Replication of tobacco mosaic virus VII. Further characterization of single- and double-stranded virus-related RNAs from TMV-infected plants

The Forgotten Tobamovirus Genes Encoding the 54 kDa Protein and the 4-6 kDa Proteins

This article reviews the literature concerning the largely forgotten tobamovirus gene products for which no functions have been ascribed. One of these gene products is the 54 kDa protein, representing the RNA-dependent RNA polymerase segment of the 183 kDa protein translated from the I1-subgenomic mRNA, but which has been found only by in vitro translation and not in plants. The other is a collection of small proteins, expressed from alternative reading frames (likely from internal ribosome entry sites) in either or both the movement protein gene or the capsid protein gene. Previously, two small proteins were referred to as the 4-6 kDa proteins, since only single proteins of such size had been characterized from tobacco mosaic virus and tomato mosaic virus genomes. Such putative proteins will be referred to here as P6 proteins, since many new proposed P6 open reading frames could be discerned, from an analysis of 45 of 47 tobamovirus genomes, with a coding capacity of >15 amino acids up to 94 amino acids, whereas other peptides with ≤15 amino acids were not considered here. The distribution of the putative P6 proteins among these tobamoviruses is described, as well as the various classes they fall into, based on their distribution with regard to the organization of other genes in the viral genomes. Models also are presented for possible functions of the 54 kDa protein and the P6 proteins, based on data in the literature.

Evaluation of potential RNA-interference-target genes to control cotton mealybug, Phenacoccus solenopsis (Hemiptera: Pseudococcuidae)

RNA interference (RNAi) of vital insect genes is a potential tool for targeted pest control. However, selection of the right target genes is a challenge because the RNAi efficacy is known to vary among insect species. Cotton mealybug, Phenacoccus solenopsis, is a phloem-feeding economically important crop pest. We evaluated the RNAi of 2 vital genes, Bursicon (PsBur) and V-ATPase (PsV-ATPase) as potential targets in P. solenopsis for its control. PCR fragments of PsBur and PsV-ATPase were amplified using cDNA synthesized from the total RNA. The PCR amplicons were cloned into Potato virus X (PVX) to develop recombinant PVX for the inoculation of Nicotiana tabacum plants for bioassays with healthy P. solenopsis. Reverse-transcription-polymerase chain reaction (RT-PCR) was used to validate the expression of transgenes in the recombinant-PVX-inoculated plants (treated), and suppression of the target genes in the mealybugs exposed to them. The RT-PCR confirmed the expression of transgenes in the treated plants. Mealybug individuals on treated plants either died or showed physical deformities. Further, the population of mealybug was significantly reduced by feeding on N. tabacum expressing RNAi triggers against PsBur and PsV-ATPase. The results conclude that RNAi is activated in P. solenopsis by feeding on N. tabacum expressing RNAi triggering elements of PsBur and PsV-ATPase genes through recombinant PVX vector. Further, V-ATPase and Bursicon genes are potential targets for RNAi-mediated control of P. solenopsis.

Revisiting the Roles of Tobamovirus Replicase Complex Proteins in Viral Replication and Silencing Suppression

Tobamoviral replicase possesses an RNA-dependent RNA polymerase (RDR) domain and is translated from genomic (g)RNA via a stop codon readthrough mechanism at a one-to-ten ratio relative to a shorter protein lacking the RDR domain. The two proteins share methyltransferase and helicase domains and form a heterodimer implicated in gRNA replication. The shorter protein is also implicated in suppressing RNA silencing-based antiviral defenses. Using a stop codon mutant of Oilseed rape mosaic tobamovirus (ORMV), we demonstrate that the readthrough replicase (p182) is sufficient for gRNA replication and for subgenomic RNA transcription during systemic infection in Nicotiana benthamiana and Arabidopsis thaliana. However, the mutant virus displays milder symptoms and does not interfere with HEN1-mediated methylation of viral short interfering (si)RNAs or plant small (s)RNAs. The mutant virus tends to revert the stop codon, thereby restoring expression of the shorter protein (p125), even in the absence of plant Dicer-like activities that generate viral siRNAs. Plant RDR activities that generate endogenous siRNA precursors do not prevent replication or movement of the mutant virus, and double-stranded precursors of viral siRNAs representing the entire virus genome are likely synthesized by p182. Transgenic expression of p125 partially recapitulates the ORMV disease symptoms associated with overaccumulation of plant sRNAs. Taken together, the readthrough replicase p182 is sufficient for viral replication and transcription but not for silencing suppression. By contrast, the shorter p125 protein suppresses silencing, provokes severe disease symptoms, causes overaccumulation of unmethylated viral and plant sRNAs but it is not an essential component of the viral replicase complex.

Inoculation of Nicotiana tabacum with recombinant potato virus X induces RNA interference in the solenopsis mealybug, Phenacoccus solenopsis Tinsley (Hemiptera: Pseudococcidae)

OBJECTIVES

The chitin synthase 1 (CHS1) gene in Phenacoccus solenopsis (PsCHS1) was evaluated as a potential target of RNA interference (RNAi) by using Potato virus X (PVX) as a vector (recombinant PVX) for expressing RNAi triggering elements in Nicotiana tabacum L.

