应用聚合酶链式反应扩增和光敏生物素标记的cDNA探针检测马铃薯纺锤块茎类病毒

以含马铃薯纺锤块茎类病毒(potato spindle tuber viroid,PSTV)RNA的总核酸为模板,加入人工合成的互补DNA引物,用反转录酶合成PSTV cDNA;在聚合酶链式反应系统中,用两个PSTV特异性引物进行cDNA扩增,用以制备光敏生物素标记的PSTV cDNA探针。用此探针进行斑点杂交检测含PSTV的马铃薯核酸提取液和汁液均出现阳性杂交信号,而健康马铃薯的核酸提取液和汁液的结果均为阴性。光敏生物素标记探针检测纯化PSTV的灵敏度可达5pg;检测感染PSTV的马铃薯块茎汁液的可测出最高稀释度为1:400。     

Determination of potato spindle tumor viroid and chrysanthenum stund viroid using biotinylated olideoxyribonucleotides]

A 26 base long oligodeoxyribonucleotide complementary to a common RNA sequence of potato spindle tuber viroid (PSTV) and chrysantemum stunt viroid (CSV) was synthesized. The 3'-end biotinylated one was used for the detection of PSTV and CSV RNA immobilized on nitrocellulose filters by nucleic acid hybridization. Visualization of hybridization results was performed by two ways, either by streptavidin-alkaline phosphatase conjugate or streptavidine and biotinylated alkaline phosphatase. It was possible to detect 0.65 ng of purified CSV and PSTV RNA. The suggested system of viroid diseases detection can be used by agricultural and horticultural enterprises.     

Oligomeric forms of potato spindle tuber viroid (PSTV) and of its complementary RNA are present in nuclei isolated from viroid-infected potato cells

Different oligomeric forms of PSTV are detected in nuclei isolated from PSTV-infected potato cells by means of molecular hybridization, using as probes synthetic oligodeoxyribonucleotides with sequence specificity for (+)PSTV and for (?)PSTV. In addition to several species of longer-than-unit-length (?)PSTV molecules, two oligomeric forms os (+)PSTV are detected, which correspond in size to RNA strands of approximately two and three times viroid unit-length. They must be considered as the precursors os the circular and linear (+)PSTV monomers accumulating in the cell nucleus.     

Contitions for optimal growth of a PSTV-infected potato cell suspension and detection of viroid-complementary longer-than-unit-length RNA in these cells

A suspension culture from potato spindle tuber viroid (PSTV)-infected cells of the wild type potato (Solanum demissum) has been established, which is a suitable model system for studying PSTV replicationin vivo. The conditions for rapid growth of these cells and for permanent extensive viroid biosynthesis within them are described. Biosynthesis of PSTV in the potato cells was demonstrated by³²P-incorporation into nucleic acids and their subsequent electrophoretic analysis on polyacrylamide gels. Under optimum culture conditions the amount of³²P-orthophosphate incorporation into PSTV reached 10% of that incorporated into the 2 M LiCl-soluble cellular RNA. (+)PSTV and its complementary form, i.e. (?)PSTV were identified after their electrophoretic separation on polyacrylamide and agarose gels by molecular hybridization. This analysis revealed the presence of six high molecular weight(?)PSTV species, which are possibly multimers of the unit length(+)PSTV molecule consisting of 359 nucleotides.     

Highly sensitive fluorescent-labeled probes and glass slide hybridization for the detection of plant RNA viruses and a viroid

