Use of [32P]RNA probes for the dot-hybridization detection of potato spindle tuber viroid

Development of the molecular methods for potato virus and viroid detection and prevention

Potato is the fourth most important food crop in the world and it forms the diet of a billion consumers in developing countries, where potato production is increasing rapidly. However, potato virus diseases in developing countries are one of the major causes of lower yields. Their control requires the development of appropriate virus-detection and seed-production technologies for the region. Recent progress in developing nucleic acid based virus detection methods are reviewed. Refinements of the protocols applicable to the laboratories located in seed producing areas are discussed. Nucleic acid spot hybridization (NASH) and reverse transcription polymerase chain reaction (RT-PCR) methods are described for the detection of viruses and viroids in dormant seed tubers and insect vectors. Although the potato crop is susceptible to over 25 virus and viroid diseases, only universally economically important viruses have been dealt with here. The progress of pathogen-derived resistance for the control of potato virus diseases is elaborated, and the results of field tests indicate their feasibility in virus control.Key words: dot-blot, spot-hybridization, reverse transcription, polymerase chain reaction, transgenic plants.

A mixture of synthetic oligonucleotide probes labeled with biotin for the sensitive detection of potato spindle tuber viroid

Five kinds of synthetic oligonucleotide probes labeled with biotin (BIO) were designed for the detection of potato spindle tuber viroid (PSTVd), and their sensitivities were compared with that of a digoxigenin (DIG)- or BIO-labeled cDNA probe. Although each oligonucleotide probe alone was less sensitive than the DIG-cDNA probe, sensitivity was increased by using a mixture of two or all of the five oligonucleotide probes. The sensitivity of a PSmix1-5 probe, which was a mixture of five oligonucleotides, was the same as that of a DIG-labeled cDNA probe, which can detect 7.8 pg of purified PSTVd and PSTVd in nucleic acids, equivalent to extracts from 20 microg of infected potato leaf and 310 microg of infected potato tuber. Using the PSmix1-5 probe, PSTVd in all leaves and tubers of seven potato cultivars could be detected without any background. Moreover, with the PSmix1-5 probe, the hybridization time could be shortened to 2 h without any decrease in sensitivity, whereas the sensitivity of the cDNA probes clearly decreased when the hybridization time was shortened. Hybridization using a mixture of several oligonucleotide probes may be applicable to the gene diagnosis of other viroids and viruses.

Multimeric non-radioactive cRNA probes improve detection of potato spindle tuber viroid (PSTVd)

Experimental data showed that multimeric, complementary RNA (cRNA) probes, labelled with non-radioactive digoxigenin (DIG), improved sensitivity of detection of the potato spindle tuber viroid (PSTVd) RNA by 2- to 30-fold as compared with corresponding multimeric cDNA probes. The degree of PSTVd detectability improvement depended upon the type of alkaline phosphatase substrate (colorimetric vs. chemiluminescent) used. Use of hexameric DIG-labelled cRNA probes in combination with chemiluminescent (Lumi-Phos 530) substrate resulted in detection of 0.48 pg of PSTVd RNA. The size of the synthesized cRNA probes corresponded to the size of the respective PSTVd cDNA templates. Interestingly, there was no relationship between the size of the synthesized, DIG-labelled DNA probes and that of the PSTVd cDNA template. This type of anomaly was not observed with other plant viral cDNA templates. Monomeric or multimeric cDNA probes detected both a mild and a severe PSTVd strain in viroid-infected potato leaf extracts diluted 1024 to 2048 times. In comparison, cRNA probes exhibited a much greater dilution end point; PSTVd RNA was detectable in viroid-infected potato leaf tissue diluted up to 16,384 times. Comparable levels of PSTVd sensitivity of detection were obtained with viroid-infected potato tuber tissue.