RESULTS

RT-PCR analysis confirmed the expression of PsCHS1 in N. tabacum inoculated with recombinant-PVX-PsCHS1 (treated). RT- and multiplex-PCR further showed a reduction in mRNA levels of the target gene in mealybugs feeding on treated plants. Mortality in parent adults and emerging nymphs (21 and 29%) exposed to the treated plants was significantly higher (P < 0.05) than those exposed to uninoculated (-ve control) or inoculated with non-recombinant PVX (PVX-control). The number of surviving adults and the combined number of adults and nymphs (47 and 60%) was significantly (P < 0.05) lower on the treated plants than the -ve (76%) or PVX (74%) control. The visual observations verified the physical deformities in mealybugs exposed to the treated plants.

CONCLUSION

chitin synthase 1 is a potential RNAi target in P. solenopsis and the recombinant PVX can be used as a tool to evaluate candidate RNAi triggering elements in plants.

RNA Interference towards the Potato Psyllid, Bactericera cockerelli, Is Induced in Plants Infected with Recombinant Tobacco mosaic virus (TMV)

The potato/tomato psyllid, Bactericera cockerelli (B. cockerelli), is an important plant pest and the vector of the phloem-limited bacterium Candidatus Liberibacter psyllaurous (solanacearum), which is associated with the zebra chip disease of potatoes. Previously, we reported induction of RNA interference effects in B. cockerelli via in vitro-prepared dsRNA/siRNAs after intrathoracic injection, and after feeding of artificial diets containing these effector RNAs. In order to deliver RNAi effectors via plant hosts and to rapidly identify effective target sequences in plant-feeding B. cockerelli, here we developed a plant virus vector-based in planta system for evaluating candidate sequences. We show that recombinant Tobacco mosaic virus (TMV) containing B. cockerelli sequences can efficiently infect and generate small interfering RNAs in tomato (Solanum lycopersicum), tomatillo (Physalis philadelphica) and tobacco (Nicotiana tabacum) plants, and more importantly delivery of interfering sequences via TMV induces RNAi effects, as measured by actin and V-ATPase mRNA reductions, in B. cockerelli feeding on these plants. RNAi effects were primarily detected in the B. cockerelli guts. In contrast to our results with TMV, recombinant Potato virus X (PVX) and Tobacco rattle virus (TRV) did not give robust infections in all plants and did not induce detectable RNAi effects in B. cockerelli. The greatest RNA interference effects were observed when B. cockerelli nymphs were allowed to feed on leaf discs collected from inoculated or lower expanded leaves from corresponding TMV-infected plants. Tomatillo plants infected with recombinant TMV containing B. cockerelli actin or V-ATPase sequences also showed phenotypic effects resulting in decreased B. cockerelli progeny production as compared to plants infected by recombinant TMV containing GFP. These results showed that RNAi effects can be achieved in plants against the phloem feeder, B. cockerelli, and the TMV-plant system will provide a faster and more convenient method for screening of suitable RNAi target sequences in planta.

Characterization of the subgenomic RNAs produced by Pelargonium flower break virus: Identification of two novel RNAs species

Pelargonium flower break virus (PFBV), a member of the genus Carmovirus, has a single-stranded positive-sense genomic RNA (gRNA) of 3.9kb. The 5' half of the gRNA encodes two proteins involved in replication, the p27 and its readthrough product, p86 (the viral RNA dependent-RNA polymerase, RdRp), and the 3' half encodes two small movement proteins, p7 and p12, and the coat protein (CP). As other members of the family Tombusviridae, carmoviruses express ORFs that are not 5'-proximal from subgenomic RNAs (sgRNAs). Analysis of double-stranded RNAs extracted from PFBV-infected leaves and Northern blot hybridizations of total RNA from infected plants or protoplasts revealed than PFBV produces four 3'-coterminal sgRNAs of 3.2, 2.9, 1.7 and 1.4kb, respectively. The 5' termini of the 1.7 and 1.4kb sgRNAs mapped 26 and 143 nt upstream of the initiation codons of the p7 and CP genes, respectively, whereas the 5'-ends of the 3.2 and 2.9kb sgRNAs were located within the readthrough portion of the RdRp gene. The PFBV sgRNAs begin with a motif which is also present at the 5' terminus of the gRNA and the minus polarity of the regions preceding their corresponding start sites (in the gRNA) may be folded into hairpin structures resembling those found for the sgRNA promoters of other carmoviruses. The results indicate that, besides the sgRNAs involved in the translation of the movement proteins and the CP identified in most carmoviral infections, PFBV produces two additional sgRNAs whose biological significance is currently unknown. The possible participation of the 3.2 and 2.9kb PFBV sgRNAs in the expression of readthrough portions of the RdRp is discussed.

