Biological activity of transcripts synthesized in vitro from full-length and mutated DNA copies of tobacco rattle virus RNA 2

Characterization of an infectious clone of pepper ringspot virus and its use as a viral vector

The genus Tobravirus comprises three species: Tobacco rattle virus, Pea early-browning virus and Pepper ringspot virus. The genomes of tobraviruses consist of two positive-sense single-stranded RNA segments (RNA1 and RNA2). Infectious clones of TRV are extensively used as virus-induced gene-silencing (VIGS) vectors for studies of virus-host interactions and functions of plant genes. Complete infectious clones of pepper ringspot virus (PepRSV), the only tobravirus present in Brazil, however, have not yet been reported. Infectious clones will help to identify unique features of PepRSV RNA2 and provide another option for development of VIGS vectors. We constructed infectious clones based on two PepRSV isolates, CAM (RNA1 and RNA2) and LAV (RNA2). The cDNA constructs for both homologous (RNA1 and RNA2 of the CAM isolate) and heterologous (RNA1/CAM and RNA2/LAV) combinations were infectious in Nicotiana benthamiana plants. VIGS vector constructs with green fluorescent protein or phytoene desaturase genes inserted in RNA2 silenced the target genes. The systemic translocation of the PepRSV RNA1 construct alone (nonmultiple infection) was also confirmed in an N. benthamiana plant. These results are similar to those reported for tobacco rattle virus.

Improving initial infectivity of the Turnip mosaic virus (TuMV) infectious clone by an mini binary vector via agro-infiltration

BACKGROUND

The in vivo infectious clone of Turnip mosaic virus (TuMV), p35S-TuMV, was used on plant pathology research for many years. To activate p35S-TuMV, the plasmid was mechanically introduced to the local lesion host Chenopodium quinoa. However, low infectivity occurred when the TuMV from C. quinoa was transferred to the systemic host Nicotiana benthamiana.

RESULTS

To increase the efficiency of initial infectivity on N. benthamiana, the expression of the TuMV infectious clone by a binary vector that directly activates viral RNA through agro-infiltration is considered to be a good alternative. The size of the binary vector by agro-infiltration is usually large and its backbone has numerous restriction sites that increase difficulty for construction. In this study, we attempted to construct a mini binary vector (pBD003) with less restriction sites. The full-length cDNA of TuMV genome, with or without green fluorescence protein, was inserted in pBD003 to generate pBD-TuMV constructs, which were then individually introduced to N. benthamiana plants by agro-infiltration. Symptom development and ELISA positivity with TuMV antiserum indicated that the pBD-TuMV constructs are infectious. Moreover, the initial infectivity of a mild strain TuMV-GK, which contains an R₁₈₂K mutation on HC-Pro, constructed in the pBD003 vector was significantly increased by agro-infiltration.

CONCLUSION

Thus, we concluded that the newly constructed mini binary vector provides a more feasible tool for TuMV researches in areas, such as creating a mild strain for cross-protection, or a viral vector for foreign gene expression. In addition, the multiple cloning sites will be further cloned in pBD003 for convenience in constructing other viral infectious clones.

Translational initiation at the coat-protein gene of phage MS2: native upstream RNA relieves inhibition by local secondary structure

Maximal translation of the coat-protein gene from RNA bacteriophage MS2 requires a contiguous stretch of native MS2 RNA that extends hundreds of nucleotides upstream from the translational start site. Deletion of these upstream sequences from MS2 cDNA plasmids results in a 30-fold reduction of translational efficiency. By site-directed mutagenesis, we show that this low level of expression is caused by a hairpin structure centred around the initiation codon. When this hairpin is destabilized by the introduction of mismatches, expression from the truncated messenger increases 20-fold to almost the level of the full-length construct. Thus, the translational effect of hundreds of upstream nucleotides can be mimicked by a single substitution that destabilizes the structure. The same hairpin is also present in full-length MS2 RNA, but there it does not impair ribosome binding. Apparently, the upstream RNA somehow reduces the inhibitory effect of the structure on translational initiation. The upstream MS2 sequence does not stimulate translation when cloned in front of another gene, nor can unrelated RNA segments activate the coat-protein gene. Several possible mechanisms for the activation are discussed and a function in gene regulation of the phage is suggested.

Developments in the understanding of the particle structure of tobraviruses

Particles of tobraviruses resemble those of tobacco mosaic tobramovirus (TMV) in having helical symmetry and in being rod-shaped. However, isolated tobravirus coat protein and TMV coat protein respond to changes in the ionic strength and pH of the solute in contrasting ways. The types of aggregate formed in solutions of coat protein also differ which may be related to differences in the apparent mechanism of reconstitution of virus particles from isolated protein and RNA. The amino acid sequences of tobravirus and tobramovirus coat proteins have been shown to be similar in some regions known to be important for the structure of TMV particles. These alignments also show that tobravirus proteins are larger than tobramoviral proteins in part because of extra residues at the C-terminus. Tobravirus particles give a signal in proton NMR spectroscopy but TMV particles do not. The signal is caused by segmental mobility of the C-terminal peptide. This difference between TMV and tobraviruses may be related to a property not shared by tobraviruses and TMV and it is therefore speculated that the mobile C-terminal peptide of tobravirus coat proteins may be important in the transmission of tobravirus particles by nematode vectors.

