Isolation and replication of mutant populations of wound tumor virions lacking certain genome segments

Evolution and emergence of plant viruses

Viruses are common agents of plant infectious diseases. During last decades, worldwide agriculture production has been compromised by a series of epidemics caused by new viruses that spilled over from reservoir species or by new variants of classic viruses that show new pathogenic and epidemiological properties. Virus emergence has been generally associated with ecological change or with intensive agronomical practices. However, the complete picture is much more complex since the viral populations constantly evolve and adapt to their new hosts and vectors. This chapter puts emergence of plant viruses into the framework of evolutionary ecology, genetics, and epidemiology. We will stress that viral emergence begins with the stochastic transmission of preexisting genetic variants from the reservoir to the new host, whose fate depends on their fitness on each hosts, followed by adaptation to new hosts or vectors, and finalizes with an efficient epidemiological spread.

Replication of Plant Viruses

Viruses replicate using both their own genetic information and host cell components and machinery. The different genome types have different replication pathways which contain controls on linking the process with translation and movement around the cell as well as not compromising the infected cell. This chapter discusses the replication mechanisms, faults in replication and replication of viruses co-infecting cells.

Viruses replicate using both their own genetic information and host cell components and machinery. The different genome types have different replication pathways which contain controls on linking the process with translation and movement around the cell as well as not compromising the infected cell. This chapter discusses the replication mechanisms, faults in replication and replication of viruses coinfecting cells.

Structural properties of double-stranded RNAs associated with biological control of chestnut blight fungus

Double-stranded RNAs (ds RNAs) are thought to be the cytoplasmic determinants responsible for the phenomenon of transmissible hypovirulence in the chestnut blight fungus Endothia parasitica [Murr.] Anderson. The three major ds RNA components associated with the North American hypovirulent strain, Grand Haven 2, were characterized with respect to molecular-hybridization specificity and RNase T1-digestion patterns. The large (L-RNA; approximately 9 kilobase pairs) and middle-sized (M-RNA; approximately 3.5 kilobase pairs) ds RNA components cross-hybridized under stringent conditions and exhibited indistinguishable partial and complete RNase T1 digestion patterns relative to their 5' and 3' termini. These results suggest that M-RNA was derived from L-RNA by an internal deletion event. The small (S-RNA; approximately 1 kilobase pair) RNA was unrelated to L- and M-RNA by these criteria. However, all three ds RNA components contained RNase T1-resistant oligonucleotides at one 5' terminus and at the corresponding 3' terminus of the complementary strand. These RNase T1-resistant species exhibited properties consistent with stretches of poly(uridylic acid) and poly(adenylic acid), respectively. The combined results are discussed in terms of the structural organization of hypovirulence-associated ds RNA molecules and their similarities to "double-stranded" RNA molecules observed in plant and animal cells infected with single-stranded RNA viruses.

Identification and characterization of double-stranded RNA associated with cytoplasmic male sterility in Vicia faba

The cytoplasmic male sterility (CMS) trait of at least one line of Vicia faba plants is always associated with the presence of high molecular weight double-stranded RNA in the leaf tissue extracts. Subcellular fractions of leaf tissue from CMS and fertile maintainer plants were initially analyzed in an attempt to locate, identify, and characterize the genetic material involved with the sterility trait. This CMS-associated high molecular weight RNA was found only in the cytosol of the "447" male sterile line of V.faba plants and could not be isolated from the recurrent parent (maintainer), from lines that had been fertility-restored, or from lines that had reverted from the sterile condition. We have been able to move the CMS-associated RNA from donor to fertile host plants through a dodder bridge. These hots not only contain the RNA but now exhibit a male sterile phenotype, as detected by visual examination of the flower, the pollen, morphological characteristics, and pollen staining ability.

Expression of wound tumor virus gene products in vivo and in vitro

Infection of Agallia constricta vector cell monolayers with wound tumor virus results in the synthesis of 12 virus-specific polypeptides. Confirmation that these polypeptides are virus encoded rather than virus induced was obtained by cell-free translation of in vitro synthesized viral mRNA. In addition, transcription by purified wound tumor virus particles was coupled with translation of the resulting transcripts in a wheat embryo cell-free extract. Six previously described structural polypeptides, one presumptive structural polypeptide, and five previously unidentified nonstructural polypeptides were synthesized in infected vector cell monolayers, in cell-free extracts directed by in vitro synthesized viral mRNA, and in the homologous plant cell-free system, in which viral transcription was coupled with translation. Pulse-chase experiments revealed no evidence of precursor-product relationships for the wound tumor virus-specific polypeptides.