Chimeras between oilseed rape mosaic virus and tobacco mosaic virus highlight the relevant role of the tobamoviral RdRp as pathogenicity determinant in several hosts

Oilseed rape mosaic virus (ORMV) is a tobamovirus taxonomically distinct from the type member of the genus, Tobacco mosaic virus (TMV). Both viruses display a specific host range, although they share certain hosts, such as Arabidopsis thaliana, Nicotiana benthamiana and N. tabacum, on which they induce different symptoms. Using a gain-of-symptom approach, we generated chimeric viruses, starting from a TMV infectious clone, over which different regions of ORMV were exchanged with their corresponding regions in the TMV genome. This approach allowed the association of pathogenicity determinants to certain genes within the ORMV genome. A general trend was observed associating the viral origin of the RNA-dependent RNA-polymerase (RdRp) gene and the gain of symptoms. In A. thaliana and N. benthamiana, chimeric viruses were unable to reproduce the symptoms induced by the parental viruses, leading to disease states which could be described as intermediate, and variable in some cases. In contrast, a hypersensitive reaction caused by both of these viruses on N-gene-bearing tobaccos could be found in resistance reactions to all chimeric viruses, suggesting that the avirulence determinant maps similarly in both viruses. A systemic necrotic spotting typical of non-N-gene tobaccos infected with ORMV was associated with the polymerase domain of RdRp. To our knowledge, this is the first time that this controversial portion of the tobamovirus genome has been identified directly as a pathogenicity determinant. None of the reactions of the chimeric viruses could be correlated with increases or decreases in virus titres in the infections.

Biological activity of T7 transcripts of a prototype clone and a sequence variant clone of a satellite RNA of cucumber mosaic virus

Molecular cloning of the (D)CARNA 5 (previously known as n-CARNA 5) necrosis-inducing satellite RNA of cucumber mosaic virus produced a prototype clone (pDsat4) and a sequence variant clone (pDsat1). pDsat1 contained 10 nucleotide changes between positions 70 and 160 which rendered that region identical to the corresponding region of a satellite RNA which does not induce necrosis. T7 RNA polymerase transcripts of each clone replicated in both tobacco and tomato, and the progeny satellite RNAs did not retain the 57-nucleotide non-satellite sequence at the 5' ends of the T7 transcripts. RNase T1 fingerprint analysis of both T7 transcripts and progeny satellite RNAs proved that the satellite sequence portion of each transcript was faithfully replicated in tobacco, and the variations in pDsat1 relative to pDsat4 were maintained. Replication of transcripts of either pDsat4 or pDsat1 in tomato resulted in lethal necrosis, suggesting that the determinant of necrosis induction lies outside the region between nucleotides 70 and 160.

The nature and biological significance of linear potato spindle tuber viroid molecules

"Naturally occurring" linear potato spindle tuber viroid (PSTVL) was shown to be as infectious as circular PSTV (PSTVc). The occurrence of PSTVL was shown not to be (a) an artifact of the extraction procedure per se; (b) due to the presence of metal ions in extraction buffers; or (c) related to the host species used for propagation, to a particular PSTV strain, or to the duration of infection. From labeling and blot-hybridization experiments, it was concluded that in infected tissue PSTVc appears first followed by PSTVL, which is produced as the result of cleavage of PSTVc at specific sites. One of the sites of cleavage of PSTVc was delineated by 5'-end labeling PSTVL, digesting it with RNase T1, separating the fragments by two-dimensional gel electrophoresis, and sequencing the major RNase T1-resistant fragments. The major site of in vitro labeling was shown to be variable, but was confined to the right-hand loop of PSTVc, i.e., between nucleotides 177 and 182. Furthermore, the right-hand end stem and loop of PSTVc contains sequences which are similar to a rDNA gene promoter sequence, and thus we suggest that DNA-dependent RNA polymerase I may be involved in viroid biosynthesis. Other cleavage sites in PSTV were determined by primer extension cDNA synthesis and by dideoxynucleotide chain termination, and were shown to correspond to nucleotides 113-114 and 80-81 and to sequences in the region of 334-340, 300-312, and 271-275. The significance of these cleavage sites is discussed.

In vitro translation products of mrnas derived from TMV-infected tobacco exhibiting a hypersensitive response

Expression of the hypersensitive response (HSR) to tobacco mosaic virus (TMV) infection in Nicotiana tabacum L. cv. Xanthi-nc (genotype NN) is controlled by the single dominant "N" gene and is temperature sensitive. TMV-infected Xanthi-nc tobacco plants grown at the HSR-restrictive temperature of 31 degrees for 3 days postinoculation show necrosis approximately 8 hr after the temperature shift to the HSR-permissive temperature of 25 degrees . Both polyribosomal and total cytoplasmic poly(A)-containing RNAs were isolated at various times after the temperature shift from leaves of TMV-infected and mock-infected Xanthi-nc tobacco plants and from TMV-infected Turkish Samsun tobacco plants (genotype nn; systemic for TMV infection). The RNAs were translated in vitro and the products were analyzed by polyacrylamide gel electrophoresis. A minimum of four polypeptide translation products specific to both the polyribosomal and total cytoplasmic poly(A)-containing RNAs derived from hypersensitively responding Xanthi-nc were observed.

Artifacts are responsible for the translational activity of polyribosome preparations isolated from alfalfa mosaic virus-infected tobacco leaves

We observed that polyribosome preparations isolated from alfalfa mosaic virus (A1MV)-infected tobacco leaves were contaminated with virion-derived material which could not be removed completely by sucrose gradient centrifugation or by magnesium ion precipitation. Upon incubation of polyribosome preparations with S 100 extracts from reticulocyte lysates, viral-encoded proteins were produced. Aurintricarboxylic acid (ATA), an inhibitor of initiation of translation, was used to inhibit de novo translation of the RNAS contaminating the polyribosome preparations. ATA concentrations, which did not inhibit peptide chain elongation on in vitro-produced polyribosomes, completely inhibited the translational activity of the tobacco polyribosomes. Hence the protein synthetic capacity of the tobacco polyribosome preparations is due to de novo translation of virion-derived material by vacant ribosomes present in the complementing S 100 extract. Efforts to activate the tobacco polyribosomes remain unsuccessful.