In this study, a modified method of the conventional RNA dot-blot hybridization was established, by replacing ~(32)p labels with CY5 labels and replacing nylon membranes with positive-charged glass slides, for detecting plant RNA viruses and a viroid. The modified RNA dot-blot hybridization method was named glass slide hybridization. The optimum efficiency of RNA binding onto the surfaces of activated glass slide was achieved using aminosilane-coated glass slide as a solid matrix and 5×saline sodium citrate (SSC) as a spotting solution. Using a CY5-labeled DNA probe prepared through PCR amplification, the optimized glass slide hybridization could detect as little as 1.71 pg of tobacco mosaic virus (TMV) RNA. The sensitivity of the modified method was four times that of dot-blot hybridization on nylon membrane with a ~(32)P-labeled probe. The absence of false positive within the genus Potyvirus [potato virus A, potato virus Y (PVY) and zucchini yellow mosaic virus] showed that this method was highly specific. Furthermore, potato spindle tuber viroid (PSTVd) was also detected specifically. A test of 40 field potato samples showed that this method was equivalent to the conventional dot-blot hybridization for detecting PVY and PSTVd. To our knowledge, this is the first report of using dot-blot hybridization on glass slides with fluorescent-labeled probes for detecting plant RNA viruses and a viroid.     

Separation of the Infectious Ribonucleic Acid of Potato Spindle Tuber Virus from Double-Stranded Ribonucleic Acid of Plant Tissue Extracts

The infectious ribonucleic acid (RNA) of potato spindle tuber virus (PSTV) can be separated by hydroxyapatite chromatography from double-stranded RNA detectable in low amounts in both infected and uninfected plant tissue extracts. The chromatographic behavior of ribonuclease-sensitive PSTV RNA resembles that of transfer RNA.     

Non-radioactive diagnosis of viral infections using "DNA-peroxidase" probes]

DNA-peroxidase probes were synthesized according to a modified method (Renzetal) for the detection of lambda phage DNA (model system), polio, potato X and M, tobacco mosaic viral RNAs by spot hybridization onto nitrocellulose membranes. cDNAs (300-1400 bases) complementary to the viral RNAs were cloned in M13 phage DNA or pTZ19. Efficacy of each step of the probe construction and the diagnostic procedure were thoroughly examined. Peroxidase activity manifested with non-toxic stain (NTS) was 3-5 fold more sensitive in comparison with alpha-Cl-naphthol or bisanisidine. It was found that HRP became much more stable to heat in diluted samples and was 2-3 fold more active after coupling with polyethylene imine spacer. Also, sodium borohydride reduction of the cDNA and PEI-HRP adduct crosslinked by the glutardialdehyde resulted in the stabilization of the probes. Target nucleic acids or diagnostic samples were efficiently fixed onto nitrocellulose membranes by a short-time UV irradiation. Diagnostics of cellular extracts with the preliminary prepared probes takes 4-5 hours due to express hybridization (1 hr) with 100-200 ng/ml of specific nucleotide sequence. Up to 20 pg (less than 10(-17) M) of the purified viral nucleic acids and 30-50 pg of them in the total fraction of the cellular nucleic acids isolated from the infected cells were identified with the probes. 50-10000 fold diluted lysate of the HeLa cells infected with poliovirus (PV1) and both crude extracts of potato tuber or potato and tobacco leaf tissues infected with PVX, PVM or TMV displayed specific signals with the respective DNA-HRP probes.     

Production of Potato Spindle Tuber Viroid (PSTV) by Large Scale Fermentation of PSTY-Infected Potato Cell Suspension Cultures

Berlin, J., Wray, V., Forche, E., Reng, H.–G , Schler,H, Luckinger, R. and Mhlbach, H.–P. 1985. Production ofpotato spindle tuber viroid (PSTV) by large scale fermentationof PSTV–infected potato cell suspension cultures.—J.exp. Bot 36: 1985–1995. Cell suspension cultures of Solatiumdemissum, infected with the potato spindle tuber viroid (PSTV),were scaled up to volumes of up to 800 dm³ to provide sufficientand uniform plant material for subsequent studies on viroidbiosynthesis. Here we describe the technological aspects ofproducing the required amounts of biomass and viroid. The cells,which had been maintained on a medium containing expensive coconutmilk, were first adapted to rapid growth on the less expensiveB5–medium. The physiological state of the cells was monitoredby in vivo ³¹P–NMR spectroscopy Under the chosen conditionsthe scale–up from 10 dm³ inoculum from shake flasks tothe harvest of the 800 dm³ stirred fermenter lasted 38 d andprovided 112 kg biomass. Growth characteristics and viroid productionin shake flasks and large bioreactors were rather similar. Gelelectrophoretic analysis of isolated nucleic acids using silverstaining and Northern blot hybridization revealed a PSTV–contentof approximately 700 µg PSTV per kg fresh mass of culturedcells. Key words: Solanum demissum, plant cell cultures, potato spindle tuber viroid, biomass production, fermentation, in vivo ³¹P-NMR     

