoa Willd. Considering these singularities, we propose that CLBV should be included in a new virus genus.

Genome characterization of Botrytis virus F, a flexuous rod-shaped mycovirus resembling plant 'potex-like' viruses

This study reports the first sequence of a flexuous rod-shaped mycovirus and also the first molecular characterization of a virus that infects the plant-pathogenic fungus BOTRYTIS: cinerea. The mycovirus BOTRYTIS: virus F (BVF) contains an ssRNA genome of 6827 nucleotides and a poly(A) tract at or very near the 3' terminus. Computer analysis of the genomic cDNA sequence of BVF revealed two potential open reading frames (ORFs) encoding proteins of 212 kDa (ORF1) and 32 kDa (ORF2). ORF1 showed significant sequence identity to the RNA-dependent RNA polymerase (RdRp)-containing proteins of plant 'tymo-' and 'potex-like' viruses. However, the ORF1 protein contained an opal putative readthrough codon between the helicase and RdRp regions, a feature not seen in this position in 'tymo-' and 'potex-like' replicases sequenced to date. ORF2 shared amino acid similarity with coat proteins of plant 'potex-like' viruses. Three untranslated regions were present in the genome, comprising a region of 63 nucleotides preceding the initiation codon of ORF1, a 93 nucleotide stretch between ORFs 1 and 2 and a 3'-terminal region of 70 nucleotides preceding the poly(A) tract. The nucleotide sequence of a putative defective RNA (D-RNA) of 829 nucleotides was also determined. The D-RNA contained one potential ORF comprising the N-terminal region of the replicase fused in-frame to the C-terminal region of the coat protein. It is proposed that the mycovirus BVF belongs to a new, as yet unassigned genus in the plant 'potex-like' virus group.

Transgenic Nicotiana occidentalis Plants Expressing the 50-kDa Protein of Apple chlorotic leaf spot virus Display Increased Susceptibility to Homologous Virus, but Strong Resistance to Grapevine berry inner necrosis virus

ABSTRACT The 50-kDa protein (P50) encoded by the open reading frame 2 of Apple chlorotic leaf spot virus (ACLSV), a putative movement protein, was expressed in transgenic Nicotiana occidentalis plants. P50 in transgenic plants was mainly detected in a modified form in the cell wall fraction, similar to that in infected leaves. The P50-expressing plants (P50 plants) complemented the systemic spread of the P50-defective mutants of an infectious cDNA clone of ACLSV (pCLSF), indicating that P50 in transgenic plants was functional. Severity of symptoms was greatly enhanced and accumulation of virus in upper leaves was increased in P50 plants inoculated with pCLSF or ACLSV compared with that in nontransgenic control plants (NT plants). Conversely, transgenic plants expressing the coat protein of ACLSV (CP plants) showed a significant delay in symptom development and a reduction of virus accumulation. However, most P50 plants inoculated with Grapevine berry inner necrosis virus (GINV), another species of the genus Trichovirus, neither developed obvious symptoms nor supported virus accumulation in inoculated or upper leaves. In contrast, systemic symptoms developed and virus accumulated equally in NT and CP plants inoculated with GINV. After inoculation with Apple stem grooving virus or Apple stem pitting virus, there was no difference in symptom development and virus accumulation among P50, CP, and NT plants. Our results indicate that transgenic plants expressing a functional P50 were more susceptible to homologous virus and, on the contrary, showed strong resistance to the heterologous virus GINV.

Specific Detection of Cherry Mottle Leaf Virus Using Digoxigenin-Labeled cDNA Probes and RT-PCR

Cherry mottle leaf virus (CMLV)-associated double-stranded RNA (dsRNA) was isolated from the propagation host Chenopodium quinoa. The dsRNA band, with a molecular weight estimated at 7.0 × 10⁶ Da, was used to produce cDNA. Two recombinant plasmids from the cloned cDNA library were identified that specifically bound with CMLV-associated RNA in dot blot hybridization studies. The cDNA inserts were sequenced, and oligonucleotide primers were designed that specifically amplify an 848-bp fragment of the CMLV genome by reverse-transcription polymerase chain reaction. Also, a poly(T) primer was reliably used for reverse transcription, with specific amplification using the CMLV primers, suggesting polyadenylation of the virus genome. Search of the database revealed some sequence homology of the partially characterized genome of CMLV with that of apple chlorotic leafspot virus. Additional sequence data are required, however, to establish the taxonomic position of the filamentous CMLV.