Replication of tobacco mosaic virus. VIII. Characterization of a third subgenomic TMV RNA

In an earlier study we concluded that tobacco mosaic virus (TMV) infections engender a third subgenomic RNA in infected tissue (P. Palukaitis, F. Garcia-Arenal, M. A. Sulzinski, and M. Zaitlin (1983), Virology 131, 533-545). This RNA of approximate MW of 1.1 x 10(6), termed I1-RNA, was shown to be polyribosome-associated and thus was presumed to serve as a messenger RNA in vivo. Upon in vitro translation of I1-RNA in a rabbit reticulocyte lysate system, a major product of MW approximately 50K was generated. When RNA isolated from polyribosomes of infected tissues was analyzed with clones representing distinct regions of the TMV genome, the I1-RNA was shown to be a subset of the TMV genome, representing the 3'-half of the molecule. A TMV-specific DNA fragment (from a phage M13 clone) containing sequences overlapping the 5' end of I1-RNA was used in nuclease S1-mapping experiments with TMV-RNAs isolated from polyribosomes. I1-RNA was thus shown to be a distinct RNA species and not a class of heterogeneous molecules of approximately the same size. The I1-RNA 5' terminus is residue 3405 in the genome. Based on these findings and on consideration of the TMV-RNA sequence, we propose a model for the translation of I1-RNA: after an untranslated sequence of 90 bases, an AUG codon at residues 3495-3497 initiates a protein of MW 54K, terminating at residue 4915. Thus, the amino acid sequence of the 54K protein is coincident with those residues of the carboxy terminus of the well-known 183K TMV protein.

Subgenomic RNAs with nucleotide sequences derived from RNAs 1 and 2 of cucumber mosaic virus can act as messenger RNAs in vitro

Encapsidated RNAs of cucumber mosaic virus (CMV) were analyzed by hybridization to specific probes after gel electrophoresis. [32P]-complementary DNA (cDNA) probes were prepared by transcription of genomic RNA 1 and RNA 2 nucleotide sequences that had been cloned in a bacteriophage M13 vector. Probes that correspond to unique sequences near the 3' ends of RNA 1 and RNA 2 revealed over 20 smaller RNAs. The subgenomic RNAs derived from each genomic RNA were analyzed more definitively by hybrid selection from total encapsidated RNA, using minus DNA clones derived from sequences in either RNA 1 or RNA 2, and a cDNA probe for the 3' sequence conserved among all the genomic RNAs. Different patterns of over 20 minor RNA species, which were 3'-coterminal with RNAs 1 and 2, were detected, and they were reproducible irrespective of the host, cucumber or Nicotiana clevelandii, from which the virus was isolated. The same RNA patterns were found in RNA extracted from the particulate fraction of CMV-infected cucumber orN. clevelandii. In order to determine whether the subgenomic RNAs could function as messenger RNAs, hybrid-selected RNAs were tested by in vitro translation, using the rabbit reticulocyte lysate. The subgenomic RNAs from RNA 1 produced over 10 major polypeptides from Mr 27,000 to Mr 90,000 all of which could be translated from a few RNA species over about 2,300 nucleotides long. The 3'-coterminal subgenomic RNAs derived from RNA 2 gave less than 10 products from Mr, 17,000 toM(r) 85,000. The smallest product (Mr 17,000) was produced by an RNA about 880 nucleotides long, whereas longer RNAs from 1400 to 2500 nucleotides were efficient mRNAs for polypeptides from Mr 30,000 up to the largest translation products consistent with the size of the RNA.

Satellite RNAs of cucumber mosaic virus: characterization of two new satellites

Two new satellite RNAs of cucumber mosaic virus (CMV) which did not induce necrosis on tomato in the presence of CMV, B-sat RNA, and WL-sat RNA, were shown to be related by sequence to two well-characterized satellite RNAs of CMV: G-sat RNA (non-necrotic on tomato) and n-CARNA 5 (necrotic on tomato). Using the techniques of molecular hybridization analysis, RNA fingerprinting and partial RNA sequencing, B-sat RNA and WL-sat RNA were shown to be more closely related to each other (probably differing by only a small number of nucleotides) than to the other two satellite RNAs. Furthermore, B-sat RNA and WL-sat RNA showed greater sequence homology with G-sat RNA than with n-CARNA 5. WL-sat RNA, which induces a "white-leaf" disease on tomato in the presence of CMV [Gonsalves et al. (1982)., exhibited heterogeneity of sequence in at least one nucleotide position.

ORF6 of Tobacco mosaic virus is a determinant of viral pathogenicity in Nicotiana benthamiana

Tobacco mosaic virus (TMV) contains a sixth open reading frame (ORF6) that potentially encodes a 4.8 kDa protein. Elimination of ORF6 from TMV attenuated host responses in Nicotiana benthamiana without alteration in virus accumulation. Furthermore, heterologous expression of TMV ORF6 from either potato virus X (PVX) or tobacco rattle virus (TRV) vectors enhanced the virulence of both viruses in N. benthamiana, also without effects on their accumulation. By contrast, the presence or absence of TMV ORF6 had no effect on host response or virus accumulation in N. tabacum plants infected with TMV or PVX. TMV ORF6 also had no effect on the synergism between TMV and PVX in N. tabacum. However, the presence of the TMV ORF6 did have an effect on the pathogenicity of a TRV vector in N. tabacum. In three different types of assay carried out in N. benthamiana plants, expression of TMV ORF6 failed to suppress gene silencing. Expression in N. benthamiana epidermal cells of the encoded 4.8 kDa protein fused to the green fluorescent protein at either end showed, in addition to widespread cytosolic fluorescence, plasmodesmatal targeting specific to both fusion constructs. The role of the ORF6 in host responses is discussed.