Primary and secondary structure of a 360-nucleotide isolate of potato spindle tuber viroid

Full-length complementary DNAs (cDNA) of a mild (KF5) and a severe (S-PSTVd) isolate of potato spindle tuber viroid (PSTVd) were constructed. DNA sequencing of four KF5 cDNA clones (M3, M4, M5, and M7) revealed that KF5 is comprised of 360 nucleotides. By comparison, all three cDNA clones (S2, S9, and S10) of S-PSTVd possess 359 nucleotides. Sequence microheterogeneity was observed among the KF5 cDNA clones. Clone M5 differs from mild PSTVd isolate KF6 by a U-to-A transversion at position 303 followed by an A addition at the lower half of the "virulence-modulating" (VM) region. These changes modified the PSTVd consensus sequence of the VM region from 5' UCUAUCU 3' to 5' UCAAAUCU 3'. Additionally, clones M4 and M7 have a G-to-A transition at position 65 of the pathogenic domain, and M3 has a G-to-A transition at position 133 of the variable domain. The sequence of the three cDNA clones of S-PSTVd was identical to that of PSTVd isolate 440-1. An improved computer program was used to predict the secondary structure of the above two sequence variants as well as that of other PSTVd variants of which the structure has been reported previously. The data provides support for the hypothesis that increasing thermodynamic instability of the VM region is correlated with increasing virulence of the respective naturally occurring PSTVd isolate.

Chemiluminescent detection of potato and pome fruit viroids by digoxigenin-labeled dot blot and tissue blot hybridization

A chemiluminescent molecular hybridization protocol was compared to 32P autoradiography for detecting potato spindle tuber viroid (PSTVd) and apple scar skin group viroids (ASSVd). Labeled cRNA probes for PSTVd and ASSVd were synthesized by SP6 RNA polymerase transcription using digoxigenin-11-UTP or alpha-[32P]UTP. Dot blot hybridization of purified viroids and sap extracts from infected plants showed that chemiluminescent detection using digoxigenin-labeled probes was as sensitive as autoradiography using 32P probes. A minimum of 2.0-2.5 pg purified viroid was detected. ASSVd could be detected in as little as 0.4 ng of total nucleic acid extract from infected tissue or in sap extracts diluted to 10(-3) with healthy extracts. Tissue blots of PSTVd-infected potato tubers and tomato roots, stems and leaves and ASSVd-infected apple fruit, stems and petioles, gave positive reactions when hybridized with the digoxigenin probe. No reaction with similar tissues from healthy plants was observed.

A rapid chemiluminescent detection method for barley yellow dwarf virus

Barley yellow dwarf virus (BYDV-PAV-IL) was detected with biotinylated in vitro transcript cDNA using a chemiluminescent substrate on nylon membranes. Signals were detected on X-ray film and quantified using either a densitometer or an ELISA plate reader. The time required for sample preparation was reduced so that the entire protocol could be completed in two days. The in vitro transcript probes could detect 1 ng of purified virus and as little as 1 microliter of sap extracts prepared from infected oat shoots.

Highly sensitive digoxigenin-labelled DNA probe for the detection of potato spindle tuber viroid

A molecular probe pSPAv6.2(+), with concatameric insert representing 6.2-times repeated copy of potato spindle tuber viroid (PSTV) RNA, was labelled with digoxigenin and used to detect PSTV by dot-blot hybridization assay. The probe was highly sensitive and specific, detecting as little as 2.5 pg of PSTV RNA. Both severe and mild PSTV strains were detectable in 64-512-times diluted crude extracts from infected tomato leaves, and potato leaves, sprouts, and seeds. For extraction of plant tissue three buffers were compared to determine the lowest non-specific background and the highest sensitivity. The results showed that the digoxigenin-labelled probe is as sensitive as the 32P-labelled probe and can replace radioactive techniques in PSTV detection. With such high sensitivity, the probe is also potentially useful for detecting the viroid in composite samples of mass-indexing programs.

