Mapping local and systemic symptom determinants of cucumber mosaic cucumovirus in tobacco

Cucumber mosaic cucumovirus (CMV) can be divided into two subgroups, I and II. LS-CMV and most other subgroup II strains cause a mild, systemic mottle on tobacco and can induce a necrotic etching (necrotic rings) symptom on inoculated tobacco leaves. In contrast, Fny-CMV and most other subgroup I strains cause severe, systemic mosaic symptoms on tobacco, but do not induce the necrotic etching symptom. Full-length cDNA clones of all three genomic RNAs of LS-CMV were constructed and infectious RNAs were generated from these clones. Using pseudorecombinants constructed from the infectious transcripts of LS-CMV and Fny-CMV, we found that both RNAs 1 and 2 of Fny-CMV are involved in determining the severity of systemic symptom on tobacco, and that LS-CMV RNA 3 contains the determinant for the necrotic etching symptom. Chimeras formed between Fny- and LS-CMV RNA 3 were used to demonstrate that the inducer of the necrotic etching symptoms mapped to the 5' 618 nucleotides of LS-CMV RNA 3, and required sequences in both the 5' non-translated region, as well as the 3a gene of CMV.

The 3a protein from cucumber mosaic virus increases the gating capacity of plasmodesmata in transgenic tobacco plants

The 3a protein, encoded by RNA 3 of cucumber mosaic virus (CMV), is the putative movement protein of viral progeny in infected plants. An analysis of transgenic tobacco plants constitutively expressing the CMV 3a protein showed that the protein is accumulated in leaves at every stage of development. In fully expanded leaves the protein is immunodetectable mostly in a cell-wall-enriched fraction. Dye-coupling experiments using fluorescent-dextran probes were performed on fully expanded leaves to study the modifying effect of CMV 3a protein on the gating capacity of plasmodesmata. Movement of fluorescein-isothiocyanate-labelled dextran with a mean molecular mass of 10,000 Da, and an approximate Stokes' radius of 2.3 nm, was detected between cells of the 3a protein transgenic plants, but not in the control plants. These results are consistent with the idea that the CMV 3a protein is involved in the modification of plasmodesmata and, therefore, in the cell-to-cell spread of the virus.

Amplification in vivo of brome mosaic virus RNAs bearing 3' noncoding region from cucumber mosaic virus

The 3' noncoding aminoacylatable regions of the three genomic RNAs of brome mosaic (BMV) and cucumber mosaic (CMV) viruses are highly conserved and exhibit extensive similarities in their primary and secondary structures. To investigate the functional significance of these conserved features, the 3' 186 nucleotide sequence of Fny-CMV RNA3 was incorporated into the 3' end of full-length genomic BMV RNA2 and RNA3 and their replicative competence and infectivity were examined in barley protoplasts and Chenopodium quinoa plants, respectively. In barley protoplasts, functional replicase provided by wild-type BMV RNAs 1 and 2 successfully interacted with the CMV 3' end when present on RNA3 and resulted in the proliferation and accumulation of chimeric progeny RNA3 and RNA4. In contrast, when CMV 3' end sequences were present on RNA2 no amplification of chimeric RNA occurred. Inoculation of chimeric RNAs to C. quinoa revealed that systemic infections were derived from the selection of higher fitness recombinant sequences over lower fitness chimeric RNAs.

Nucleotide sequence and infectious in vitro transcripts of RNA 3 of tomato aspermy virus pepper isolate

The nucleotide sequence of a cDNA clone corresponding to the entire RNA 3 of a pepper isolate of tomato aspermy cucumovirus (P-TAV) was determined. The 2222 nucleotides (nt) long RNA 3 is dicistronic and codes a 3a (280 amino acids) and a coat protein (cp, 218 amino acids). The nucleotide sequence of P-TAV RNA 3 shows a high sequence identity (99%) with that of C-TAV RNA 3 and the amino acid sequences of the 3a and the coat proteins between these two TAV strains are also very similar. The transcription start site of the subgenomic RNA 4 was mapped to the G at the position of 1148 of RNA 3. A full-length cDNA copy of P-TAV RNA-3 was cloned downstream of the phage T7 promoter. Transcripts synthesized in vitro had no extra nucleotides at the 5' end, but there were nine non-viral nucleotides at the 3' terminus. The transcripts of TAV RNA 3 were infectious when coinoculated into test plants in the presence of purified RNA 1 and 2 of P-TAV or Trk7-CMV respectively. Northern blot analysis of RNA extracted from inoculated plants showed the expected genomic and subgenomic RNAs.