Specific binding of Bluetongue virus NS2 to different viral plus-strand RNAs

The Reoviridae have double-stranded RNA genomes of 10-12 segments, each in a single copy in the mature virion. The basis of genome segment sorting during virus assembly that ensures each virus particle contains the complete viral genome is unresolved. Bluetongue virus (BTV) NS2 is a single-stranded RNA-binding protein that forms inclusion bodies in infected cells. Here, we demonstrate that the specific interaction between NS2 and a stem-loop structure present in BTV S10 RNA, and phylogenetically conserved in other BTV serotypes, is abolished by mutations predicted to disrupt the structure. Subsequently, we mapped RNA regions in three other genomic segments of BTV that are bound preferentially by NS2. However, structure probing of these RNAs did not reveal secondary structure motifs that obviously resembled the stem-loop implicated in the NS2-S10 interaction. In addition, the specific binding by NS2 to two different viral RNAs was found to occur independently. Together, these data support the hypothesis that the recognition by NS2 of different RNA structures may be the basis for discrimination between viral RNAs during virus assembly.

Studies on overwintering of bluetongue viruses in insects

Bluetongue viruses (BTVs) are economically important arboviruses that affect sheep and cattle. The overwintering mechanism of BTVs in temperate climates has eluded researchers for many years. Many arboviruses overwinter in their invertebrate vectors. To test the hypothesis that BTVs overwinter in their vertically infected insect vectors, Culicoides sonorensis larvae were collected from long-term study sites in northern Colorado, USA, and assayed for the presence of BTV RNA by nested RT-PCR. Sequences from BTV RNA segment 7 were detected in 30 % (17/56) of pools composed of larvae and pupae collected in 1998 and in 10 % (31/319) of pools composed of adults reared from larvae collected in 1996. BTV was not isolated from the insects. Additionally, Culicoides cell-culture lines derived from material collected at one of the sites, or derived from insect samples collected during a BTV outbreak, contained BTV RNA segment 7. In contrast, segment 2 RNA was detected at half the rate of segment 7 RNA in the field-collected larvae and was only detected in the Culicoides cell lines with one of two primer sets. These data suggest that BTVs could overwinter in the insect vector and that there is reduced expression of the outer capsid genes during persistent infection.

Variability and genetic structure of plant virus populations

Populations of plant viruses, like all other living beings, are genetically heterogeneous, a property long recognized in plant virology. Only recently have the processes resulting in genetic variation and diversity in virus populations and genetic structure been analyzed quantitatively. The subject of this review is the analysis of genetic variation, its quantification in plant virus populations, and what factors and processes determine the genetic structure of these populations and its temporal change. The high potential for genetic variation in plant viruses, through either mutation or genetic exchange by recombination or reassortment of genomic segments, need not necessarily result in high diversity of virus populations. Selection by factors such as the interaction of the virus with host plants and vectors and random genetic drift may in fact reduce genetic diversity in populations. There is evidence that negative selection results in virus-encoded proteins being not more variable than those of their hosts and vectors. Evidence suggests that small population diversity, and genetic stability, is the rule. Populations of plant viruses often consist of a few genetic variants and many infrequent variants. Their distribution may provide evidence of a population that is undifferentiated, differentiated by factors such as location, host plant, or time, or that fluctuates randomly in composition, depending on the virus.

Evidence for a phytoreovirus associated with tobacco exhibiting leaf curl symptoms in South Africa

