Complete nucleotide sequence and genome organization of Calibrachoa mottle virus (CbMV)--a new species in the genus Carmovirus of the family Tombusviridae

Complete genomic sequence of the viral RNA of Calibrachoa mottle virus (CbMV) has been determined. The CbMV genome has a positive-sense single-stranded RNA of 3919 nucleotides in length and encodes five open reading frames (ORFs). ORF1 encodes a protein with predicted molecular weight of 28 kDa (p28). ORF2 extends through the amber stop codon of ORF1 to give a protein with a predicted molecular weight of 87 kDa (p87). The readthrough domain of p87 contains the GDD motif common to RNA-dependent RNA polymerases (RdRp). ORF3 and ORF4 encode two small overlapping polypeptides of 8 kDa (p8) and 9 kDa (p9), respectively. The 3'-proximal ORF5 encodes a capsid protein (CP) of 37 kDa (p37). The untranslated 5'- and 3'-terminal regions are composed of 34 and 234 non-coding nucleotides, respectively. Comparisons of amino acid sequences of the ORFs of CbMV with members of Tombusviridae show that CbMV is closely related to members of the genus Carmovirus. Phylogenetic analyses based on the amino acid sequences of RdRp and coat protein and nucleotide sequences of the whole genome reveal that CbMV forms a subgroup with several carmoviruses. Therefore, the genome organization, physico-chemical properties, sequence alignments and phylogenetic analysis support the classification of CbMV as a new species in the genus Carmovirus, family Tombusviridae.

New isolates of carnation Italian ringspot virus differ from the original one by having replication-associated proteins with a typical tombusvirus-like N-terminus and by inducing peroxisome- rather than mitochondrion-derived multivesicular bodies

Five new isolates of carnation Italian ringspot virus (CIRV) from cherry trees, Gypsophila and surface water differ from the original carnation isolate (CIRV-car) and also from Pelargonium necrotic spot virus (PelNSV) by having an ORF 1/ORF1-RT with a typical tombusvirus-like 5'end and by inducing the formation of peroxisome- rather than mitochondrion-derived multivesicular bodies (MVBs). This supports with natural isolates earlier conclusions reached by others with artificially produced hybrid viruses that the 5'end of ORF 1 determines from which organelle the MBVs will be derived. CIRV-car might have resulted from a natural recombination event with genome elements of a PelNSV-like virus.

Characterization of Distinct Tombusviruses that Cause Diseases of Lettuce and Tomato in the Western United States

A soilborne disease of lettuce, associated with necrosis and dieback, has been found with increasing frequency in California and Arizona over the last 10 years. An isometric virus, serologically related to Tomato bushy stunt virus (TBSV), was consistently isolated from lettuce plants with these disease symptoms. Back-inoculation to healthy lettuce plants and subsequent reisolation of the virus from symptomatic lettuce leaves suggested that this virus was the causal agent of this disease. A tombusvirus was also associated with a necrosis disease of greenhouse-grown tomatoes in Colorado and New Mexico. Complementary DNA representing the 3' end of viral genomic RNAs recovered from diseased lettuce and tomato plants had identical nucleotide sequences. However, these sequences were divergent (12.2 to 17.1%) from sequences of the previously described strains of TBSV, Petunia asteroid mosaic virus (PAMV), Artichoke mottled crinkle virus, and Carnation Italian ringspot virus. Additional tombusvirus isolates were recovered from diseased lettuce and tomato plants and these were most closely related to the TBSV-cherry strain (synonymous with PAMV) and to Cucumber necrosis virus based on comparison of 3'-end sequences (0.1 to 0.6% and 4.8 to 5.1% divergence, respectively). Western blot analysis revealed that the new tombusvirus isolated from diseased lettuce and tomato plants in the western United States is serologically distinct from previously described tombusvirus species and strains. Based on genomic and serological properties, we propose to classify this virus as a new tombusvirus species and name it Lettuce necrotic stunt virus.