Detection of hepatopancreatic parvovirus in Thai shrimp Penaeus monodon by in situ hybridization,dot blot hybridization and PCR amplification

Hepatopancreatic parvovirus (HPV) infects the hepatopancreas in penaeid shrimp and retards their growth. The DNA sequence of HPV from Thai shrimp Penaeus monodon (HPVmon) differs from HPV of Penaeus chinensis (HPVchin) by approximately 30%. In spite of this difference, commercial PCR primers (DiagXotics) developed from HPVchin to yield a 350 bp PCR product do give a 732 bp product with HPVmon DNA template. On the other hand, the sensitivity of HPVmon detection with these primers and with hybridization probes designed for HPVchin is significantly lower than it is with HPVchin. To improve sensitivity for HPVmon detection, we used the sequence of the 732 bp HPVmon PCR amplicon described above to develop specific PCR primers (H441F and H441R) and hybridization probe. The primers could detect as little as 1 fg of purified HPVmon DNA while the 441 bp digoxygenin-labeled PCR product gave strong, specific reactions with in situ hybridization and with hybridization blots. In contrast, negative results were obtained using DNA from all other pathogens tested and from DNA of P. monodon. Supernatant solution from boiled, fresh shrimp fecal and postlarval samples homogenized in 0.025% NaOH/0.0125% SDS could be used to detect as little as 0.1 pg HPVmon DNA by the PCR reaction. By dot blot hybridization, a visible signal was obtained with purified HPVmon DNA at 0.01 pg, but detection in spiked feces and postlarval samples was only 1 and 0.1 pg, respectively.     

Subcellular localization of viroids in highly purified nuclei from tomato leaf tissue

Approximately 95% of the viroid RNA which is present in potato spindle tuber viroid (PSTV)-infected tomato plant leaf issue, is associated with the nucleolar fraction obtained from purified nuclei. Viroids were released from the nucleolar fraction by increasing the ionic strength of the medium to 0.66 suggesting that viroid RNA is present in these subnuclear components in a protein-nucleic acid complex. A purification procedure for nuclei from leaf tissue had to be newly developed; it involves two Percoll density centrifugations as final steps. The nuclei were sonicated and the sonicate fractionated into fractions either highly enriched in nucleoli or in broken chromatin and ribonucleoprotein particles. The viroid content in the different samples was determined by gel electrophoresis. Depending upon the progress of the disease, viroid copy numbers between 200 and 10,000 per cell were observed in homogenized tissue, purified nuclei and in the nucleolar fraction. In chloroplasts, practically no viroids were detected. The results are discussed in the light of current hypotheses about the replication, pathogenicity and origin of viroids.     

Identification of Mycoplasma hyopneumoniae with a DNA probe

From a genomic library of Mycoplasma hyopneumoniae a 1.3 kb DNA fragment was cloned which showed specific Southern hybridization and dot hybridization with the type strain of several porcine and bovine Mycoplasma species. This probe selectively recognized M. hyopneumoniae sequences in purified DNA or in broth-grown organisms. The 35S-labelled probe could detect as little as 100 pg of DNA or 10(5) colour changing units. This is a possible alternative diagnostic procedure for enzootic pneumonia of pigs.     