ABSTRACT Three forms of tobacco leaf curl (termed classes I, II, and III, based on symptomatology) recently have been described in southern Africa. Numerous attempts to isolate virus particles responsible for a nongeminivirus-induced leaf curl disease (class I) of tobacco in South Africa have been unsuccessful. Recently, 12 dsRNA segments were isolated from tobacco exhibiting class I leaf curl symptoms, suggesting a possible reovirus genome. The objective of our study was to confirm whether the dsRNA segments are associated with a reovirus. Isolation of icosahedral particles with an outer core 60 to 65 nm in diameter and an inner core 40 to 45 nm in diameter was achieved. Twelve distinct nonpolyadenylated dsRNAs were isolated from purified virions, and the total molecular masses of the dsRNAs ranged from 17.86 to 18.40 x 10(6) Da in polyacrylamide and agarose gels, respectively. Using hybridization analysis, dsRNAs were identified as non-homologous distinct segments. Comparisons with other known reoviruses revealed a unique banding pattern that was most similar to the wound tumor virus (WTV), the type species of the genus Phytoreovirus. Hybridizations of WTV cloned DNA probes (segments S4 and S6 to S9) and dsRNAs from infected tobacco indicated no significant sequence similarity, whereas indirect enzyme-linked immunosorbent assay with a polyclonal antiserum to WTV showed strong positive cross-reactivity to tobacco virions. Our results indicate a virus with features consistent with those of phytoreoviruses. This is the first report of a plant reovirus in tobacco, the first record in Africa, and the second example of a field-isolated dicot phytoreovirus.

Precise packaging of the three genomic segments of the double-stranded-RNA bacteriophage phi6

Bacteriophage phi6 has a genome of three segments of double-stranded RNA. Each virus particle contains one each of the three segments. Packaging is effected by the acquisition, in a serially dependent manner, of the plus strands of the genomic segments into empty procapsids. The empty procapsids are compressed in shape and expand during packaging. The packaging program involves discrete steps that are determined by the amount of RNA inside the procapsid. The steps involve the exposure and concealment of binding sites on the outer surface of the procapsid for the plus strands of the three genomic segments. The plus strand of segment S can be packaged alone, while packaging of the plus strand of segment M depends upon prior packaging of S. Packaging of the plus strand of L depends upon the prior packaging of M. Minus-strand synthesis begins when the particle has a full complement of plus strands. Plus-strand synthesis commences upon the completion of minus-strand synthesis. All of the reactions of packaging, minus-strand synthesis, and plus-strand synthesis can be accomplished in vitro with isolated procapsids. Live-virus constructions that are in accord with the model have been prepared. Mutant virus with changes in the packaging program have been isolated and analyzed.

The loss of outer capsid protein P2 results in nontransmissibility by the insect vector of rice dwarf phytoreovirus

A transmission-defective (TD) isolate of rice dwarf phytoreovirus lacked the ability to infect cells when derived from the virus-free insect vector Nephotettix cincticeps. Analysis by sodium dodecyl sulfate-polyacrylamide gel electrophoresis of the purified virus showed that among six structural proteins, the P2 outer capsid protein (encoded by genome segment S2) was absent from the TD isolate, whereas all six proteins were present in the transmission-competent (TC) isolate. P2 was not detected on immunoblots of rice plants infected with the TD isolate. Genome segment S2 and its transcript were detected in both TD and TC isolates. Sequence analysis of the S2 segment of the TD isolate revealed the presence of a termination codon due to a point mutation in the open reading frame, which might explain the absence of P2 in the TD isolate. These results demonstrate that the P2 protein is one of the factors essential for infection by the virus of vector cells and, thus, influences transmissibility by vector insects.

Heterogeneity of rice ragged stunt oryzavirus genome segment 9 and its segregation by insect vector transmission

Genomic heterogeneity of genome segment 9 (S9) of rice ragged stunt virus (RRSV) was investigated and a point mutation was found to be responsible for an electrophoretic mobility shift of S9 on polyacrylamide gel electrophoresis (PAGE). A new form of S9 (S9L) which migrated slightly faster than natural S9 (S9U) had the same length with A-->C transversion at nt 843. Synthetic S9 with a C:G pair at nt 843 migrated slightly faster than that with an A:U pair. Therefore, we conclude that the single point mutation shifts the electrophoretic mobility. Using polymerase chain reaction-single strand conformation polymorphism (PCR-SSCP), we could detect S9U and S9L alone or mixture in insect vectors after acquisition as well as in infected rice plants.