Two classes of subgenomic RNA of grapevine virus A produced by internal controller elements

Grapevine virus A (GVA), a species of the recently established genus Vitivirus, consists of an approximately 7.3-kb single-stranded RNA genome of positive polarity, organized into five open reading frames (ORFs). The virus, which is closely associated with the grapevine rugose wood disease complex, has been poorly investigated genetically. We explored the production of viral RNAs in a GVA-infected Nicotiana benthamiana herbaceous host and characterized one nested set of three 5'-terminal sgRNAs of 5.1, 5.5, and 6.0 kb, and another, of three 3'-terminal sgRNAs of 2.2, 1.8, and 1.0 kb that could serve for expression of ORFs 2-3, respectively. Neither 3'- nor 5'-terminal sgRNAs, which would correspond to ORF5, was detected, suggesting that expression of this ORF occurs via a bi- or polycistronic mRNA. The 5'-terminal sgRNAs were abundant in dsRNA-enriched extracts. Cloning and sequence analysis of the 3' end of 5.5-kb 5'-terminal sgRNA and the 5' end of the 1.8-kb 3'-terminal sgRNA suggested that a mechanism other than specific cleavage was involved in production of these sgRNAs. Apparently, the production of the 5'- and 3'-terminal sgRNAs was controlled by sequences upstream of the 5'-terminus of each of ORFs 2-4. Detection of both plus and minus strands of the 5'- and 3'-terminal sgRNAs, though in different levels of accumulation, suggested that each of these cis-acting elements is involved in production of four RNAs: a 3'-terminal plus-strand sgRNA which could act as an mRNA, the corresponding 3'-terminal minus-strand RNA, a 5'-terminal plus-strand sgRNA, and the corresponding 5'-terminal minus-strand RNA.

P0 of beet Western yellows virus is a suppressor of posttranscriptional gene silencing

Higher plants employ a homology-dependent RNA-degradation system known as posttranscriptional gene silencing (PTGS) as a defense against virus infection. Several plant viruses are known to encode proteins that can suppress PTGS. Here we show that P0 of beet western yellows virus (BWYV) displays strong silencing suppressor activity in a transient expression assay based upon its ability to inhibit PTGS of green fluorescent protein (GFP) when expressed in agro-infiltrated leaves of Nicotiana benthamiana containing a GFP transgene. PTGS suppressor activity was also observed for the P0s of two other poleroviruses, cucurbit aphid-borne yellows virus and potato leafroll virus. P0 is encoded by the 5'-proximal gene in BWYV RNA but does not accumulate to detectable levels when expressed from the genome-length RNA during infection. The low accumulation of P0 and the resulting low PTGS suppressor activity are in part a consequence of the suboptimal translation initiation context of the P0 start codon in viral RNA, although other factors, probably related to the viral replication process, also play a role. A mutation to optimize the P0 translation initiation efficiency in BWYV RNA was not stable during virus multiplication in planta. Instead, the P0 initiation codon in the progeny was frequently replaced by a less efficient initiation codon such as ACG, GTG, or ATA, indicating that there is selection against overexpression of P0 from the viral genome.

Elucidation of the genome organization of tobacco mosaic virus

Proteins unique to tobacco mosaic virus (TMV)-infected plants were detected in the 1970s by electrophoretic analyses of extracts of virus-infected tissues, comparing their proteins to those generated in extracts of uninfected tissues. The genome organization of TMV was deduced principally from studies involving in vitro translation of proteins from the genomic and subgenomic messenger RNAs. The ultimate analysis of the TMV genome came in 1982 when P. Goelet and colleagues sequenced the entire genome. Studies leading to the elucidation of the TMV genome organization are described below.

Replication of tobacco mosaic virus RNA

The replication of tobacco mosaic virus (TMV) RNA involves synthesis of a negative-strand RNA using the genomic positive-strand RNA as a template, followed by the synthesis of positive-strand RNA on the negative-strand RNA templates. Intermediates of replication isolated from infected cells include completely double-stranded RNA (replicative form) and partly double-stranded and partly single-stranded RNA (replicative intermediate), but it is not known whether these structures are double-stranded or largely single-stranded in vivo. The synthesis of negative strands ceases before that of positive strands, and positive and negative strands may be synthesized by two different polymerases. The genomic-length negative strand also serves as a template for the synthesis of subgenomic mRNAs for the virus movement and coat proteins. Both the virus-encoded 126-kDa protein, which has amino-acid sequence motifs typical of methyltransferases and helicases, and the 183-kDa protein, which has additional motifs characteristic of RNA-dependent RNA polymerases, are required for efficient TMV RNA replication. Purified TMV RNA polymerase also contains a host protein serologically related to the RNA-binding subunit of the yeast translational initiation factor, eIF3. Study of Arabidopsis mutants defective in RNA replication indicates that at least two host proteins are needed for TMV RNA replication. The tomato resistance gene Tm-1 may also encode a mutant form of a host protein component of the TMV replicase. TMV replicase complexes are located on the endoplasmic reticulum in close association with the cytoskeleton in cytoplasmic bodies called viroplasms, which mature to produce 'X bodies'. Viroplasms are sites of both RNA replication and protein synthesis, and may provide compartments in which the various stages of the virus mutiplication cycle (protein synthesis, RNA replication, virus movement, encapsidation) are localized and coordinated. Membranes may also be important for the configuration of the replicase with respect to initiation of RNA synthesis, and synthesis and release of progeny single-stranded RNA.

