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Helical plant viruses are arranged into four families: Flexiviridae, Tobamoviridae, Hordeiviridae, and Tobraviridae. Further division of these families into genera and subgenera is shown. A family-specific, constant amount of RNA per unit virion length and a distinct radial location of RNA from the center of the helix are considered as basic criteria for establishment of these families.
Cowpea chlorotic mottle virus RNA has been prepared in comparatively high yield (at least 50%) by a modified phenol extraction method. The preparation, which has high biological activity, has been resolved into four components by zonal centrifugation on a 15-40% (w/v) sucrose density gradient. The components obtained have been tested for biological activity against whole plants and plant protoplasts. Each of the two largest components RNA 1 and RNA 2 was by itself infective (50-90% of the specific infectivity of the whole genome) and produced virus-specific proteins (coat protein and P2) and RNAs ("RNA 3" and "RNA 4"). Contamination by small proportions (less than 10%) of neighbouring RNAs is presumed to be involved in this infectivity. The two smallest components were obtained in an almost pure form.
Plant viruses pose a significant threat to global agriculture and require efficient tools for their timely detection. We present AutoPVPrimer, an innovative pipeline that integrates artificial intelligence (AI) and machine learning to accelerate the development of plant virus primers. The pipeline uses Biopython to automatically retrieve different genomic sequences from the NCBI database to increase the robustness of the subsequent primer design. The design_primers_with_tuning module uses a random forest classifier that optimizes parameters and provides flexibility for different experimental conditions. Quality control measures, including the evaluation of poly-X content and melting temperature, increase primer reliability. Unique to AutoPVPrimer is the visualize_primer_dimer module, which supports the visual evaluation of primer dimers-a feature missing in other tools. Primer specificity is validated via primer BLAST, which contributes to the overall efficiency of the pipeline. AutoPVPrimer has been successfully applied to the tomato mosaic virus, proving its adaptability and efficiency. The modular design allows customization by the user and extends the applicability to different plant viruses and experimental scenarios. The pipeline represents a significant advance in primer design and provides researchers with an effective tool to accelerate molecular biology experiments. Future developments aim to extend compatibility and incorporate user feedback to consolidate AutoPVPrimer as an innovative contribution to the bioinformatics toolbox and a promising resource for the advancement of plant virology research.
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To facilitate the recognition of plant viruses with similar characteristics a dendrogram of characterized viruses was constructed. The sequence of criteria included: type of nucleic acid; single or double stranded; presence or absence of lipid envelope; helical or nonhelical symmetry; and divided or single genome. Nonhelical RNA viruses with divided genomes were further divided into viruses with one or more than one capsid size. Those with one capsid size were subdivided into viruses with one or more than one sedimenting component. Nonhelical RNA viruses with a single genome were divided according to their RNA size, and their sensitivity to sodium dodecyl sulfate and ethylenediaminetetraacetic acid.
Some characteristics of a microplate method for the detection and assay of plant viruses using enzyme-labelled antibodies are described. The method enabled the highly sensitive detection of a number of morphologically different viruses in purified preparations and in unclarified extracts of herbaceous hosts and of infected crop plants. Virus concentrations were estimated by photometric measurement of the colour intensity of the hydrolysed substrate. The suitability of the tehcnique for various field and research applications is considered.
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Plant-infecting viruses spread through their hosts by transporting their infectious genomes through intercellular nano-channels called plasmodesmata. This process is mediated by virus-encoded movement proteins. Whilst the sub-cellular localisations of movement proteins have been intensively studied, live-cell RNA imaging systems have so far not been able to detect viral genomes inside the plasmodesmata. Here, we describe a highly sensitive RNA live-cell reporter based on an enzymatically inactive form of the small bacterial endonuclease Csy4, which binds to its cognate stem-loop with picomolar affinity. This system allows imaging of plant viral RNA genomes inside plasmodesmata and shows that potato virus X RNA remains accessible within the channels and is therefore not fully encapsidated during movement. We also combine Csy4-based RNA-imaging with interspecies movement complementation to show that an unrelated movement protein from tobacco mosaic virus can recruit potato virus X replication complexes adjacent to plasmodesmata. Therefore, recruitment of potato virus X replicase is mediated non-specifically, likely by indirect coupling of movement proteins and viral replicase via the viral RNA or co-compartmentalisation, potentially contributing to transport specificity. Lastly, we show that a 'self-tracking' virus can express the Csy4-based reporter during the progress of infection. However, expression of the RNA-binding protein in cis interferes with viral movement by an unidentified mechanism when cognate stem-loops are present in the viral RNA.
The localization of the RNA in a spherical plant virus is established by neutron diffraction. For BMV, this localization is different at low pH than it is at high pH (swollen virus).
Recent experiments on the disassembly and assembly of some flexuous plant viruses and their proteins are described. The properties of reconstituted potato virus X and those of assembled potato virus Y protein are considered as well as the suitability of other flexuous viruses for reconstitution studies.
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Potyviridae is the largest family of plant-infecting RNA viruses. All members of the family (potyvirids) have single-stranded positive-sense RNA genomes, with polyprotein processing as the expression strategy. The 5'-proximal regions of all potyvirids, except bymoviruses, encode two types of leader proteases: the serine protease P1 and the cysteine protease HCPro. However, their arrangement and sequence composition vary greatly among genera or even species. The leader proteases play multiple important roles in different potyvirid-host combinations, including RNA silencing suppression and virus transmission. Here, we report that viruses in the genus Arepavirus, which encode two HCPro leader proteases in tandem (HCPro1-HCPro2), can naturally lose the coding sequences for these two proteins during infection. Notably, this loss is associated with a shift in foliage symptoms from severe necrosis to mild chlorosis or even asymptomatic infections. Further analysis revealed that the deleted region is flanked by two short repeated sequences in the parental isolates, suggesting that recombination during virus replication likely drives this genomic deletion. Reverse genetic approaches confirmed that the loss of leader proteases weakens RNA silencing suppression and other critical functions. A field survey of areca palm trees displaying varied symptom severity identified a transitional stage in which full-length viruses and deletion mutants coexist in the same tree. Based on these findings, we propose a scenario in which full-length isolates drive robust infections and facilitate plant-to-plant transmission, eventually giving rise to leader protease-less variants that mitigate excessive damage to host trees, allowing long-term coexistence with the perennial host. To our knowledge, this is the first report of potyvirid self-attenuation via coding sequence loss.
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Extracts from the seeds of 15 species of legume inhibited the infection of plants by viruses. Extracts could be divided into those with marked inhibitory activity reducible on heating and those with less marked inhibitory activity which increased on heating. Evidence is given is given to suggest that seed extracts contain both virus inhibitors and augmenters and that the inhibitors are high molecular weight proteins possibly related to lectins.