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

A dot-hybridization assay using 32P-labelled RNA probes (+RNA and cRNA) transcribed from potato spindle tuber viroid (PSTV) cDNA was described. A complete cDNA copy of PSTV, originally cloned in pBR 322 (pAV 401) was subcloned in the BamHI site of a 'Riboprobe' cloning vectors pSP 64 and pSP 65 in opposite orientations. The reconstructed plasmids were designated pDX 1 and pDX 4, respectively. Transcription of pDX 1 and pDX 4 plasmids by SP6 RNA polymerase resulted in the generation of PSTV-specific RNA (+RNA) and PSTV complementary RNA (cRNA), respectively. The cRNA probe was much more sensitive than the +RNA probe and the nick-translated cDNA probe from the plasmid pAV 401 for the detection of PSTV in clarified plant sap. As little as 1.4 pg of purified PSTV mixed in clarified sap from uninoculated tomato leaves has been detected using cRNA probe. A relatively simple procedure using cetyltrimethyl ammonium bromide (CTAB) as nucleic acid precipitant and an enrichment step for the purification of PSTV was described.

Rice stripe virus: prototype of a new group of viruses that replicate in plants and insects

The unusual filamentous particles of rice stripe virus contain four species of single-stranded RNA. Similar filamentous particles are common in other planthopper-borne viruses of the rice stripe virus group, of which a type virus, rice stripe virus, is reviewed.

Infectious mutants of cassava latent virus generated in vivo from intact recombinant DNA clones containing single copies of the genome

Intact recombinant DNAs containing single copies of either component of the cassava latent virus genome can elicit infection when mechanically inoculated to host plants in the presence of the appropriate second component. Characterisation of infectious mutant progeny viruses, by analysis of virus-specific supercoiled DNA intermediates, indicates that most if not all of the cloning vector has been deleted, achieved at least in some cases by intermolecular recombination in vivo between DNAs 1 and 2. Significant rearrangements within the intergenic region of DNA 2, predominantly external to the common region, can be tolerated without loss of infectivity suggesting a somewhat passive role in virus multiplication for the sequences in question. Although packaging constraints might impose limits on the amount of DNA within geminate particles, isolation of an infectious coat protein mutant defective in virion production suggests that packaging is not essential for systemic spread of the viral DNA.

Regulation of expression of the wound tumor virus genome in persistently infected vector cells is related to change in translational activity of viral transcripts

The interaction between a plant virus and its insect vector was studied at the molecular level by examining wound tumor virus (WTV) gene expression in cultured cells derived from its leafhopper vector. Infection of vector cells by WTV is noncytopathic and results in an acute phase (through day 5), followed by persistence beginning with the first cell passage. Viral-specific polypeptide synthesis and viral genome RNA accumulation increased to a maximum level during the first 5 days following inoculation and then decreased as infected cells were passaged (to 5 to 20% of the level observed during the acute phase by passages 10 to 15). In contrast, viral-specific mRNAs were present at approximately the same level in the acute phase and in the early stage (passage 10) of the persistent phase of infection. Although viral transcripts isolated at different times after inoculation exhibited identical electrophoretic migration patterns, they had different functional activities in cell-free translation systems. Transcripts isolated from persistently infected cells were inefficiently translated in vitro, reflecting the situation in infected cells. These results indicate that the decline in the level of viral polypeptide synthesis associated with the persistent phase of WTV infection is related to a change in the translational activity of viral transcripts.

The nucleotide sequence of tobacco vein mottling virus RNA

The nucleotide sequence of the RNA of tobacco vein mottling virus, a member of the potyvirus group, was determined. The RNA was found to be 9471 residues in length, excluding a 3'-terminal poly(A) tail. The first three AUG codons from the 5'-terminus were followed by in-frame termination codons. The fourth, at position 206, was the beginning of an open reading frame of 9015 residues which could encode a polyprotein of 340 kDa. No other long open reading frames were present in the sequence or its complement. This AUG was present in the sequence AGGCCAUG, which is similar to the consensus initiation sequence shared by most eukaryotic mRNAs. The chemically-determined amino acid compositions of the helper component and coat proteins were similar to those predicted from the nucleotide sequence. Amino acid sequencing of coat protein from which an amino-terminal peptide had been removed allowed exact location of the coat protein cistron. A consensus sequence of V-(R or K)-F-Q was found on the N-terminal sides of proposed cleavage sites for proteolytic processing of the polyprotein.

Detection of double-stranded RNA by immunoblot electrophoresis

A procedure is described which permits the serological detection of double-stranded RNA (dsRNA) which has been electrophoretically transferred from agarose gels to Zeta-Probe blotting membranes. Cucumber mosaic virus replicative forms of RNAs 1-3 and cassava (Manihot esculenta) clone 'Secundina' dsRNAs can be routinely detected from 1 g of leaf tissue. This procedure allows for the detection and size estimation of dsRNAs in crude nucleic acid preparations.