Nucleotide sequence and rt-PCR detection of a virus associated with grapevine rupestris stem-pitting disease

ABSTRACT Grapevine rupestris stem pitting (RSP) is a graft-transmissible disease of unknown etiology. We have characterized a virus associated with this disease. The entire genomic sequence (GenBank accession number AF026278) consisted of 8,725 nucleotides excluding a poly(A) tail. Six open reading frames (ORF) were found. ORF1 potentially encodes a polypeptide with a methyltransferase domain, a papain-like proteinase domain, a helicase domain, and a RNA-dependent RNA polymerase domain; ORF2, ORF3, and ORF4 compose a triple-gene block; ORF5 encodes a coat protein; and ORF6 is located near the 3' end with unknown function. Sequence analysis indicated that the virus is most similar to apple stem-pitting virus and may be allied with the carla- and potexviruses and grouped with other viruses that infect woody hosts. A specific reverse-transcription polymerase chain reaction (RT-PCR)-based detection method was developed. Among 62 grapevine sources known to be infected with rupestris stem-pitting disease, 60 sources tested positive by RT-PCR. Among 43 healthy vines tested, all were negative. The name grapevine rupestris stem-pitting-associated virus is proposed.

In vitro translation of apple chlorotic leaf spot virus (ACLSV) RNA

The genomic RNA of apple chlorotic leaf spot virus was translated in a rabbit reticulocyte lysate system, yielding a large, 190 K product as well as several other polypeptides of smaller size (60, 56, 22 and 15 kDa). The 22 kDa product was immunoprecipitated by an anti-ACLSV serum and comigrated with purified ACLSV coat protein. In vitro translation of RNA transcripts prepared from cloned ACLSV cDNAs demonstrates that the coat protein is synthesised by initiation on the second in frame AUG codon of the 28 kDa open reading frame located at the 3' end of the genome. In the in vitro translation system used, the ability of various ACLSV-derived RNAs to direct the synthesis of the coat protein appears to be the result of initiation on the internal AUG codon.

Gene expression from viral RNA genomes

This review is centered on the major strategies used by plant RNA viruses to produce the proteins required for virus multiplication. The strategies at the level of transcription presented here are synthesis of mRNA or subgenomic RNAs from viral RNA templates, and 'cap-snatching'. At the level of translation, several strategies have been evolved by viruses at the steps of initiation, elongation and termination. At the initiation step, the classical scanning mode is the most frequent strategy employed by viruses; however in a vast number of cases, leaky scanning of the initiation complex allows expression of more than one protein from the same RNA sequence. During elongation, frameshift allows the formation of two proteins differing in their carboxy terminus. At the termination step, suppression of termination produces a protein with an elongated carboxy terminus. The last strategy that will be described is co- and/or post-translational cleavage of a polyprotein precursor by virally encoded proteinases. Most (+)-stranded RNA viruses utilize a combination of various strategies.

Principles of molecular organization, expression, and evolution of closteroviruses: over the barriers

This chapter focuses on the molecular organization, evolution, and expression of closterovirus genomes, as well as on their unique particle structure. The closterovirus group combines several positive-strand RNA viruses with very flexuous filamentous particles, of which beet yellows virus (BYV) is the type virus. Closteroviruses are distinct from other RNA viruses of plants in some important phenomenological aspects. They have genomes of up to 20 kilobases (kb), a value comparable only to those of the animal coronaviruses and toroviruses, which have the largest RNA genomes of all positive-strand RNA viruses. The existence of such genomes having a coding capacity several times that of an average RNA virus genome raises questions as to the trend whereby the long genomes have evolved and the possible novel functions they have acquired. The dramatic increase in the closterovirus genome coding capacity may be linked to the distinct ecological niche they occupy. Thus, closteroviruses are the only elongated plant viruses known so far to cause phloem-limited infections in plants and to persist in their insect vectors for many hours, in contrast to only minutes.