Consequences of gene transfer between distantly related tombusviruses

Hybrid cDNA clones were constructed by fusing the coat protein-encoding gene and/or the 3'-terminal region (including the 22- and 19-kDa protein-encoding genes) derived from a clone of artichoke mottled crinkle tombusvirus to the 5'-terminal region of a full-length clone of cymbidium ringspot tombusvirus. In vitro transcripts from recombinant clones were infectious when inoculated into Nicotiana clevelandii plants. Inoculated plants showed symptoms different from those induced by parent viruses. In particular, systemic invasion depended very much, although not exclusively, on the type of protein that coated progeny viral RNA, suggesting a role of the capsid protein in the long-distance movement of tombusvirus infections.

Nucleotide sequence of the coat protein gene of pelargonium leaf curl virus and comparison of the deduced coat protein amino acid sequence with those of other tombusviruses

The sequence of 1,787 nucleotides (nts) in the genomic RNA of pelargonium leaf curl virus (PLCV) was determined. It included the entire coat protein (cp) gene (nts 585 to 1,754), 558 nts of the 3' end of the putative RNA polymerase gene, 26 nts of an intercistronic region between the two genes and 33 nts downstream of the stop codon of the cp gene. The cp gene was cloned into the expression vector pET8c and expressed in E. coli. The deduced cp amino acid sequence of PLCV was compared with those of five other tombusviruses. The closer the degree of serological relatedness between two viruses, the more similarity was found in their cp amino acid sequences not only in the protruding domains, but also in their random and shell domains and in the arm regions. Nucleic acid hybridization tests, cp amino acid comparisons and serological tests all suggest the same order of sequence for the relationships in the tombusvirus group.

Tombusvirus genome may encode the sixth small protein near its 3' terminus

A short open reading frame (ORF), ORF6, potentially encoding a polypeptide (pX) of 32-69 amino acids, was revealed upon computer translation of the 3' terminal regions of tomato bushy stunt, cymbidium ringspot, cucumber necrosis and artichoke mottled crinkle tombusviruses. ORF6 has an initiating AUG codon in a favorable context and is evaluated as expressible, judging the distribution of guanosine residues within the codons. Inspection of the alignment of the four putative products encoded by ORF6 shows statistically significant sequence conservation over 11 SD above the random expectation. Secondary structure predictions based on the Garnier method demonstrate strict conservation of a loop between two beta-strands, thus suggesting functional conservation of pXs. It is suggested that pX is not involved in tombusvirus genome replication and encapsidation in cis.

The complete genome structure and synthesis of infectious RNA from clones of tomato bushy stunt virus

The complete sequence of the genome of the cherry strain of tomato bushy stunt virus (TBSV), a member of the tombusvirus group, was determined. A full-length clone of the genome containing a bacteriophage T7 RNA polymerase promoter was assembled from partial cDNA clones. In vitro transcripts of the genome, either with or without a 5' cap structure, were highly infectious. In addition, a genomic clone modified to contain an EcoRI restriction site as a signature mutation was infectious. Five genes are encoded by the TBSV genome. The first ORF from the 5' terminus encodes a p33 protein as well as a p92 product translated by read-through of the amber terminator for p33. The capsid protein gene resides internally, and two ORFs for proteins of 19 and 22 kDa reside at the 3' terminus. These last three genes are expressed from two subgenomic RNAs. The genomic organization of TBSV agrees with previous models for tombusviruses. Computer alignments of TBSV proteins with those of two other tombusviruses suggest greater relatedness among the members of this group than previously reported.

Organization of tomato bushy stunt virus genome: characterization of the coat protein gene and the 3' terminus

We have synthesized cDNA clones of the genome of the cherry strain of tomato bushy stunt virus (TBSV-cherry) and have used them as hybridization probes to identify and position two 3' coterminal subgenomic RNAs of approximately 2.2 and 0.9 kilobases (kb) in length. The 5' termini of the two subgenomic RNAs have been mapped to positions located 2156 and 936 nucleotides respectively from the 3' terminus of the viral genome. The nucleotide sequence of cDNA clones encompassing the region of the genome containing both of the subgenomic RNAs has been determined. The sequence data indicate that two nested open reading frames (ORFs) occur in the most 3' proximal location on the genome suggesting that the 0.9-kb subgenomic RNA potentially encodes two polypeptides of 19,397 and 21,610 Da. Comparison of the amino acid sequence of a potential translation product of 41,024 Da encoded by the first ORF of the 2.2-kb subgenomic RNA with the published capsid protein amino acid sequence of the BS-3 strain of TBSV indicates that the 2.2-kb subgenomic RNA encodes the capsid protein. The TBSV coat protein cistron is located internally on the genome and thus its genetic organization differs from that reported for most other small, spherical viruses with monopartite genomes. Amino acid sequence comparisons of analogous regions of the cucumber necrosis virus (CNV) genome confirms a close relationship between the viruses.