RNA 2 of tobacco rattle virus strain TCM encodes an unexpected gene

The sequence of the 3'-terminal 1210 nucleotides of RNA 1 and the complete sequence of 3389 nucleotides of RNA 2 of tobacco rattle virus (TRV) strain TCM has been deduced. The sequence of the 3'-terminal 1099 nucleotides of RNAs 1 and 2 was found to be identical. Thus the genome of this TRV strain is partially diploid, encoding a 16K protein in both RNA 1 and RNA 2. The sequence that is unique to RNA 2 contains two open reading frames: the coat protein cistron and a cistron for a 29.1K protein, which shows no homology with the RNA 1 encoded 28.8K protein. cDNA probes corresponding to these two open reading frames cross-hybridized to pea early-browning virus RNA 2, but not to RNA 2 of five other tobraviruses tested.

Genetic recombination between RNA components of a multipartite plant virus

Genetic recombination of DNA is one of the fundamental mechanisms underlying the evolution of DNA-based organisms and results in their diversity and adaptability. The importance of the role of recombination is far less evident for the RNA-based genomes that occur in most plant viruses and in many animal viruses. RNA recombination has been shown to promote the evolutionary variation of picornaviruses, it is involved in the creation of defective interfering (DI) RNAs of positive- and negative-strand viruses and is implicated in the synthesis of the messenger RNAs of influenza virus and coronavirus. However, RNA recombination has not been found to date in viruses that infect plants. In fact, the lack of DI RNAs and the inability to demonstrate recombination in mixedly infected plants has been regarded as evidence that plants do not support recombination of viral RNAs. Here we provide the first molecular evidence for recombination of plant viral RNA. For brome mosaic virus (BMV), a plus-stranded, tripartite-genome virus of monocots, we show that a deletion in the 3' end region of a single BMV RNA genomic component can be repaired during the development of infection by recombination with the homologous region of either of the two remaining wild-type BMV RNA components. This result clearly shows that plant viruses have available powerful recombinatory mechanisms that previously were thought to exist only in animal hosts, thus they are able to adapt and diversify in a manner comparable to animal viruses. Moreover, our observation suggests an increased versatility of viruses for use as vectors in introducing new genes into plants.

Association of tobacco etch virus related RNA with chloroplasts in extracts of infected plants

The RNA in various subcellular fractions of tobacco etch virus (TEV) infected tissue was analyzed for the presence of complementary viral RNA, and double-stranded viral RNA by hybridization with 32P-labeled viral RNA or cDNA probes. Although viral RNA was detected in several cellular fractions, the complementary RNA of full-length size was found exclusively associated with fractions containing chloroplasts. Treatment of RNAs with RNase before hybridization suggested that the virus-related complementary RNA was present in double-stranded form.

Characterization of viruses infecting a eukaryotic Chlorella-like green alga

Nineteen plaque-forming viruses of the unicellular, eukaryotic Chlorella-like green alga, strain NC64A, were isolated from various geographic regions in the United States and characterized. Like the previously described virus, PBCV-1, all of the new viruses were large polyhedrons, sensitive to chloroform, and contained large dsDNA genomes of ca. 300 kbp. All of the viral DNAs contained 5-methyldeoxycytidine which varied from 0.1 to 47% of the deoxycytidine. In addition, 10 of the viral DNAs contained N6-methyldeoxyadenosine which varied from 8.1 to 37% of the deoxyadenosine. These viruses, along with 11 previously described viruses which replicate in the same Chlorella host, were grouped into 11 classes based on at least one of the following properties: plaque size, reaction with PBCV-1 antiserum, or the nature and abundance of methylated bases in their genomic DNA.

Detection of Fiji disease virus in infected sugarcane by nucleic acid hybridization

Clones of Fiji disease virus were obtained by cDNA synthesis from isolated viral genomic double-stranded RNA. Nick-translated probes made from a mixture of clones specifically detected Fiji disease virus in infected sugarcane galls, leaves and growing tips. This method for detection of Fiji disease virus is extremely sensitive, and can be used as a rapid screening procedure for the virus with very small tissue samples.

Synthesis of viral DNA forms in Nicotiana plumbaginifolia protoplasts inoculated with cassava latent virus (CLV); evidence for the independent replication of one component of the CLV genome

Totipotent leaf mesophyll protoplasts of Nicotiana plumbaginifolia, Viviani were inoculated with cassava latent virus (CLV) or with full length copies of CLV genomic DNAs 1 and 2 excised from replicative forms of M13 clones. Virus specific DNAs began to appear 48-72h after inoculation with virus or cloned DNAs, coincident with the onset of host cell division. Infected cells accumulated supercoiled forms of DNAs 1 and 2 as well as progeny single-stranded (ss) virion (+) sense DNAs representing each component of the genome. Both supercoiled and ss molecules were synthesised by cells inoculated with cloned DNA 1 alone but DNA 2 failed to replicate independently.