Historical overview of research on the tobacco mosaic virus genome: genome organization, infectivity and gene manipulation

Early in the development of molecular biology, TMV RNA was widely used as a mRNA [corrected] that could be purified easily, and it contributed much to research on protein synthesis. Also, in the early stages of elucidation of the genetic code, artificially produced TMV mutants were widely used and provided the first proof that the genetic code was non-overlapping. In 1982, Goelet et al. determined the complete TMV RNA base sequence of 6395 nucleotides. The four genes (130K, 180K, 30K and coat protein) could then be mapped at precise locations in the TMV genome. Furthermore it had become clear, a little earlier, that genes located internally in the genome were expressed via subgenomic mRNAs. The initiation site for assembly of TMV particles was also determined. However, although TMV contributed so much at the beginning of the development of molecular biology, its influence was replaced by that of Escherichia coli and its phages in the next phase. As recombinant DNA technology developed in the 1980s, RNA virus research became more detached from the frontier of molecular biology. To recover from this setback, a gene-manipulation system was needed for RNA viruses. In 1986, two such systems were developed for TMV, using full-length cDNA clones, by Dawson's group and by Okada's group. Thus, reverse genetics could be used to elucidate the basic functions of all proteins encoded by the TMV genome. Identification of the function of the 30K protein was especially important because it was the first evidence that a plant virus possesses a cell-to-cell movement function. Many other plant viruses have since been found to encode comparable 'movement proteins'. TMV thus became the first plant virus for which structures and functions were known for all its genes. At the birth of molecular plant pathology, TMV became a leader again. TMV has also played pioneering roles in many other fields. TMV was the first virus for which the amino acid sequence of the coat protein was determined and first virus for which cotranslational disassembly was demonstrated both in vivo and in vitro. It was the first virus for which activation of a resistance gene in a host plant was related to the molecular specificity of a product of a viral gene. Also, in the field of plant biotechnology, TMV vectors are among the most promising. Thus, for the 100 years since Beijerinck's work, TMV research has consistently played a leading role in opening up new areas of study, not only in plant pathology, but also in virology, biochemistry, molecular biology, RNA genetics and biotechnology.

Transgenically expressed cucumber mosaic virus RNA 1 simultaneously complements replication of cucumber mosaic virus RNAs 2 and 3 and confers resistance to systemic infection

Tobacco plants transformed with a cDNA copy of RNA 1 of the Fny strain of cucumber mosaic virus (CMV) promoted the asymptomatic accumulation of inoculated viral RNAs 2 and 3, which could be detected in noninoculated leaves, suggesting that the transgene also permitted viral long-distance movement. Typical symptoms of infection appeared later and correlated with the appearance of viral RNA 1 regenerated from the transgenic mRNA. Although all R0-generation plants were susceptible to Fny-CMV, one line displaying variable susceptibility to the virus in R1-and R2-generations led to selected R3-generation lines with systemic resistance to Fny-CMV. In the inoculated leaves of resistant plants, a dramatic decrease in the accumulation of viral RNA 1 was observed, relative to susceptible plants. No viral RNAs were detected in noninoculated leaves of the resistant plants, but such leaves were susceptible to infection. Furthermore, these leaves could sustain replication of inoculated CMV RNAs 2 and 3, indicating that a complete transgene-silencing had not been induced. Although a transgene-mediated, CMV RNA 1-suppression occurred in the inoculated leaf of resistant plants, the absence of a complete systemically acquired silencing suggests the existence of additional interferences with viral infection that prevented systemic infection by viral RNAs 2 and 3.

Cell-to-cell movement of beet necrotic yellow vein virus: I. Heterologous complementation experiments provide evidence for specific interactions among the triple gene block proteins

Cell-to-cell movement of beet necrotic yellow vein virus (BNYVV) requires three proteins encoded by a triple gene block (TGB) on viral RNA 2. A BNYVV RNA 3-derived replicon was used to express movement proteins to functionally substitute for the BNYVV TGB proteins was tested by coinoculation of TGB-defective BNYVV with the various replicons to Chenopodium quinoa. Trans-heterocomplementation was successful with the movement protein (P30) of tobacco mosaic virus but not with the tubule-forming movement proteins of alfalfa mosaic virus and grapevine fanleaf virus. Trans-complementation of BNYVV movement was also observed when all three TGB proteins of the distantly related peanut clump virus were supplied together but not when they were substituted for their BNYVV counterparts one by one. When P30 was used to drive BNYVV movement in trans, accumulation of the first TGB protein of BNYVV was adversely affected by null mutations in the second and third TGB proteins. Taken together, these results suggest that highly specific interactions among cognate TGB proteins are important for their function and/or stability in planta.