Nucleotide sequence and infectivity of cucumber mosaic cucumovirus (strain K) RNA2 involved in breakage of replicase-mediated resistance in tobacco

Replicase-mediated resistance represents a genetically engineered form of resistance against viral infections and is established by using an intact or modified viral polymerase (replicase) gene for the transformation of the host. The K strain of cucumber mosaic cucumovirus (K-CMV) has been shown to break replicase-mediated resistance generated using a modified RNA2 of the subgroup I strain Fny-CMV. A full-length cDNA clone of K-CMV RNA2 was generated and RNA transcripts were shown to be infectious in combination with Fny-CMV RNAs 1 and 3. We further demonstrate that the ability of K-CMV to overcome resistance in the transgenic plants maps to RNA2. The complete nucleotide sequence of this RNA was determined and sequence differences from Fny-CMV RNA2 are discussed with regard to functional domains and their possible involvement in resistance breakage.

Specificity of replicase-mediated resistance to cucumber mosaic virus

Plants transformed with a nucleotide sequence coding for a truncated RNA 2 replicase gene of the subgroup I strain of cucumber mosaic virus, Fny-CMV, are resistant to cucumber mosaic disease. Two resistant lines representing independent transformations in the original study have been propagated, and their progeny have been examined. Resistance to Fny-CMV was genetically integrated and was retained in the R4 generation. Fourteen subgroup I CMV strains, 6 strains uncharacterized as to subgroup, and 4 subgroup II CMV strains, as well as potato virus X, tobacco mosaic virus, tomato aspermy virus, tobacco etch virus, and peanut stunt virus were inoculated mechanically to R2 generation plants of these two lines. Resistance was found to 12 subgroup I CMV strains and to all of the subgroup-uncharacterized strains. No resistance was found to subgroup II CMV strains nor to the other viruses listed above. However, the two plant lines behaved differently in response to 3 subgroup I strains, K-CMV, PRC-CMV, and MB-CMV, where one line (5) was more resistant than the other (2). RNase protection analyses indicated that these 3 strains vary more in sequence from Fny-CMV than do the other subgroup I strains tested. Resistance was also shown when aphids were used to inoculate plants with either of 2 subgroup I CMV strains; no resistance was observed when aphids were used to transmit a subgroup II CMV strain. Inoculation of transgenic plants with pseudorecombinants produced with the RNAs derived from Fny-CMV to which the plants are resistant, and LS-CMV, a subgroup II strain to which they are susceptible, indicated that the resistance-breaking capacity of LS-CMV is a function of RNA 2.

Requirement of 3'-terminal guanosine in (-)-stranded RNA for in vitro replication of cucumber mosaic virus satellite RNA by viral RNA-dependent RNA polymerase

The 3' terminus of the (-) RNA strand in the replicative forms of several (+)-stranded RNA viruses possesses an unpaired guanosine with unknown function. This unpaired guanosine is also found at the 3' terminus of the (-) strand in the double-stranded form of two cucumoviral satellite RNAs. Using a cucumber mosaic virus (CMV) RNA-dependent RNA polymerase capable of replicating the satellite RNA in vitro, the 3'-terminal guanosine of the satellite (-) strand was shown to be an absolute requirement for satellite (+) strand synthesis. If genomic RNA synthesis of CMV and other members of the alphavirus-like superfamily that produce (-) strands terminating in an unpaired 3' guanosine follows a similar strategy, the work reported here would represent the first experimental support for the notion of 3'-terminal guanosine functioning as an essential recognition signal for viral replicases, enabling (+) strand RNA synthesis to be initiated internally from a (-) strand template.

Molecular cloning of coat protein gene of cucumber mosaic virus, CMV-U strain

RNA isolation from purified cucumber mosaic virus, CMV-U strain and cDNA synthesis was carried out. The coat protein gene (RNA4) region was amplified selectively by polymerase chain reaction (PCR) with CMV RNA4-specific primers. Double-stranded cDNA was cloned in PRT103 vector at Xho1/Kpn1 site and about 1kb insert obtained. The insert was partly sequenced which showed 50% sequence homology with CMV-Q, C and WL strains.

Structural features unique to a new 405-nucleotide satellite RNA of cucumber mosaic virus inducing tomato necrosis

The complete nucleotide sequence of a new satellite RNA (KN-satRNA) of cucumber mosaic virus (CMV) strain KN, isolated from tomato plants showing severe necrosis, has been determined by the analysis of a full-length cDNA clone from which biologically active transcript was produced. KN-satRNA was 405 nucleotides and is the largest among the known CMV-satRNAs. Comparison of the sequence with D-CARNA5 (335 nucleotides) revealed three extensive homologous regions, which were the 5' region (position 1-80), the 3' half (position 213-405), and a middle section (position 116-177) of the molecule. The total length of the three regions covers almost the entire molecule of D-CARNA5. Thus, it is apparent that insertions would occur at two sites of D-CARNA5, positions 81-86 and 146, to evolve the larger size satRNA. These insertions did not alter the proposed secondary structure model of Q-satRNA. The in vitro transcript of the cDNA clone of KN-satRNA induced necrosis on tomato which was identical to that of native KN-satRNA. The 3'half of the RNA contained the "necrogenic consensus" sequence reported for other satRNAs, to which the pathogenicity of KN-satRNA may be attributed.