Infection of a Chlorella-like alga with the virus PBCV-1: transcriptional studies

Infection of the unicellular, eukaryotic Chlorella-like green alga NC64A by the large dsDNA containing virus PBCV-1 immediately reduced host RNA synthesis. Chloroplast rRNAs, but not cytosolic rRNAs, were degraded following viral infection. Northern blot analysis utilizing four cloned fragments of PBCV-1 DNA as probes, which represent about 12% of the viral genome, revealed several properties of PBCV-1 transcription: A few viral transcripts were detected within 5 min after infection. Each PBCV-1 DNA clone hybridized to both early and late transcripts which implies that early and late genes are dispersed throughout the viral genome. The transition from early to late transcription occurred between 40 and 60 min after infection coincident with the onset of viral DNA synthesis. Three of the four DNA clones hybridized to transcripts which additively were larger than the corresponding DNA probe. This could reflect RNA processing, presence of overlapping genes, or transcription from both DNA strands. A few, but not all, early transcripts were synthesized in the presence of cycloheximide. This suggests that the virus either carries in its own RNA polymerase or uses a host RNA polymerase for very early viral transcription and that synthesis of additional, later transcripts depends on translation of an early gene product(s).

5S RNA and tRNA-like molecules are associated with killer virus dsRNA of yeast

A population of oligonucleotides co-purified with the dsRNA genomic segments of the killer virus of Saccharomyces cerevisiae during electrophoresis through agarose gels. These smaller RNA molecules must be separated from the viral genome in order to determine the structure of the dsRNA molecules. Sequence analysis of these isolated oligonucleotides showed that the population contained tRNA-like molecules, as well as 5S RNA, which are presumably encoded by the host cell genome.

Taxonomy of cucurbit-infecting tobamoviruses as determined by serological and molecular hybridization analyses

A number of cucurbit-infecting tobamoviruses have been reported in the past but there is confusion about their identity and relationships. Cucumber viruses 3 (CV3) and 4 (CV4) were originally described in the United Kingdom whereas the watermelon (W) and cucumber (C) 'isolates' of cucumber green mottle mosaic virus (CGMMV) came from Japan. The results of serological studies and RNA-cDNA analyses have shown that CV3, CV4 and CGMMV-W are very closely related, whereas CGMMV-C is quite different. It is concluded that there are two distinct tobamoviruses that infect cucurbits; they are only very remotely related to each other and to a number of other tobamoviruses. It is suggested that the name CGMMV be retained to include the isolates or strains CV3, CV4 and CGMMV-W, and that a new name, kyuri green mottle mosaic virus (KGMMV), be given to CGMMV-C.

The nucleotide sequence of tobacco rattle virus RNA-2 (CAM strain)

The nucleotide sequence of the smaller genomic strand (RNA-2) of the bipartite tobacco rattle virus (CAM strain) has been determined. RNA-2 is capped at the 5' terminus and contains 1799 nucleotide residues. There is a single 223 codon long open reading frame extending from nucleotide 574 to 1242 which designates a protein of Mr 23,654. The derived amino acid composition, in percent, matches that previously determined for the virus capsid protein. The long open reading frame is flanked by 5' and 3' untranslated regions of 573 and 554 nucleotides, respectively. The 5' leader sequence contains two different sets of direct repeats, one of 119 nucleotides and the other of 76. It also contains 13 apparently unused AUG codons, four of which lie in the same frame as the capsid protein cistron. The 3' terminal sequence of RNA-2 is identical to that of the larger genomic strand (RNA-1) for 459 nucleotides.

In vitro mutagenesis of infectious viroid cDNA clone

Previously we constructed an infectious hop stunt viroid (HSV) cDNA clone, PHS-P2P, which carries two copies of full-length HSV cDNA tandemly and generates HSV RNA when it is inoculated into cucumber plants. The in vitro transcript of the cDNA clone was also infectious. To investigate the essential regions for infectivity of HSV, we introduced a short deletion or insertion into the HSV sequence of pHS-P2P using restriction sites (XhoI site for pHI-X1, PvuI site for pHI-P1, and BamHI site for pHI-B1) and assayed the infectivities of these mutagenized clones. None of these mutagenized clones and their transcripts were infectious under the conditions used. Simultaneous inoculation of two or three of non-infectious mutagenized clones or the transcripts from them did not restore the infectivity.