Linear oligomeric potato spindle tuber viroid (PSTV) RNAs are accurately processed in vitro to the monomeric circular viroid proper when incubated with a nuclear extract from healthy potato cells

A nuclear extract for the processing of oligomeric viroid RNA in vitro has been prepared from nuclei isolated from healthy potato cells grown in suspension culture. Linear RNA molecules containing concatameric units of (+) or (−) strands, respectively, of the potato spindle tuber viroid (PSTV) were synthesized in vitro with the aid of the SP6 RNA polymerase and used as substrates for processing. When oligomeric linear PSTV (+)RNAs are incubated with the nuclear extract, monomeric linear molecules are accurately excised from them, and ligated to monomeric PSTV (+)RNA circles representing the viroid proper. Oligomeric PSTV (−)RNAs are likewise processed but with a much lower efficiency. Viroid-processing operates although other nucleolytic activities are still present in the extract. These results substantiate our previous finding that oligomeric PSTV does not process autocatalytically under in vitro conditions where certain introns and other RNAs do. This is the first report of an in vitro RNA processing system derived from higher plants.     

Nucleotide sequence and proposed secondary structure of Columnea latent viroid: a natural mosaic of viroid sequences.

The Columnea latent viroid (CLV) occurs latently in certain Columnea erythrophae plants grown commercially. In potato and tomato, CLV causes potato spindle tuber viroid (PSTV)-like symptoms. Its nucleotide sequence and proposed secondary structure reveal that CLV consists of a single-stranded circular RNA of 370 nucleotides which can assume a rod-like structure with extensive base-pairing characteristic of all known viroids. The electrophoretic mobility of circular CLV under nondenaturing conditions suggests a potential tertiary structure. CLV contains extensive sequence homologies to the PSTV group of viroids but contains a central conserved region identical to that of hop stunt viroid (HSV). CLV also shares some biological properties with each of the two types of viroids. Most probably, CLV is the result of intracellular RNA recombination between an HSV-type and one or more PSTV-type viroids replicating in the same plant.     

Complexes of viroids with histones and other proteins.

Complexes of potato spindle tuber viroid (PSTV) with nuclear proteins have been studied by in vitro reconstitution of the complexes and by isolation and characterization of in vivo complexes under non-dissociating conditions. For in vitro reconstitution, nuclear proteins were separated by SDS-gel-electrophoresis, renatured and blotted onto nitrocellulose filters, and incubated with viroid. The viroid-protein complexes were crosslinked covalently, and the viroid containing protein bands were detected by northern hybridization with a radioactive cDNA probe. The histones, a 41,000 dalton protein and to a small extent a 31,000 dalton protein were found in complexes with viroids. Raising the strength to 0.4 M NaCl destroys the complexes with the 41,000 dalton proteins but not those with the histones. From nucleoli, which are known to obtain the majority of viroids under non-dissociating conditions (Schumacher et al., (1983) EMBO J. 2, 1549-1555), a nucleosomal fraction was prepared. Viroids were found predominantly in this nucleosomal fraction. They are bound in a complex of 12-15 svedberg units.     

Isolation of borrelidin as a phytotoxic compound from a potato pathogenic streptomyces strain

Streptomyces species strain GK18, isolated in Iran, induced deep-pitted lesions on potato tubers, lesions different from the raised lesions induced by the usual scab-causing phytotoxin, thaxtomin. In addition, neither thaxtomin production nor hybridization to its biosynthetic probe was detected for strain GK18, suggesting the production of a different phytotoxin. The active component was extracted with ethyl acetate from culture filtrate of strain GK18, purified by gel filtration and silica gel chromatography, and identified as an 18-membered macrolide, borrelidin, by spectroscopic analysis. The purified borrelidin induced necrosis on potato tuber slices and inhibited the growth of shoots and roots of radish seedlings. This is the first report on the phytotoxicity of borrelidin as a possible causative compound of potato scab disease.     

Differences in chromatin from normal and leukemic human cells as shown by digestion with restriction nucleases

Sequence homology was found by computer analysis between potato spindle tuber viroid (PSTV) RNA and U3B snRNA of Novikoff hepatoma cells. This homology is colinear in arrangement, extends in length to 81% of the entire U3B snRNA molecule and is involved in the PSTV molecule unique sites which, if depicted in terms of the secondary structure of the circular PSTV molecule, reveal a conspicuous regularity in their location. A strong relation in primary structure between PSTV and U3B snRNA is demonstrated by statistical analysis.