First field isolation of wound tumor virus from a plant host: minimal sequence divergence from the type strain isolated from an insect vector

A new strain of wound tumor virus (WTV) has been isolated from a periwinkle plant (Catharanthus roseus) that was among several used as bait plants in a blueberry field. The 12 segments of double-stranded RNA of the viral genome were isolated directly from infected tissue and found to have mobilities through agarose gels that were identical to those of the type strain WTV. Coupled complementary DNA (cDNA) and polymerase chain reactions (PCR) primed with oligonucleotides complementary to the termini of segments 4-12 of the type strain of WTV successfully amplified those segments. Amplification products of the 9 segments were of the size expected for the full-length segment, with no shorter than full-length products representing defective RNAs detected. PCR products representing segments 7, 11, and 12 were cloned and sequenced in their entirety. The sequence of each segment varied only slightly from the homologous segment of the type strain. Variation ranged from less than 1% for segment 12 to approximately 3% for segment 7, but even these low levels of variation were much greater than the variation found in WTV isolates maintained in the laboratory. Most of the variation in each of the three segments was confined to the coding regions, and most of the differences were third position transitions. The new WTV strain has been designated WTVNJ.

New viruses and new disease: mutation, evolution and ecology

Given the extraordinarily high mutation rate of viruses, particularly those with RNA genomes, it is not surprising that new viruses are continually evolving. However, the symptomatology of old viral diseases has remained stable for centuries. The combination of genetic and ecological factors that constrain as well as facilitate the emergence of new viruses is analyzed.

Structure-specific binding of wound tumor virus transcripts by a host factor: involvement of both terminal nucleotide domains

A gel retardation assay was used to demonstrate binding of wound tumor virus transcripts by a protein component of leafhopper vector cell extracts. Comparative binding studies employing terminally modified and internally deleted transcripts established that the segment-specific inverted repeats present in the terminal domains of the viral transcripts were necessary but not sufficient for optimal binding. An additional involvement of internal sequences in either the formation or the stabilization of the binding complex was indicated. Results of competitive binding experiments confirmed the sequence- and structure-specificity of the protein-RNA interaction and revealed apparent differences in the ability of individual viral transcripts to form a stable binding complex. Possible implications of structure-specific interactions between wound tumor virus transcripts and a host component and the role of the terminal inverted repeats are discussed.

The 3'-terminal sequence of a wound tumor virus transcript can influence conformational and functional properties associated with the 5'-terminus

We recently reported the presence of segment-specific inverted repeats within the terminal regions of wound tumor virus genomic segments (J. V. Anzol, Z. Xu, T. Asamizu, and D. L. Nuss, 1987, Proc. Natl. Acad. Sci. USA, 84, 8301-8305). This report describes a series of experiments designed to investigate potential intramolecular interactions involving the 5'- and 3'-terminal domains of wound tumor virus transcripts. A series of transcription vectors were constructed which allowed the synthesis of an exact copy of the transcript corresponding to genomic segment S8 and four analogs that differed from the authentic sequence only at the immediate 3'-terminus. Modifications designed to extend or alter the 3'-terminal inverted repeat altered the in vitro translational efficiency of the transcript and the sensitivity of phosphodiester bonds within the immediate 5'-terminal domain to digestion by nuclease T1. These results were consistent with computer-assisted secondary structure analyses of the complete nucleotide sequence of transcripts corresponding to six genomic segments which predicted intramolecular interactions involving the terminal inverted repeats. Potential roles of the terminal domains in expression, sorting and packaging of a segmented RNA genome are considered.

Assignment of wound tumor virus nonstructural polypeptides to cognate dsRNA genome segments by in vitro expression of tailored full-length cDNA clones

Presumptive full-length cDNA clones of 9 of the 12 wound tumor virus double-stranded RNA genome segments were tailored for efficient in vitro expression by a recently described strategy [Z. Xu, J.V. Anzola, and D.L. Nuss (1987) DNA6, 505-513]. In vitro synthesized polypeptides specified by synthetic transcripts corresponding to the tailored cDNAs comigrated in polyacrylamide gels with in vivo synthesized viral-specific polypeptides. This analysis confirmed the functional integrity of the tailored cDNA clones and identified cognate genome segments which encode all five viral non-structural polypeptides as well as four structural polypeptides; two which comprise the capsid, one located in the viral core and one associated with the outer protein coat.