Bidirectional transcription of maize streak virus DNA and identification of the coat protein gene

Three RNA transcripts encoded by maize streak virus DNA were detected in polyadenylated RNA from virus-infected maize leaves. Two of the transcripts, a major 0.9 kb and a minor 1.05 kb RNA, were mapped on the virion (+) sense DNA and the other minor transcript of 1.2 kb was mapped on the complementary (-) sense DNA, demonstrating that transcription of MSV DNA was bidirectional. The two virion sense transcripts were 3' coterminal at nucleotide 1114 but had 5' termini at nucleotides 2682 and 163 respectively. Virus-specific polyadenylated RNA translated in vitro to produce a 28,000 MW polypeptide, specifically immunoprecipitable by antiserum raised against whole virus. The mRNA for this protein was mapped by hybrid-arrested translation to the long open reading frame in virion sense DNA whose potential amino acid composition, calculated from nucleotide sequence data, closely agreed with that determined experimentally for the coat protein.

Nucleotide sequence and genome organization of carnation mottle virus RNA

The complete nucleotide sequence of carnation mottle genomic RNA (4003 nucleotides) is presented. The sequence was determined for cloned cDNA copies of viral RNA containing over 99% of the sequence and was completed by direct sequence analysis of RNA and cDNA transcripts. The sequence contains two long open reading frames which together can account for observed translation products. One translation product would arise by suppression of an amber termination codon and the sequence raises the possibility that a second suppression event could also occur. Sequence homology exists between a portion of the carnation mottle virus sequence and that of putative RNA polymerases from other RNA viruses.

Correlation between structure and pathogenicity of potato spindle tuber viroid (PSTV)

Sequence analysis by primer-extension at the level of their cDNA showed that the RNA genomes of various field isolates of potato spindle tuber viroid (PSTV) of different virulence differ from each other only in a few nucleotides in two distinct regions of the rod-shaped molecule. Despite insertions and deletions the chain length of 359 nucleotides is strictly conserved in all the isolates studied. Thermodynamic calculations revealed that due to the observed sequence differences the region located at the left hand part of the rod-like secondary structure of the PSTV molecule, denoted 'virulence modulating (VM) region', becomes increasingly unstable with the increasing virulence of the corresponding isolate. Based on these data we propose in molecular terms a model for the mechanism of viroid pathogenicity. It implies that the nucleotides of the VM region specify and modulate the binding- and hence the competition-potential of the PSTV RNA molecule for a still unknown host factor(s) and thus determine the virulence of PSTV.

Infectivity studies on different potato spindle tuber viroid (PSTV) RNAs synthesized in vitro with the SP6 transcription system

We have constructed two sets of clones in which one to six head-to-tail connected DNA copies of the potato spindle tuber viroid (PSTV) RNA genome were inserted into the plasmid pSP62- Pl downstream of the promoter for SP6 RNA polymerase. In vitro transcription of these constructs with the promoter-specific SP6 RNA polymerase yielded the corresponding oligomeric single-stranded linear PSTV RNA molecules of (+) and (-) polarity. Except for short vector-derived terminal sequences these in vitro synthesized PSTV RNA forms are equivalent to the RNA intermediates of the PSTV replication cycle which are present in vivo only in extremely low concentrations. From each DNA template molecule up to 600 RNA copies could be transcribed in vitro and yields > 100 microg were obtained. When mechanically inoculated to tomato seedlings the PSTV (+) RNA oligomers were as infectious as the natural PSTV (+) RNA monomers. Surprisingly, the corresponding oligomeric PSTV (-) RNAs wer approximately 10(4)-fold less infectious. However, when these (-) RNAs were partially protected prior to inoculation by mixing or hybridizing them with non-infectious (+) RNA fragments or by 'capping' their 5' terminus, an increase in the number of infections was observed. The in vitro synthesis of infectious RNA from cloned cDNA means that, in principle, it should be possible to develop vector systems from pathogens with RNA genomes.

Infectivity and in vitro mutagenesis of monomeric cDNA clones of citrus exocortis viroid indicates the site of processing of viroid precursors

Monomeric cDNA clones of citrus exocortis viroid (CEV) were constructed in the plasmid vector pSP6-4 and the infectivity of the clones plus in vitro-synthesized RNA transcripts determined by inoculation onto tomato seedlings. Infectivity was dependent on the site of the viroid molecule used for cloning and the orientation of the cDNA insert. Only the plus BamHI cDNA clone was infectious and produced progeny viroid with wild-type sequence at the region corresponding to the BamHI cloning site. Infectivity correlated with the terminal repetition of 11 nucleotides of viroid sequence, 5'GGATCCCCGGG 3', in the vector adjacent to the insert. The 11-nucleotide sequence lies within the highly conserved central region of viroids. Site-directed mutagenesis of a single nucleotide in the repeat at the 5'-end of the CEV insert to 5' GGATCCCC(T,A)GG 3' gave two point mutants. The two mutant CEV inserts, when excised from the vector, were not infectious. However, plasmid DNA and RNA transcripts from non-excised mutant CEV inserts were infectious. The progeny of one of these clones was examined and contained wild-type sequence. It was concluded that in vivo processing of longer-than-unit-length CEV occurs at one of three adjacent sites in the 11 nucleotide sequence and that the G nucleotide at position 97 is important for viroid replication.

