Three-dimensional model of the potyviral genome-linked protein

The full sequence of the genome-linked viral protein (VPg) cistron located in the central part of potato virus Y (common strain) genome has been identified. The VPg gene codes for a protein of 188 amino acids, with significant homology to other known potyviral VPg polypeptides. A three-dimensional model structure of VPg is proposed on the basis of similarity of hydrophobic-hydrophilic residue distribution to the sequence of malate dehydrogenase of known crystal structure. The 5' end of the viral RNA can be fitted to interact with the protein through the exposed hydroxyl group of Tyr-64, in agreement with experimental data. The complex favors stereochemically the formation of a phosphodiester bond [5'-(O4-tyrosylphospho)adenylate] typical for representatives of picornavirus-like viruses. The chemical mechanisms of viral RNA binding to VPg are discussed on the basis of the model structure of protein-RNA complex.

Digoxigenin-labelled molecular probe for the simultaneous detection of three potato pathogens: potato spindle tuber viroid (PSTVd), potato virus Y (PVY), and potato leafroll virus (PLRV)

A molecular probe, p3POT, was constructed of PSTVd, PVY, PLRV cDNA fragments introduced into pUC18 vector. Sequencing of the inserts revealed that cloned fragments covered conservative parts of pathogenic genomes. Dot-blot hybridization of digoxigenin-labelled construct to crude extracts from plants infected with different potato viruses proved high sensitivity and specificity of the p3POT probe. This makes p3POT probe an useful tool for the routine testing, and selection of virus-free potatoes.

Detection of potato spindle tuber viroid (PSTV) in dormant potato tubers by concatameric cDNA probe

The 32P-labelled concatameric insert cut out from a plasmid pSPAv6.2(+), containing 6.2 copies of a full-length PSTV, was used to detect PSTV in dormant potato tubers by dot-blot hybridisation assay. The concatameric insert probe was 4 times more sensitive than the monomeric one. This allowed the detection of 0.5 pg of viroid RNA. The sensitivity makes th eoligomeric cDNA probe a useful alternative to cDNA probes.

Characterisation of synthetic DNA probe detecting potato spindle tuber viroid

Chemically synthesized DNA fragments complementary to selected regions of the potato spindle tuber viroid (PSTV) genome were cloned into Escherichia coli plasmid pUC9. One of the recombinant plasmids (pIBB4) with a 87 bp insert representing the central region of the PSTV genome (nucleotides 88 to 174) was used after labelling by nick translation for detecting PSTV by dot-blot hybridization. The molecular probe was almost as sensitive as the one carrying the full genomic PSTV copy (pAV401), detecting down to 20 pg of PSTV RNA in 8-15 micrograms of infected tissue. The specificity of the test was high; no signals were created by extracts from healthy plants or plants infected with a variety of common potato viruses. The probe is potentially useful in studies on mixed infections of potatoes with different viruses, and in selection of certified seed material.