Papain-like proteinase of turnip yellow mosaic virus: a prototype of a new viral proteinase group

Sequence comparisons predicted a potential papain-like proteinase domain in the N-terminal cleavage product (NRP) of the large nonstructural replicase polyprotein (RP) of turnip yellow mosaic virus (TYMV). Replacement of the predicted catalytic amino acids, Cys-783 by Ser, or of His-869 by Glu, abolished cleavage of the 206K RP into a approximately 150 K NRP and a approximately 78 K C-terminal product in reticulocyte lysates, while other substitutions exerted no apparent influence on proteolysis. The proteinase-deficient mutant RPs could not be cleaved in trans by as much as an eight-fold molar excess of wild-type proteinase. Deletion experiments have excluded the possible influence on autoproteolysis of amino acid sequences 1-708 and 982-1204 flanking the proteinase domain. Thus, the proteinase of TYMV with a papain-like dyad of essential amino acids has been mapped just upstream from the putative NTPase domain. Statistically significant sequence similarities with the TYMV proteinase were found for the similarly located domains of the replicase polyproteins of carlaviruses, capilloviruses, apple stem pitting virus and apple chlorotic leaf spot virus as well as for those of other tymoviruses and for the domain located downstream from the putative NTPase domain of the large polyprotein of beet necrotic yellow vein furovirus. All these domains are not significantly similar to other known proteinases, although they conserve papain-like Cys- and His-containing motifs. Thus these domains constitute a compact group of related enzymes, the tymo-like proteinases, within the proposed papain-like proteinase supergroup. The resulting alignment of 10 tymo-like proteinase sequences has revealed a third highly conserved residue--Gly (Gly821 in TYMV RP) followed by a hydrophobic residue. We speculate that all the tymo-like proteinase domains of the viral replicative proteins may share common biochemical and biological features.

Nucleotide sequence of the 3' terminal region of the RNA of two filamentous grapevine viruses

The 3' terminal region of grapevine virus A (GVA) and grapevine virus B (GVB), encompassing 1883 and 2136 nucleotides, respectively, was sequenced by the deoxynucleotide chain termination method. Three putative open reading frames (ORF) were identified in both genomic viral RNAs, denoted 1 to 3 in the 5' to 3' direction. ORF 1 encoded a polypeptide with estimated M(r) of 31 kDa (GVA) and 36.5 kDa (GVB), possessing the G/D motif of the "30 K superfamily" movement proteins, and showing good alignments with putative movement proteins of trichoviruses and capilloviruses. ORF 2 was identified as the coat protein (CP) cistron, coding for polypeptides with an estimated M(r) of 21.5 kDa (GVA) and 21.6 kDa (GVB). These CPs showed substantial sequence homology with one another and with CPs of tricho- and capilloviruses, but not of closteroviruses. ORF 3 potentially coded for two small polypeptides with estimated M(r) of 10 kDa (GVA) and 14 kDa (GVB). The ORF 3 product of GVB (14 K), but not that of GVA, shared some homology with the 3' terminal polypeptides of different plant viruses that exhibit the "zinc finger domain" of proteins with nucleic acid-binding properties. GVA and GVB have many properties in common with trichoviruses but possess an extra open reading frame (ORF 3). Whether this finding may have a bearing on the classification of these viruses is unclear. However, until the taxonomic significance of this difference in genome structure is established, it seems plausible to include GVA and GVB as tentative species in the Trichovirus genus.

Nucleotide sequence of the 3'-terminal region of citrus tatter leaf virus RNA

The 3'-terminal sequence of citrus tatter leaf virus lily isolate (CTLV-L) was determined from cloned cDNA. The sequence contains two open reading frames (ORFs). ORF1 encodes a protein that contains consensus sequences associated with the RNA-dependent RNA polymerase. ORF2, which is in a different reading frame within ORF1, can encode a 36 kD protein, putatively identified as a movement protein. CTLV-L coat protein (CP) was found to be located in the C-terminal region of the polyprotein encoded by ORF1. Evolutionary relationships and classification of capilloviruses is discussed.