Molecular cloning and characterization of the genome of wound tumor virus: a tumor-inducing plant reovirus

The double-stranded RNA genome of the tumor-inducing plant pathogen, wound tumor virus, was converted to double-stranded DNA and cloned into plasmid pBR322. Multiple apparent full-length copies of 9 of the 12 wound tumor virus genome segments were identified. The entire sequence of cloned genome segment S12, the smallest of the genome segments, was determined. This genome segment was found to be 851 nucleotides in length and to possess a single long open reading frame that extends 178 codons from the first AUG triplet (residues 35-37): information sufficient to encode a protein of the size estimated for the smallest of the previously identified wound tumor virus primary gene products, Pns 12. Sequence data obtained from analysis of cloned cDNA copies of several genome segments and from direct analysis of the 3' termini of the double-stranded genome RNAs revealed that each wound tumor virus genome segment possesses the common terminal sequences: (+) 5'GGUAUU ... UGAU 3' (-) 3'CCAUAA ... ACUA 5'.

Unusual properties of two branched RNA's with circular and linear components

Irradiation with ultraviolet light was used to create two nonlinear RNA molecules. Circular potato spindle tuber viroid (PSTV) RNA was crosslinked at a single site to generate a figure eight-shaped molecule; 5S rRNA from HeLa cells was transformed into an alpha-shaped molecule with a small circular element and two arms (1). Crosslinked RNA's could be separated from their untreated counterparts by electrophoresis in polyacrylamide gels containing urea. The gel mobility of crosslinked PSTV was not altered by boiling, treatment with E. coli RNase III or glyoxalation. However, mild nuclease digestion ("nicking") produced derivatives which migrated more slowly than the starting material in gels of certain polyacrylamide concentrations, but not in others. Limited nuclease digestion of crosslinked 5S rRNA did not generate any detectable products with reduced mobility in the gels tested. Thus, the ability of the "nicking assay" to reveal circular elements within nonlinear RNA's can vary depending upon the composition of the gel chosen for analysis and on the size of the circular element relative to the rest of the molecule.

Immunological detection of the messenger RNA cap-binding protein

The 24-kilodalton messenger RNA cap-binding protein (CBP) was purified from the rabbit reticulocyte postribosomal supernatant fraction using an affinity resin consisting of the p-aminophenyl gamma-ester of m7GTP coupled to Sepharose. The affinity-purified CBP was used to raise a goat antiserum. Anti-CBP antibodies were purified by adsorption to CBP coupled to either Controlled-Pore Glass or diazobenzyloxymethyl paper. The affinity-purified antibodies reacted specifically with only the 24-kilodalton polypeptide in whole reticulocyte lysate and in initiation factors prepared from the same source. During a conventional (nonaffinity) purification of CBP from a high salt extract of the ribosomal pellet, immunological reactivity paralleled the ability to reverse cap analogue inhibition of translation, indicating that the 24-kilodalton polypeptide present in the postribosomal supernatant fraction is immunologically cross-reactive with the CBP purified from ribosomes. Fractionation of whole reticulocyte lysate by sucrose gradient sedimentation followed by immunoblotting revealed that CBP was present in the supernatant fraction and the region of the gradient corresponding to ribosomal subunits but not in mono- or polysomes. The CBP to ribosome ratio was found to be approximately 0.02, assuming that the m7GTP-Sepharose retains all of the protein. This is considerably lower than that of other initiation factors and suggests that CBP may be the limiting polypeptide factor involved in the initiation of protein synthesis. The antibodies also inhibited the translation of a capped messenger RNA (globin). Inhibition of the translation of an uncapped RNA (satellite tobacco necrosis virus) was also observed, but to a lesser degree than with globin mRNA.

Taxonomy and nomenclature of viruses

In his article The species concept in plant virology Milne1 describes the CMI/AAB Descriptions of Plant Viruses2 as providing the 'creeping barrage' (for the 'anti-species' views of many plant virologists and others) in the seemingly unending trench warfare over virus taxonomy and nomenclature. As an editor since 1970 (with BD Harrison) of this continuing series, I am moved to fire a few additional shots in support of Milne's thesis.