The use of filter hybridization techniques for the identification, differentiation and classification of plant viruses

In attempts to use dot-blot hybridization tests for the identification of viruses or for assigning them to a certain taxonomic group we found that hybridization signals may be given not only by the homologous virus, but also by heterologous viruses belonging to the same or different taxonomic groups. Possible reasons for this phenomenon, which was observed with uncloned as well as with cloned cDNAs, are discussed. Quantitative dot-blot hybridization tests with extracted viral RNAs proved to be very sensitive in differentiating closely related viruses which were barely distinguishable in serological tests. Estimates on the degree of homology between the RNAs of different viruses may be influenced by a number of experimental parameters, such as competition for the available cDNA between homologous and heterologous RNAs or homologous RNAs in different concentrations on the same sheet of nitrocellulose, saturation phenomena due to close packaging of highly concentrated RNA on the blot and, of course, stringency conditions during washing procedures. Taking these parameters into account we have reestimated the degree of homology between the RNAs of 5 tombusviruses. Our new data suggest that the order of sequence for the relationships among these 5 tombusviruses is similar to that proposed by Koenig and Gibbs (1986) on the basis of serological data.

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.

The classification of tymoviruses by cDNA-RNA hybridization and other measures of relatedness

The relationships of twelve tymoviruses have been assessed by cDNA-RNA hybridization. In addition, the percentage molar nucleotide composition of the genome of the PD strain of Kennedya yellow mosaic virus and the percentage molar amino acid composition of the coat proteins of cacao yellow mosaic, Kennedya yellow mosaic and turnip yellow mosaic (Cardamine strain) viruses were estimated. These as well as published serological comparisons and genome and coat protein composition determinations were used to compute classifications of tymoviruses using various "metrics", and simple numerical methods were used to compare the classifications. Measures of relatedness estimated from cDNA-RNA hybridization and base ratio data correlated significantly with each other, but were less closely correlated with those calculated from amino acid data, and did not correlate with those calculated from serological tests. The serological relationships correlated significantly with estimates of relatedness calculated from amino acid data, but not with those based on hybridization or base ratio data. The differences between these classifications mostly resulted from the anomalous behaviour of eggplant mosaic virus, its particles are serologically close to those of other tymoviruses that naturally infect species of the tobacco family, whereas in cDNA-RNA hybridization tests eggplant mosaic virus is closest to the tymoviruses that infect legumes. Similar but smaller anomalies in the characteristics of other tymoviruses were also found.

Gel electrophoresis of intact subcellular particles

The review describes the application of gel electrophoresis to the characterization and separation of viruses, ribosomes, vesicles and other subcellular particles. The preparation of the sample, the choice of the buffer, the gel medium, the apparatus and the detection of the particle (staining and scanning) as well as the necessary theory are discussed. This includes the mathematical evaluation of experimental data on the basis of Ferguson plots using the extended Ogston theory. Simple methods and sophisticated computer simulation techniques are described and exemplified in application to the determination of particle size and charge, the pore size of the gel (unpublished data) and the two-dimensional agarose electrophoresis (unpublished). It is shown that the nature of the particle (e.g. spherical or rod-shaped, pliable or rigid texture) determines the shape of the non-linear Ferguson plot. In addition, the review gives a number of practical applications of gel electrophoresis, isoelectric focusing, titration curves and immuno-electrophoresis to subcellular particles. Pros and cons are evaluated. A comparison with other analytical procedures is made. The review is concluded by a futuristic outlook.