Multipartite nature of potato virus X

Potato virus X (PVX) was among the first viruses to be purified. Nonetheless, properties of the purified virus remain contentious. The literature has been heavily influenced by the concept of a virus as a monopartite entity. Despite the fact that electron micrographs invariably show large proportions of shorter virus particles, the latter are universally ignored. Seven distinct classes of particle lengths were detected. Seven RNA species of approximate sizes 6.4, 3.6, 3.0, 2.1, 1.8, 1.4, and 0.9 kb were extracted from these purified virus preparations. This study shows clearly that shorter PVX particles are not breakage products and indicates that they may reflect fundamental properties of the genome strategy. Furthermore, other potexviruses have been found to contain many shorter particles, and the level of these particles is stable during purification. PVX is generally believed to consist of particles of single length even though the literature does not confirm this conclusion. The notion of a single particle length appears to reflect historical concepts of what a virus should be rather than what PVX is. This report considers whether shorter rods present in virus preparations of PVX are distinctive products of infection. The problem addressed is significant because if affects conclusions concerning the mechanisms of PVX biosynthesis and replication.

Efficient cell-to-cell movement of beet necrotic yellow vein virus requires 3' proximal genes located on RNA 2

RNA 2 of beet necrotic yellow vein virus (BNYVV) carries six open reading frames. The four 3' proximal frames encode the proteins P42, P13, P15, and P14. The first three species present homologies to proteins encoded by three overlapping open reading frames (the triple gene block) in potexviruses, carlaviruses, and barley stripe mosaic virus. P14 does not display homology with other known plant viral proteins. The functions of P42, P13, P15, and P14 were investigated by site-directed mutagenesis. Full-length transcripts of wild-type BNYVV RNAs 1 and 2 were infectious when coinoculated to protoplasts or leaves of Chenopodium quinoa. RNA 2 transcripts in which P42, P13, and P15 were prematurely terminated by frameshift mutations replicated in protoplasts (when inoculated with wild-type RNA 1) but were not infectious to leaves, indicating that the triple gene block proteins of BNYVV are essential for viral cell-to-cell spread. Mutations in P14 were not lethal in leaf infections but smaller local lesions and lesser amounts of viral RNA were produced. RNA 2-related subgenomic RNA species of 2.6, 1.4, and 0.7 kb were detected; they presumably direct synthesis of P42, P13, and P14. No species of the length predicted for a P15-specific subgenomic RNA was detected.

Differential interactions among strains of tomato aspermy virus and satellite RNAs of cucumber mosaic virus

Tomato and tobacco plants were inoculated with either of two strains of tomato aspermy virus, 1-TAV or V-TAV, and each of six isolates of cucumber mosaic virus satellite RNA (CMV-satRNA), B1, B2, B3, Ix, or WL2. Ribonuclease protection assays, used to detect total satRNA and encapsidated satRNA, revealed that G-satRNA generated new satellite RNA not of the inoculated sequence. The other CMV-satRNAs were compared for their ability (1) to replicate, (2) to modulate symptoms, (3) to reduce TAV accumulation, and (4) to alter the extent of encapsidation of TAV genomic RNAs. The fraction of B2- and B3-satRNAs encapsidated was greater for 1-TAV than for V-TAV, although spread and accumulation of the satRNA were similar for both helper viruses. These results suggest that CMV-satRNA may spread in a nonencapsidated form. Accumulation of CMV-satRNA in systemically infected leaves was detected for all inoculum combinations except V-TAV and Ix-satRNA, for which the satellite RNA increased only in protoplasts and inoculated leaves of tobacco or tomato. In such inoculated leaves, Ix-satRNA was not detected in capsids. Thus the effectiveness of the TAV helpers of CMV-satRNAs may be controlled in at least some instances by the extent of satRNA spread or encapsidation rather than by the efficiency of satRNA replication. In contrast to infections initiated by inoculation of CMV and CMV-satRNA, inoculation of 1-TAV or V-TAV and CMV-satRNA did not alter the relative amounts of viral genomic RNAs encapsidated or result in accumulation of large amounts of double-stranded satRNA.

Helper virus-dependent replication, nucleotide sequence and genome organization of the satellite virus of maize white line mosaic virus

Virus like particles (17 nm in diameter) associated with maize white line mosaic virus (MWLMV) were shown to be a satellite virus of MWLMV (SV-MWLMV) on the basis of the following properties: (1) The SV-MWLMV was dependent upon the presence of MWLMV for replication in maize, while the latter virus could replicate independently of the SV particles. (2) No nucleotide sequence homology was detected between the SV-MWLMV and MWLMV, using complementary DNA probes prepared to the two RNAs, in a Northern blot hybridization analysis. (3) The RNA of the SV-MWLMV translated in vitro to produce a protein of the same Mr (24,000) as that found associated with the SV particles. This protein could be immunoprecipitated with an antiserum to the SV particles. And (4), there was no serological relationship between the coat proteins of MWLMV and the SV-MWLMV. The complete nucleotide sequence of the SV-MWLMV RNA (1168 nucleotides) was determined. The SV-MWLMV RNA contains a single open reading frame encoding a polypeptide of Mr 23,961. Computer analysis revealed no significant homology between SV-MWLMV RNA and any other viral or satellite RNAs. However, the putative SV-MWLMV capsid protein is predicted to share some structural features with the capsid protein of the satellite virus of panicum mosaic virus.