The replication of plant virus RNA

The roles of plant-encoded RNA-dependent RNA polymerases and viral RNA replicases in the replication of plant viral RNA are reviewed with respect to the positive single-stranded TYMV, CPMV and BMV.

Nucleotide sequence of the satellite of peanut stunt virus reveals structural homologies with viroids and certain nuclear and mitochondrial introns

Peanut stunt virus-associated RNA 5 (PARNA 5), the satellite of a plant cucumovirus, is a linear RNA of 393 nucleotides with a 5' cap and a 3' hydroxyl group. Determination of its nucleotide sequence has revealed two consecutive open reading frames that together extend most of its length. Sequences at the 5' and 3' ends are homologous with those of the satellite of the related cucumber mosaic virus, and the double-stranded forms of both satellites contain an unpaired guanosine at the 3' end of the minus strand. However, little other homology exists between the two satellites. In contrast, PARNA 5 has several regions of 90% sequence homology with various plant viroids, including sequences of the conserved central region of most viroids. Such homologies suggest a common origin with viroids coupled with specific adaptation as a linear RNA. The presence within PARNA 5 of conserved intron sequences essential to proper RNA processing suggests a possible origin from plant introns and/or involvement of such sequences in the processing of PARNA 5 multimers to monomers at some stage of replication.

Eleven new sequence variants of citrus exocortis viroid and the correlation of sequence with pathogenicity

Full-length double-stranded cDNA was prepared from purified circular RNA of two new Australian field isolates of citrus exocortis viroid (CEV) using two synthetic oligodeoxynucleotide primers. The cDNA was then cloned into the phage vector M13mp9 for sequence analysis. Sequencing of nine cDNA clones of isolate CEV-DE30 and eleven cDNA clones of isolate CEV-J indicated that both isolates consisted of a mixture of viroid species and led to the discovery of eleven new sequence variants of CEV. These new variants, together with the six reported previously, form two classes of sequence which differ by a minimum of 26 nucleotides in a total of 370 to 375 residues. These two classes correlate with two biologically distinct groups when propagated on tomato plants where one produces severe symptoms and the other gives rise to mild symptoms. Two regions of the native structure of CEV, comprising 18% of the total residues, differ between the sequence variants of mild and severe isolates. Whether or not both of these regions are essential for the variation in pathogenicity has yet to be determined.

Characterisation of DNA forms associated with cassava latent virus infection

In addition to the major encapsidated DNA species found in preparations of cassava latent virus (genomic DNAs 1 and 2) there are minor DNA populations of twice (dimeric) and approximately half genome length. Both minor species resemble the genomic DNAs in that they are composed of predominantly circular single-stranded DNA. All of these size groups have a corresponding covalently-closed circular double-stranded DNA form in infected tissue. Infectivity studies using cloned DNAs 1 and 2 show that dimeric DNA routinely appears, suggesting it to be an intermediate in the DNA replicative cycle that can be encapsidated at low efficiency. In contrast, half unit length DNA has not yet been detected after multiple passaging of virus derived from the cloned DNA inoculum. Half unit length DNAs appear to be derived exclusively from DNA 2 and consist of a population of molecules exhibiting a relatively specific deletion. As they have an inhibitory effect on virus multiplication, their encapsidated forms are analogous to defective interfering particles associated with other eukaryotic DNA containing viruses. Small primer molecules associated with the genomic single-stranded DNAs, as reported for another geminivirus, have not been detected in CLV.

Usefulness and limitations of the species concept for plant viruses

Continuing concerns among virologists are what range of isolates is covered by one virus name and whether such names relate to categories broadly equivalent to biological species of higher organisms. In the potyviruses, tobamoviruses, and probably other groups of plant viruses with monopartite RNA genomes, exchange of genetic information among isolates is not known to occur; our ability to delineate separate viruses apparently depends on the extent to which biological fitness involves several correlated changes in the genomes of variant clones. Although some such correlated changes are found where viruses infect different plant families, intergrading forms occur in many instances where the host ranges of variants overlap. In plant viruses with multipartite RNA or DNA genomes, the extent of gene pools can be assessed from the ability of isolates to form pseudo-recombinants by reassortment of their genome parts. In the nepoviruses, clusters of virus strains sharing a gene pool resemble, but seem more sharply delimited than, the clusters based on nucleotide sequence homology or serological specificity. In the tobraviruses gene pools do not coincide with serological groupings, and in the geminiviruses biologically very distinct entities have much genome homology and are closely related serologically. The biological species concept seems inappropriate or impractical for many plant viruses, and a more flexible and pragmatic approach to assigning virus isolates to nameable categories is advocated.