A rapid and versatile method for cloning viroids or other circular plant pathogenic RNAs

We surveyed the occurrence of unique restriction sites on the cDNAs of viroids, virusoids, and plant viral satellite RNAs that have a circular RNA as an intermediate of replication and found that four such sites would linearize their circular cDNAs. A rapid and simple method was then developed for cloning a naturally occurring viroid from Nematanthus wettsteinii plants. First-strand cDNA was synthesized using random hexanucleotide DNA primers and M-MuLV reverse transcriptase (Superscript RT). Second-strand DNA was synthesized by employing the replacement synthesis method using Escherichia coli RNase H, E. coli DNA polymerase I, E. coli DNA ligase, and beta-NAD+. The circular double-stranded DNA was analyzed for the presence of commonly available, unique restriction sites and subsequently linearized with a selected restriction enzyme. The linear cDNA was ligated to dephosphorylated plasmid vector pGEM 3Z f(+) and cloned in E. coli strain DH5 alpha. This cDNA cloning procedure is suitable for cloning sequence variants of well-characterized viroids, virusoids, certain plant viral satellite RNAs, and new such pathogens of unknown sequence.

RNA progeny of an infectious two-base deletion cDNA mutant of potato spindle tuber viroid (PSTV) acquire two nucleotides in Planta

Deletion mutations were generated in four structural domains of a potato spindle tuber viroid (PSTV) complementary DNA (cDNA) clone. Deletions of 3 to 5 nucleotides at the central conserved domain (CCGGG, positions 94 to 98), variable domain (GCCG, positions 146 to 149) and pathogenicity domain (CGA, positions 286 to 288) abolished infectivity of dimeric or trimeric cDNA constructs, or their in vitro transcripts. By contrast, a clone (St4) with a deletion of two nucleotides (UU, positions 339 and 340), located at the left terminal domain, retained infectivity when DNA or in vitro transcribed (+)RNA was used as inoculum. Sequencing of four cDNA clones of such viroid progeny demonstrated that two nucleotides were added at the deletion site. Two of the viroid progeny contained a CG addition. A third clone possessed a GU addition, whereas the fourth clone had a UU addition which represents a true reversion to full-length wild-type PSTV RNA. Ribonuclease protection assay of viroid progeny from St4-infected tomato plants suggested that only a negligible proportion of the St4 progeny were true revertants.

Comparison of nonradioactive cDNA probes for detection of potato spindle tuber viroid by dot-blot hybridization assay

Six nonradioactive cDNA probes were compared for their sensitivities for detecting potato spindle tuber viroid (PSTVd) by dot-blot hybridization assay. Three biotinylated PSTVd cDNA probes, labeled by photoactivation with photobiotin, by nick translation or by random priming with biotinylated deoxyribonucleotides, were all capable of detecting 20 pg of purified PSTVd by a colorimetric assay and 2-20 pg by a chemiluminescent assay. Digoxigenin-labeled probe was able to detect 200 pg of purified PSTVd. Two biotinylated probes prepared with polymerase chain reaction (PCR) incorporating biotinylated dUTP or dATP were the most sensitive: 0.2-2 pg of PSTVd was detectable by both assays. All six probes could detect PSTVd also in extracts of infected tomato leaves at a dilution of up to 1/250-1/1250. These nonradioactive probes are equal to radioactive probes in their sensitivity, and the biotinylated probes produced with PCR amplification are particularly suitable for practical diagnosis, as they are sensitive and rapidly prepared in large quantities.

cDNA cloning and analysis of RNA 2 of a Prunus stem pitting isolate of tomato ringspot virus

Recombinant plasmids containing sequences derived from the genome of a tomato ringspot virus (TomRSV) isolate associated with both stem pitting disease of stone fruits and apple union necrosis and decline were constructed. Selected inserts were subcloned into the polylinker region of the SP6 transcription vector pSP64. Using the SP6 promoter flanking this region, high specific activity 32P-labelled cRNA probes were generated by SP6 RNA polymerase. cRNA probes were specific for TomRSV RNA 2 present in purified virions or in extracts from woody and herbacous hosts. No sequence relatedness was detected between TomRSV RNA 2 and genomic RNA from tobacco ringspot, arabis mosaic, strawberry latent ringspot, or cucumber mosaic virus in Northern blot analysis using TomRSV cRNA probes. These probes detected TomRSV infection in woody and herbaceous hosts in dot-blot hybridization assays.