Effect of beet necrotic yellow vein virus RNA composition on transmission by Polymyxa betae

Beet necrotic yellow vein virus (BNYVV) is naturally transmitted by the soil-borne fungus Polymyxa betae and usually remains confined to the roots of infected sugarbeets. In naturally infected sugarbeets the virion RNA always consists of four components which are uniform in size in different isolates but when BNYVV is propagated by mechanical inoculation to leaves of Chenopodium quinoa the two smallest RNA components, RNA-3 and -4, may undergo deletion or disappear from the isolate, suggesting that they are only essential for the natural mode of infection. To test this hypothesis, several C. quinoa isolates of BNYVV with different RNA-3 and -4 contents have been retransmitted to sugarbeet root via P. betae. The results show that the two isolates containing no detectable full-length RNA-3 and -4 are poorly transmitted and that cases of successful infection are associated with the reappearance of full-length RNA-3 and -4.

Segment-specific inverted repeats found adjacent to conserved terminal sequences in wound tumor virus genome and defective interfering RNAs

Defective interfering (DI) RNAs are often associated with transmission-defective isolates of wound tumor virus (WTV), a plant virus member of the Reoviridae. We report here the cloning and characterization of WTV genome segment S5 [2613 base pairs (bp)] and three related DI RNAs (587-776 bp). Each DI RNA was generated by a simple internal deletion event that resulted in no sequence rearrangement at the deletion boundaries. Remarkably, although several DI RNAs have been in continuous passage for more than 20 years, their nucleotide sequences are identical to that of corresponding portions of segment S5 present in infrequently passaged, standard, transmission-competent virus. The positions of the deletion breakpoints indicate that the minimal sequence information required for replication and packaging of segment S5 resides within 319 bp from the 5' end of the (+)-strand and 205 bp from the 3' end of the (+)-strand. The terminal portions of segment S5 were found to contain a 9-bp inverted repeat immediately adjacent to the conserved terminal 5'-hexanucleotide and 3'-tetranucleotide sequences shared by all 12 WTV genome segments. The presence of a 6- to 9-nucleotide segment-specific inverted repeat immediately adjacent to the conserved terminal sequences was found to be a feature common to all WTV genome segments. These results reveal several basic principles that govern the replication and packaging of a segmented double-stranded RNA genome.

A defective interfering RNA that contains a mosaic of a plant virus genome

A symptom-modulating RNA associated with tomato bushy stunt virus (TBSV) was investigated with respect to physical and biological properties. Linear RNA of approximately 396 nucleotides was packaged in viral coat protein and was dependent on TBSV for replication. Coinoculation of the small RNA with TBSV resulted in the attenuation of TBSV-induced symptoms and depression of virus synthesis in whole plants. Nucleotide sequence analysis revealed that the symptom-modulating RNA was derived from 5', 3', and internal segments of the TBSV genome. The identification of this symptom-modulating RNA as a co-linear deletion mutant of the helper virus genome establishes it as the first definitive defective interfering RNA (DI RNA) to be identified in association with a plant virus.

Variant dsRNAs associated with transmission-defective isolates of wound tumor virus represent terminally conserved remnants of genome segments

Variant double-stranded RNAs are often associated with the genome of transmission-defective isolates of wound tumor virus. These RNAs are replicated and packaged into virus particles in systemically infected plants and are transcribed in vitro by the virion-associated transcriptase. Direct physical evidence that the variant RNAs are remnants of particular WTV genome segments was provided by molecular hybridization studies. Subsequently, ribonuclease T1 digestion products of 3'-end-labeled genome and remnant RNAs were analyzed by one- and two-dimensional electrophoretic techniques. One-dimensional partial and complete digestion patterns were indistinguishable, indicating that the guanosine positions relative to the 3' terminus of the corresponding strands of a particular genome segment and its remnant RNA are the same for at least 40 nucleotides from each end. Fingerprints of the 3' terminal ribonuclease T1-resistant fragments were identical, showing that the nucleotide composition of the 3' terminal ends of the corresponding strands of a particular genome segment and its remnant RNA are also identical. These results indicate that variant RNAs associated with transmission-defective WTV isolates are formed by deletion of an internal portion (as much as 85%) of genomic RNA segments yielding terminally conserved genomic remnants that are functional with respect to transcription, replication, and packaging.

In Vitro Synthesis and Modification of mRNA by Exvectorial Isolates of Wound Tumor Virus

Nontransmissible (exvectorial) isolates of wound tumor virus retain the ability to catalyze in vitro synthesis of RNA. Furthermore, exvectorial virus particles exhibit mRNA-2′- O -methyltransferase activity even after long-term (30-year) passage in a host that lacks this enzyme activity.