Progress towards a higher taxonomy of viruses

The current consensus view is that a higher hierarchical taxonomy of viruses cannot be established for two reasons. Firstly, viruses appear to be polyphyletic in origin, with several sets of viruses arising by different, independent routes at different times. Secondly, subsequent virus adaptation for survival in different host/vector combinations has involved the selective acquisition of additional genes by a process of cassette or modular evolution, with these additional gene modules coming from other viruses or host genetic material. Thus, depending on the gene product used for comparison, different phylogenetic relationships can be deduced. Further virus adaptation can arise by reassortment of segmented genomes, gene duplication, deletions, frameshift mutations, point mutations or de novo development of new gene products from existing, unused reading frames. The solution to the first objection is to place all viruses in a separate kingdom and assign the current viruses to several phyla that reflect these diverse origins. The solution to the second objection is to consider the core module of replication machinery as the major criterion on which to make the initial assignments to classes and orders. For RNA viruses, the major criterion is the sequence identity of the RNA-dependent RNA polymerase. Using this criterion, the positive strand RNA viruses can be assigned to five classes that correspond to the recently recognized supergroups of RNA viruses. These five classes contain four, three, three, three and one order(s) respectively. These fourteen orders contain 31 virus families (including 17 families of plant viruses) and 48 genera (including 30 genera of plant viruses). This approach confirms the separation of the alphaviruses and flaviviruses into two families, the Togaviridae and Flaviridae, but suggests that several other current taxonomic assignments, such as the pestiviruses, hepatitis C virus, rubiviruses, hepatitis E virus and arteriviruses, may be wrong. The coronaviruses and toroviruses appear to be distinct families in distinct orders, not distinct genera of the same family as currently classified. In addition, the luteoviruses are split into two families and apple chlorotic leaf spot virus appears not to be a closterovirus but a new genus of the Potexviridae. From an analysis of the polymerase dendrograms of the dsRNA viruses, it appears that they are not closely related to each other, but belong to four additional classes (Partitiviridae, Reoviridae, Birnaviridae and Cystoviridae) and one additional order (Totiviridae) of one of the classes of positive ssRNA viruses in the same subphylum as the positive strand RNA viruses.(ABSTRACT TRUNCATED AT 400 WORDS)

Evolution and taxonomy of positive-strand RNA viruses: implications of comparative analysis of amino acid sequences

Despite the rapid mutational change that is typical of positive-strand RNA viruses, enzymes mediating the replication and expression of virus genomes contain arrays of conserved sequence motifs. Proteins with such motifs include RNA-dependent RNA polymerase, putative RNA helicase, chymotrypsin-like and papain-like proteases, and methyltransferases. The genes for these proteins form partially conserved modules in large subsets of viruses. A concept of the virus genome as a relatively evolutionarily stable "core" of housekeeping genes accompanied by a much more flexible "shell" consisting mostly of genes coding for virion components and various accessory proteins is discussed. Shuffling of the "shell" genes including genome reorganization and recombination between remote groups of viruses is considered to be one of the major factors of virus evolution. Multiple alignments for the conserved viral proteins were constructed and used to generate the respective phylogenetic trees. Based primarily on the tentative phylogeny for the RNA-dependent RNA polymerase, which is the only universally conserved protein of positive-strand RNA viruses, three large classes of viruses, each consisting of distinct smaller divisions, were delineated. A strong correlation was observed between this grouping and the tentative phylogenies for the other conserved proteins as well as the arrangement of genes encoding these proteins in the virus genome. A comparable correlation with the polymerase phylogeny was not found for genes encoding virion components or for genome expression strategies. It is surmised that several types of arrangement of the "shell" genes as well as basic mechanisms of expression could have evolved independently in different evolutionary lineages. The grouping revealed by phylogenetic analysis may provide the basis for revision of virus classification, and phylogenetic taxonomy of positive-strand RNA viruses is outlined. Some of the phylogenetically derived divisions of positive-strand RNA viruses also include double-stranded RNA viruses, indicating that in certain cases the type of genome nucleic acid may not be a reliable taxonomic criterion for viruses. Hypothetical evolutionary scenarios for positive-strand RNA viruses are proposed. It is hypothesized that all positive-strand RNA viruses and some related double-stranded RNA viruses could have evolved from a common ancestor virus that contained genes for RNA-dependent RNA polymerase, a chymotrypsin-related protease that also functioned as the capsid protein, and possibly an RNA helicase.