Morphology and nucleic acid of rice gall dwarf virus

In negative stain preparations, the particles of rice gall dwarf virus (RGDV) had the form of angular icosahedra, approximately 65 nm in diameter, and resembled Phytoreovirus particles. The genomic double-stranded RNA of RGDV was fractionated by PAGE into 12 segments similar to those of the RNAs of the phytoreoviruses, wound tumor virus and rice dwarf virus, but of different mobilities. The RNAs were distinct from those of other plant reoviruses. RGDV therefore is confirmed as a new Phytoreovirus.

Detection of avocado sunblotch viroid by hybridization with synthetic oligonucleotide probes

Two short (20 and 17 nucleotides) DNA hybridization probes, complementary to avocado sunblotch viroid (ASBV) RNA nucleotides 68-87 and 88-104 respectively (Symons, R.H., Nucleic Acid Res. 9, 6527, 1981) were synthesized. The sensitivity and specificity of these radioactively labelled probes for hybridization with RNA of several ASBV isolates are demonstrated.

The nucleotide sequence of maize streak virus DNA

The nucleotide sequence of the DNA of maize streak virus (MSV) has been determined. The data were accommodated into one DNA circle of 2687 nucleotides, in contrast to previously characterised geminiviruses which have been shown to possess two circles of DNA. Comparison of the nucleotide sequences of the DNA of MSV with those of cassava latent virus (CLV) and tomato golden mosaic virus (TGMV) showed no detectable homology. Analysis of open reading frames revealed seven potential coding regions for proteins of mol. wt. greater than or equal to 10 000, three in the viral (+) sense and four in the complementary (-) sense. The position of likely transcription signals on the MSV DNA sequence would suggest a bidirectional strategy of transcription as proposed for CLV and TGMV. Nine inverted repeat sequences which have a potential of forming hairpin structures of delta G greater than or equal to -14 kcal/mol have been detected. Three of these hairpin structures are in non-coding regions and could be involved in the regulation of transcription and/or replication.

Cloned single- and double-stranded DNA copies of potato spindle tuber viroid (PSTV) RNA and co-inoculated subgenomic DNA fragments are infectious

A set of monomeric and oligomeric potato spindle tuber viroid (PSTV) specific DNA forms representing complete DNA copies of the circular PSTV RNA genome were constructed and cloned in plasmid pBR322 and bacteriophage M13. Both single- and double-stranded PSTV DNAs are capable of initiating viroid replication in mechanically inoculated tomato plants where it normally proceeds via the RNA-RNA pathway without DNA being involved. All dimeric and higher multimeric forms were infectious irrespective of their polarity in the case of single-stranded DNA and regardless of their orientation in the vector DNA in the case of double-stranded DNA. The vector-inserted monomeric PSTV DNA units were also found to be infectious but of low specific infectivity which was increased when these monomers had been excised. Even two subgenomic DNA fragments, representing together the 359 nucleotides of the PSTV RNA genome, initiated the synthesis of viroid RNA progeny when co-inoculated although each fragment by itself is non-infectious. These results are discussed with respect to the infectivity previously observed with certain cloned DNAs of conventional RNA and DNA viruses.

Replication of peanut stunt virus and its associated RNA 5 in cowpea protoplasts

Peanut stunt virus (PSV) RNA containing PSV-associated RNA 5 (PARNA 5) was used as the inoculum in the successful infection of cowpea protoplasts. Total nucleic acid extracts of protoplast samples at different times after inoculation were analyzed for the presence of PSV genomic RNAs and PARNA 5 using glyoxal denaturation, agarose gel electrophoresis, blotting to nitrocellulose, and hybridization to specific probes. It appears that (+)-stranded PSV genomic RNAs are synthesized up to 36 hr after inoculation after which their synthesis levels off, whereas PARNA 5 synthesis continues much later during infection. Oligomers of PARNA 5 were found in the infected protoplasts, in double-stranded RNA preparations from PSV-infected tissues, and in single-stranded PSV-RNA preparations isolated from purified virus. However, we were unable to demonstrate the presence of circular PARNA 5 molecules in infected protoplasts or tissues. These results leave open the question whether PARNA 5 is replicated via a rolling circle type replication mechanism, as proposed for viroids and tobacco ringspot virus satellite, or via a virus-like replication mechanism, as certain structural features of PARNA 5 would indicate. It is not impossible that both types of mechanisms are operative at different phases of PARNA 5 replication.

An encapsidated, subgenomic messenger RNA encodes the coat protein of carnation mottle virus

The translation strategy of carnation mottle virus (CarMV) in vitro has been generally assumed to involve internal initiation events on full-length, genomic RNA (4.3 kb). We suggest that this is, at least in part, incorrect. Encapsidated RNA, fractionated on denaturing sucrose gradients, or total RNA from CarMV-infected leaves, fractionated under non-denaturing conditions, was translated in an mRNA-dependent rabbit reticulocyte cell-free system. Evidence for subgenomic RNAs which encode a polypeptide of Mr 38 000 was found. This product was shown to be related to authentic CarMV coat protein by partial proteolysis with alpha-chymotrypsin and SDS/polyacrylamide-gel electrophoresis.