Replication of cucumber mosaic virus satellite RNA from negative-sense transcripts produced either in vitro or in transgenic plants

Both positive [(+)] and negative [(-)] sense versions of two satellite RNA (satRNA) genes from cucumber mosaic virus (CMV), the necrogenic I17N and the nonnecrogenic R, have been introduced into the genome of tobacco plants. On infection with satRNA-free CMV, satRNA was amplified in plants expressing each of the four genes. All four genes confer protection against CMV infection. However, co-inoculation of plants with viral RNA and CMV satRNA transcripts synthesized in vitro showed that (-) sense transcripts were less active than the corresponding (+) sense transcripts. This is the first report that (-) sense CMV satRNA transcripts can serve as a template for satRNA replication.

Complex interactions among several nucleotide positions determine phenotypes defective for long-distance transport in the satellite RNA of cucumber mosaic virus

Ix-satRNA is a CMV-satRNA necrogenic on tomato that is defective for long-distance systemic movement when coinoculated in tobacco with V-TAV. To analyze the determinants for this defective phenotype, full-length cDNA clones of Ix-satRNA and of the closely related, nondefective I17N-satRNA were obtained. Infectious transcripts from these clones (Ix5-satRNA and I17N1-satRNA) had the same phenotypes as the original satRNAs and differed only in four positions: positions 20 (Ix5, C; I17N1, U), 102 (Ix5, C; I17N1, U), 224 (Ix5, deleted; I17N1, A), 327 (Ix5, G; I17N1, A). By site-directed mutagenesis at positions 224 and 327 and by recombination using two common restriction sites, satRNAs in which the bases at these four positions were changed from the composition at Ix5-satRNA to the composition at I17N1-satRNA were obtained. A comparison of the phenotypes of the 13 single, double, and triple mutants (respective to Ix5-satRNA) showed that the defective phenotype of Ix5-satRNA is determined by the nature of the four positions analyzed; mutants at any of the positions 102, 224, and 327 accumulated as efficiently as I17N1-satRNA in systemically infected tobacco leaves when coinoculated with V-TAV. The change C20-->U also restored systemic movement, albeit imperfectly, giving rise to a phenotype that moved systemically less efficiently than I17N1-satRNA. This phenotype determined by U20 is expressed irrespective of the base at position 102, indicating an epistatic interaction between determinants 20 and 102; this interaction does not occur with position 224 or 327. That differences in the analyzed satRNAs are due to their being able, or not, to move systemically is shown by the fact that all of them (including Ix5-satRNA) accumulated to the same high level in directly inoculated leaves. The similarity in the sequences of the analyzed satRNAs and the complexity of the interactions among the effects of base changes at four positions scattered over the satRNA molecule suggest that the observed movement phenotypes may depend on conformational changes in the satRNAs.

The chlorosis-induction domain of the satellite RNA of cucumber mosaic virus: identifying sequences that affect accumulation and the degree of chlorosis

A number of satellite RNAs of cucumber mosaic virus (CMV) can induce chlorosis in either tobacco or tomato. A region containing the chlorosis domain was delimited, and one nucleotide position (153) regulating chlorosis induction as well as the nucleotide position (149) controlling the host specificity for chlorosis were identified. A cDNA clone of the B5-sat RNA was modified by site-directed mutagenesis to identify other nucleotides affecting chlorosis itself, as well as the extent of chlorosis and the helper virus-strain specificity for chlorosis. Four nucleotides conserved in chlorosis-inducing satellite RNAs (positions 127, 148, 149, 158) as well as two nucleotides within the chlorosis-induction domain that vary among chlorosis-inducing satellite RNAs (170, 171) were altered. Only substitutions at nucleotide positions 127 and 171 did not affect expression of the chlorosis phenotype. Alteration of position 148 affected satellite RNA accumulation. The pleiotropic effects of various sequences within the chlorosis-induction domain are discussed relative to particular sequence contexts in different chlorosis-inducing RNAs.