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.

32P- and biotin-labelled in vitro transcribed cRNA probes for the detection of potato spindle tuber viroid and chrysanthemum stunt viroid

Replacing nick-translated DNA probes by in vitro transcribed complementary RNA (cRNA) probes considerably increased the sensitivity of dot-blot detection tests of potato spindle tuber viroid and chrysanthemum stunt viroid. As compared to the limit of detection of 5-10 pg of viroid obtained with 32P-labelled DNA probes, cRNA probes allow the detection of less than 1 pg of pure viroid. When labelled with biotin by incorporation of biotin-labelled ribonucleotides, the cRNA probes have a limit of detection of approximately 5 pg of purified viroid.

Nonradioactive, photobiotin-labelled DNA probes for routine diagnosis of viroids in plant extracts

Avocado sunblotch viroid (ASBV), coconut cadang cadang viroid (CCCV), chrysanthemum stunt viroid (CSV) and potato spindle tuber viroid (PSTV) were detected in plant extracts by dot-blot hybridization using nonradioactive photobiotin-labelled nucleic acid probes. Recombinant DNA probes, containing full-length monomer viroid inserts in the plasmid vectors pSP64 or pUC9, were biotinylated with photobiotin and used as sonicated double-stranded DNA fragments. Using fresh leaf material, a general method (suitably modified for avocado tissue) was developed for the rapid preparation of purified nucleic acid extracts. Plant extracts from a range of field samples were spotted onto nitrocellulose, subjected to hybridization and the biotin-labelled DNA bound to the target nucleic acid was detected with an avidin-alkaline phosphatase conjugate. Under the stated hybridization and washing conditions, each individual viroid probe was specific. Each viroid was readily detected with a sensitivity similar to that obtained with the same (or a like) probe labelled with 32P. Healthy plant extracts gave colourless spots.

Biotinylated RNA probes for the detection of potato spindle tuber viroid (PSTV) in plants

Diseases caused by potato spindle tuber viroid (PSTV) are of significant agronomic importance, and early detection is vital. The objective of this paper was to synthesize biotinylated RNA probes in order to develop a specific, sensitive, and reliable assay system for detection of PSTV in infected plants. RNA probes were prepared by in vitro transcription of cloned PSTV, and were labelled with either biotin-11-UTP or [32P]UTP. Partially purified total RNAs from healthy and from PSTV-infected plants were spotted onto nitrocellulose filters and hybridized with either biotin-labelled or 32P-labelled probes. Our results showed that the sensitivity of biotinylated probes was similar to that for the 32P-labelled probes.

Cloned riboprobe for detection of a mycoplasmalike organism

A [32P]-labeled single stranded-RNA probe (riboprobe) was constructed with plasmid vector pSP64 and used to detect and specifically identify an uncultured pathogenic mycoplasmalike organism in infected host. The riboprobe was more sensitive and reliable than complementary double stranded-DNA probe in detection of western X mycoplasmalike organism. When concentration of a double stranded-DNA probe was increased, nonspecific hybridization signal was observed with nucleic acid from healthy plants and from plants infected by other mycoplasmalike organisms. In contrast, sensitivity of detection with the complementary riboprobe was increased at elevated probe concentrations without nonspecific hybridization.

Detection of Chrysanthemum stunt viroid (CSV) using nick translated probes in a dot-blot hybridization assay

We developed a dot-blot hydridization assay for the detection of Chrysanthemum stunt viroid (CSV) in Chrysanthemum plant samples. The probe, a recombinant plasmid containing a full-length monomeric cDNA copy of CSV, is labelled with (32P) by nick-translation. The influence of the hybridization conditions, of the sample denaturation technique and of the plant sap components on the final sensitivity has been studied. The optimized system, involving a formaldehyde denaturation step, allows the detection of as little as 5 pg of purified viroid. Under these conditions, 100 pg of pure viroid diluted in plant sap, or infected plant extract diluted 1:25 in healthy extract can be detected, showing the potential of this method for indexing of Chrysanthemum for CSV infection.