Physical structure and genetic organisation of the genome of maize streak virus (Kenyan isolate)

The structure of the maize streak virus genome (Kenyan isolate, MSV-K), as determined from the sequence of clones obtained from DNA isolated from virus particles, is composed of one major DNA component of about 2.6 kb. MSV virion DNA is partially double-stranded, composed of a full-length virion (V) strand and a short (70-80b) primer (P) strand. The primer strand has a fixed 5'-end capped with alkaline labile material, presumably 1-2 ribonucleotides. The MSV genome has two major coding regions oriented on opposite strands and flanked by two small intergenic regions. The coding region on the P strand is composed of two major open reading frames (ORFs), arranged in tandem and in the same reading frame. Because the predicted protein derived from a composite of these two ORFs closely corresponds to the product from a single ORF in the cassava latent virus genome, it is likely that this region encodes two proteins with common amino-termini, one a read-through product of the amber codon terminator in the first ORF. The intergenic regions contain potential transcription start and stop signals oriented in the direction of the two opposing coding regions. Considerable DNA sequence heterogeneity was observed, mostly silent or conservative third base substitutions in coding regions and base substitutions, small insertions and small, close-range transpositions in intergenic regions.

A revised replication cycle for viroids: the role of longer than unit length RNA in viroid replication

Longer than unit length plus and minus strand RNAs were detected in hop stunt viroid (HSV) infected cucumber leaf tissues by Northern blot hybridization analysis using strand-specific probes. To elucidate the role of these longer than unit length RNAs in the viroid replication cycle, we synthesized tandemly repeated plus and minus strand HSV RNAs in vitro from cloned HSV cDNA and assayed their infectivities. Two and four unit tandemly repeated plus strand RNAs were infectious, but one unit plus, and one, two and four unit minus strands were noninfectious. Taking these data into consideration, we propose a revised rolling circle model for viroid replication.

[Analysis of polypeptides of virus-specific informosomes induced by tobacco mosaic virus and potato virus X]

Informosome-like virus-specific ribonucleoprotein (vRNP) of tobacco mosaic virus (TMV) comprise a set of four major polypeptides having molecular weights of 17 500, 31 000, 37 000 and 39 000. Of the minor polypeptides, those of apparent molecular weights 25 000, 55 000, 68 000 and 70 000 had electrophoretic mobilities of polypeptides found in a ribonucleoprotein preparation from uninoculated plants. Polypeptide with mol.wt. 175 000 is TMV coat protein so far as: a) vRNP was precipitated with immunoglobulins against TMV and TMV coat protein; b) it had electrophoretic mobility similar to mobility of TMV coat protein; c) the peptide map of polypeptides with mol.wts 31 000, 37 000 and 39 000 are probably virus-specific-products. This is supposed because they are not present in cell informosomes protein, and they are not revealed in vRNP induced in cells after infection with potato virus X (PVX). Electrophoresis of vRNP-PVX protein reveals polypeptides of 23 000 (PVX coat protein), 55 000, 70 000, 78 000, 95 000, 120 000 and 145 000.

Double-stranded cDNAs of hop stunt viroid are infectious

Restriction fragments composed of only hop stunt viroid (HSV) cDNA were prepared from recombinant clone pHS-P4P, which carries four tandemly repeated HSV cDNAs, and inoculated into cucumber cotyledons. The results showed that double-stranded cDNAs consisting of 1 to 3 units of HSV sequences were infectious. In cucumber plants inoculated with these double-stranded cDNAs, infectious RNA molecules indistinguishable from authentic HSV were propagated.

Nucleotide sequence of cucumber pale fruit viroid: homology to hop stunt viroid

Double stranded cDNA of cucumber pale fruit viroid ( CPFV ) has been cloned by the method of Okayama and Berg (Mol.Cell.Biol.2,161-170 (1982] and the complete nucleotide sequence was established. The covalently closed circular molecules of single-stranded CPFV RNA consists of 303 nucleotides. The nucleotide sequence of CPFV was compared with the previously established sequence of hop stunt viroid (HSV), which consists of 297 nucleotides ( Ohno et al. Nucleic Acid Res.11,6185-6197 (1983]. CPFV differs from HSV in the nucleotide sequence at 16 positions which include 8 exchanges, 7 insertions and 1 deletion. Both viroids share about 95% sequence homology. Considering the pathogenic properties of both viroids together, it is concluded that CPFV is a cucumber isolate of HSV.