Mapping determinants within cucumber mosaic virus and its satellite RNA for the induction of necrosis in tomato plants

A mutant of the WL47 satellite (WL47-sat) RNA of cucumber mosaic virus (CMV), constructed in vitro, induces lethal necrosis in tomato plants when associated with either of two subgroup II strains of CMV: LS- or WL-CMV (D. E. Sleat and P. Palukaitis, Proc. Natl. Acad. Sci. USA 87:2946-2950, 1990). The phenotype of this mutant (WLM2-sat RNA) has been examined on tomato plants, after co-inoculation with a wider range of CMV strains. Necrosis was observed when WLM2-sat RNA was associated with any of the subgroup II CMV strains tested. However, WLM2-sat RNA ameliorated the symptoms induced by subgroup I CMV strains without inducing necrosis. Inoculation with WLM2-sat RNA with pseudorecombinants formed between subgroup I and subgroup II CMV strains showed an association of the necrosis induction phenotype with RNA 2 of the subgroup II strains. In contrast to WLM2-sat RNA, infectious transcripts of the naturally necrogenic D4-sat RNA induced lethal necrosis in tomato with all CMV strains tested. Experiments involving the exchange of sequences between WLM2- and D4-sat RNAs indicated that nucleotides sequences in either of two separate regions could influence the necrosis phenotype. Thus, the subgroup-specific necrosis-inducing phenotype may be due to subtle alterations in secondary and/or tertiary structure in the satellite RNA, as well as the presence or absence of particular nucleotide sequences.

Complete nucleotide sequence of the RNA 3 from subgroup II of cucumber mosaic virus (CMV) strain: Trk7

The complete nucleotide sequence (2209 nucleotides) of the RNA 3 of the cucumber mosaic virus strain Trk7 was determined. Trk7-CMV possesses two open reading frames which encode the 3a protein (279 amino acids) and the coat protein (218 amino acids). Sequence analysis proved the earlier biological and serological classification of the RNA 3 molecule of Trk7-CMV in subgroup II. A high degree of homology was found in the strains Q and Kin of CMV, while the average similarity between the two different subgroups is much lower.

New overlapping gene encoded by the cucumber mosaic virus genome

Cucumber mosaic virus (CMV) contains three genomic RNAs (RNAs 1, 2, and 3) and a subgenomic RNA (RNA 4), a shared feature of the Bromoviridae family which includes cucumoviruses, bromoviruses, alfalfa mosaic virus, and ilarviruses. We describe in this paper the molecular characterization of a novel subgenomic RNA of the Q strain of CMV (Q-CMV), RNA 4A, which was first reported in 1973 (K. W. C. Peden and R. H. Symons, Virology 53, 487-492, 1973). RNA 4A is 682 nucleotides and is identical in sequence to the 3'-terminal 682 nucleotides of RNA 2. RNA 4A encodes a small open reading frame (ORF) of 100 codons, which, in RNA 2, overlaps the C-terminal portion of the major 2a gene; thus it is likely that RNA 4A functions as the mRNA for the in vivo expression of the ORF, called ORF 2b. Polyclonal antibodies raised against a 2b fusion protein expressed in Escherichia coli specifically detected the 2b gene product in Q-CMV-infected cucumber plants by Western immunoblotting. Examination of published viral RNA sequences revealed the conservation of ORF 2b in all of the four other cucumoviruses sequenced to date; however, it is absent from the rest of the Bromoviridae. We suggest that the proposed ORF 2b may be expressed in other cucumoviruses, most likely via 4A-like subgenomic RNAs, and that the predicted gene product may have a unique functional role in the infection process of cucumoviruses.

Nucleotide sequence of RNA 3 of the British type isolate (Blencowe strain) of tomato aspermy virus

The complete sequence of RNA 3 of the Blencowe, British (B) isolate of tomato aspermy virus (TAV) is presented. The RNA 3 of TAV-B is dicistronic, encoding the putative movement protein 3a and the capsid protein.

Cucumber mosaic virus-associated RNA 5. XIII.--Opposite necrogenicities in tomato of variants with large 5' half insertion/deletion regions

Two satellite RNA of cucumber mosaic virus (CMV) designated J876-CARNA-5 (for cucumber mosaic virus-associated RNA-5) and D27-CARNA-5 have been molecularly and biologically characterized. J876-CARNA-5 (387 nucleotides (nt)) and D27-CARNA-5 (391 nt) have nearly identical 5' half insertion/deletion regions where 120 nt replace approximately 70 nt of D-CARNA-5 (335 nt), the first variant described and sequenced. J876-CARNA-5 possesses the 15-nt conserved sequence element in its 3' half which is present in all tomato necrogenic variants and induces the same level of necrosis in tomatoes as the prototype necrogenic D-CARNA-5. D27-CARNA-5 lacks the 3' half necrosis-determining element and attenuates the CMV symptoms in tomato. Transcripts of cloned cDNA of J876-CARNA-5 were stably propagated in tomato in the presence of CMV-1. Purified J876-CARNA-5 progeny, inoculated with CMV-1 in a quantitative bioassay, induced tomato necrosis at the same dilution level as the natural satellite. Several computer-generated secondary structures of CMV satellites were examined and the possible correlation of a defined secondary structural element with necrosis induction is discussed.