The nucleotide sequence of apple stem grooving capillovirus genome

The complete nucleotide sequence of apple stem grooving virus (ASGV) genome has been determined. The genome is 6496 nucleotides in length excluding a 3'-terminal poly(A) tail and contains two overlapping open reading frames (ORFs). ORF1 begins at nucleotide position 37 and is terminated at position 6341, encoding a protein with a molecular weight of 241 kDa. ORF2, which is in a different reading frame within ORF1, begins at position 4788 and can encode a 36-kDa protein. The 241-kDa protein contains two consensus sequences associated with the RNA-dependent RNA polymerase and the NTP-binding helicase. Comparisons of amino acid sequences around these conserved motifs with other RNA viruses revealed that ASGV has extensive similarities with apple chlorotic leaf spot, tymo-, carla-, and potexviruses, and is a member of the sindbis-like supergroup. ASGV coat protein is found to be located in the C-terminal region of the 241-kDa polyprotein. The 36-kDa protein encoded by ORF2 contains the consensus sequence Gly-Asp-Ser-Gly found in the active site of several cellular and viral serine proteases.

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.

Identification of the initiation codon of plum pox potyvirus genomic RNA

The expression of plum pox potyvirus (PPV) genomic RNA takes place through translation of its unique long and functional open reading frame (ORF) into a large polyprotein that undergoes extensive proteolytic processing. In this paper we show that the AUG recognized as the initiation codon of the PPV ORF by in vitro translation systems is the one found at nucleotide position 147, in spite of the presence at position 36 of an in-phase AUG that marks the start of the ORF. Deletion of a substantial part of the PPV 5' nontranslated region (5'-NTR), from nucleotide 19 to 101, does not impair the in vitro translation of PPV synthetic transcripts. By introduction of mutations that disrupt either of these two AUGs into a full-length PPV cDNA clone, it is shown that, while alteration of the first AUG does not have any effect on virus viability, growth, or symptom induction, destruction of the second renders the viral RNA noninfectious. This result indicates that the AUG employed in vivo is also the second. The hypothesis that this AUG could be recognized through a ribosomal internal entry mechanism has been tested in vitro using various bicistronic transcripts in which the PPV 5'-NTR was internally placed. The second cistron of these bicistronic RNAs was translated, but only at low levels, indicating that the PPV 5'-NTR is not able to drive in vitro an efficient internal entry of the ribosomes and suggesting that PPV RNA translation might proceed through a conventional leaky scanning mechanism.

Phylogeny of capsid proteins of rod-shaped and filamentous RNA plant viruses: two families with distinct patterns of sequence and probably structure conservation

Computer-assisted comparative analysis of all available amino acid sequences of the capsid proteins of positive strand RNA plant viruses with helical capsids is described. Two distinct families of homologous proteins were delineated through statistically significant sequence similarities, one including the capsid proteins of rod-shaped viruses (tobamo-, tobra-, hordei-, and furoviruses) and the other those of filamentous viruses (poty-, bymo-, potex-, carla-, and closteroviruses). It was concluded that the capsid proteins of all rod-shaped viruses, on the one hand, and filamentous viruses, on the other hand, evolved from common ancestors. Analysis of residue conservation patterns in the capsid proteins of rod-shaped viruses revealed maintenance of the hydrophobic core and of the (putative) salt bridge between conserved Arg and Asp residues. Sequence comparisons within the filamentous virus family expanded the observations on the relationship between the capsid proteins of potex-, carla-, poty-, and bymoviruses. Grouping of the beet yellows closterovirus capsid protein sequence, recently determined in this laboratory (Agranovsky et al., J. Gen. Virol., 1991, 72, 15-23), with those of potex- and carlaviruses was demonstrated. The coat protein of another closterovirus, apple chlorotic leaf spot virus, appeared to constitute a distinct phylogenetic lineage. Despite the lack of significant overall similarity, comparison of the alignments of the capsid proteins of the two families suggested formation of analogous salt bridges.