Mechanism of synthesis of turnip yellow mosaic virus coat protein subgenomic RNA in vivo

Turnip yellow mosaic virus (TYMV) possesses a monopartite single-stranded (+) sense RNA genome in which the coat protein (cp) gene is 3' proximal and is expressed in vivo via a subgenomic RNA. Evidence is presented here that this subgenomic RNA is synthesized in vivo by internal initiation of replication on (-) RNA strands of genomic length. The double-stranded RNAs (dsRNAs) from TYMV-infected plants have been isolated, purified, and characterized. Under native conditions, no dsRNAs (replicative intermediates and/or replicative forms) of subgenomic length corresponding to subgenomic cp RNA can be detected by ethidium bromide staining of RNA-sizing gels or by Northern blot hybridization using RNA probes. The presence of nascent subgenomic cp (+) RNA strands on the dsRNA of genomic length has been demonstrated using two different approaches: (1) Northern blot hybridization using (-) RNA probes under denaturing conditions and (2) characterization of the 5' ends of nascent (+) RNA strands upon labeling by vaccinia virus nucleoside-2'-methyltransferase.

Sequence and structure at the genome 3' end of the U2-strain of tobacco mosaic virus, a histidine-accepting tobamovirus

The primary sequence of the 3' noncoding region of U2-TMV RNA was determined. A structural model was proposed based on chemical and enzymatic structure mapping as well as on analyses of nuclease protection by aminoacyl-tRNA-synthetase. The model agrees with those proposed for TMV "vulgare" RNA and confirms their general validity for the tobamoviruses. The RNA appears to have a tRNA-like, L-shaped structure at the 3' terminus, linked to a quasi-continuous double-helical stalk, with five pseudoknots involved in the formation of the whole structure. However, the structure of U2-TMV RNA is less stringently conserved than the 3' termini of "vulgare" and other histidine-accepting tobamoviruses. This difference is reflected in the kinetics of aminoacylation of the RNA.

Characterization of cucumber mosaic virus. I. Molecular heterogeneity mapping of RNA 3 in eight CMV strains

RNAs from 13 strains of cucumber mosaic virus (CMV) were divided into two groups on the basis of their ability to hybridize to cDNA of either Fny-CMV RNA or WL-CMV RNA. The extent of the cross-hybridization within one of these groups was analyzed by an RNA protection assay. A cDNA clone of RNA 3 of the Fny strain of CMV was placed in a transcription vector between bacterial promoters T3 and T7. Labeled, minus-sense RNA transcripts prepared from all or part of the cDNA to RNA 3 of Fny-CMV were annealed to the genomic RNA of each of a number of cucumoviruses and digested with RNases. The patterns of RNA fragments protected from digestion were specific for each CMV strain and revealed the extent and location of heterogeneity among the viruses as well as within the Fny-CMV natural population. This approach will allow the differences in host range and disease processes to be correlated with variations in genomic RNAs.

Structure and expression of an alcohol dehydrogenase 1 gene from Pisum sativum (cv. "Greenfeast")

Three genomic clones for anaerobically inducible alcohol dehydrogenase (Adh) have been isolated from Pisum sativum cv. "Greenfeast" via cDNA cloning. One of these contains a complete gene, has exon sequences corresponding to one of the cDNA sequences and is likely to be an expressed gene. This gene has a structure similar to the Adh genes of maize, with introns in the same positions in the coding sequence but differing in their lengths and nucleotide sequences. At the nucleotide level the coding sequence is 75% homologous to both maize Adh1 and Adh2 and 80% homologous to the Adh gene from Arabidopsis, but has an extra coding triplet in exon 1 that is not found in the other plant Adh genes. The non-translated regions of all the gene transcripts are widely divergent between species. A short segment of the pea Adh promoter region (-290 to +57) was fused to a reporter gene and introduced into protoplasts of Nicotiana plumbaginifolia by electroporation. Transient expression of the introduced gene increased markedly when the transfected protoplasts were incubated under anaerobic conditions, showing that cis-acting regulatory signals necessary for anaerobic control of expression reside in the -290 to +57 segment. Sequence comparisons between this region and the corresponding regions of maize and Arabidopsis Adh genes have identified short sequences that may be involved in the anaerobic regulation of plant Adh genes.

Sindbis virus proteins nsP1 and nsP2 contain homology to nonstructural proteins from several RNA plant viruses

Although the genetic organization of tobacco mosaic virus (TMV) differs considerably from that of the tripartite viruses (alfalfa mosaic virus [AlMV] and brome mosaic virus [BMV]), all of these RNA plant viruses share three domains of homology among their nonstructural proteins. One such domain, common to the AlMV and BMV 2a proteins and the readthrough portion of TMV p183, is also homologous to the readthrough protein nsP4 of Sindbis virus (Haseloff et al., Proc. Natl. Acad. Sci. U.S.A. 81:4358-4362, 1984). Two more domains are conserved among the AlMV and BMV 1a proteins and TMV p126. We show here that these domains have homology with portions of the Sindbis proteins nsP1 and nsP2, respectively. These results strengthen the view that the four viruses share mechanistic similarities in their replication strategies and may be evolutionarily related. These results also suggest that either the AlMV 1a, BMV 1a, and TMV p126 proteins are multifunctional or Sindbis proteins nsP1 and nsP2 function together as subunits in a single complex.