cis-active sequences near the 5'-termini of beet necrotic yellow vein virus RNAs 3 and 4

RNAs 3 and 4 of the multicomponent genome of beet necrotic yellow vein virus are dispensable for infection of Chenopodium quinoa leaves. We have used mutagenesis of biologically active RNA 3 transcripts to identify 5'-proximal sequences essential in cis for RNA 3 amplification. One such element, Box I, (nucleotides 283-292) was complementary to the first 10 residues (Box I') following the 5'-terminal cap. A second cis-active element (Box II) was identified between nucleotides 237-244 and was complementary to nucleotides 16-23 (Box II'). Other cis-active sequences exist between Box II' and II but have not been mapped to fine scale. Most sequence substitutions in Boxes I and II or in the 5'-proximal complementary sequences were lethal but compensatory mutations designed to restore Box I/I' or Box II/II' base pairing restored viability, suggesting that secondary structure involving these elements rather than their exact sequence is the critical feature. Transcripts bearing short deletions near residue 200 were replicated but did not assemble into virions, indicating that this region contains or contributes to a cis-active encapsidation signal. Similar experiments with RNA 4 transcript have shown that 5'-proximal cis-essential elements are limited to the first 400 residues of this RNA. Essential subdomains within this region have not been mapped but there are no structures obviously homologous to Boxes I/I' and II/II' of RNA 3.

Construction and analysis of infectious transcripts synthesized from full-length cDNA clones of both genomic RNAs of pea early browning virus

Full-length cDNA clones of both RNAs of pea early browning virus have been constructed. Synthetic transcripts derived in vitro from these clones are infectious when inoculated onto plants. Electron microscopy revealed the presence of virions in transcript-inoculated plants, and both purified RNA and virions isolated from such plants could be used to infect other plants. Transcripts of RNA1 alone were able to replicate and spread systemically which is a characteristic of members of the tobravirus group of plant viruses.

Secondary structure of the ribosome binding site determines translational efficiency: a quantitative analysis

We have quantitatively analyzed the relationship between translational efficiency and the mRNA secondary structure in the initiation region. The stability of a defined hairpin structure containing a ribosome binding site was varied over 12 kcal/mol (1 cal = 4.184 J) by site-directed mutagenesis and the effects on protein yields were analyzed in vivo. The results reveal a strict correlation between translational efficiency and the stability of the helix. An increase in its delta G0 of -1.4 kcal/mol (i.e., less than the difference between an A.U and a G.C pair) corresponds to the reduction by a factor of 10 in initiation rate. Accordingly, a single nucleotide substitution led to the decrease by a factor of 500 in expression because it turned a mismatch in the helix into a match. We find no evidence that exposure of only the Shine-Dalgarno region or the start codon preferentially favors recognition. Translational efficiency is strictly correlated with the fraction of mRNA molecules in which the ribosome binding site is unfolded, indicating that initiation is completely dependent on spontaneous unfolding of the entire initiation region. Ribosomes appear not to recognize nucleotides outside the Shine-Dalgarno region and the initiation codon.

The complete nucleotide sequence of PEBV RNA2 reveals the presence of a novel open reading frame and provides insights into the structure of tobraviral subgenomic promoters

The 3374 nucleotide sequence of RNA2 from the British PEBV strain SP5 has been determined. The RNA includes three open reading frames flanked by 5' and 3' noncoding regions of 509 and 480 nucleotides. The open reading frames specify coat protein, a 29.6K product homologous to the 29.1K product of TRV(TCM) RNA2 and a 23K product not homologous to any previously described protein. The homology demonstrated between the coat proteins of PRV, TRV and PEBV indicates a common evolutionary origin for these proteins. Upstream of each ORF are located sequences homologous to those with which subgenomic RNAs of other tobraviruses start. Subgenomic RNAs for the expression of the three ORFs may start at these points. On all five tobraviral RNA2 molecules sequenced to date, these sequences were found upstream of the coat protein ORF in association with a strongly-conserved potential secondary structural element. Similar potential structures were identified upstream of other tobraviral ORFs. These structures may contribute to the activity of the tobraviral subgenomic promoter.

Interaction of RNase P from Escherichia coli with pseudoknotted structures in viral RNAs

In a previous study it was shown that RNase P from E. coli cleaves the tRNA-like structure of turnip yellow mosaic virus (TYMV) RNA in vitro (Guerrier-Takada et al. (1988) Cell, 53, 267-272). Cleavage takes place at the 3' side of the loop that crosses the deep groove of the pseudoknot structure present in the aminoacyl acceptor domain. In the present study fragments of TYMV RNA with mutations in the pseudoknot, generated by transcription in vitro, were tested for susceptibility to cleavage by RNase P. Changes in the specificity with respect to the site of cleavage and decreases in the rate of cleavage were observed with most of these substrates. The behaviour of various mutants in the reaction catalyzed by RNase P is in agreement with the present model of the TYMV RNA pseudoknot (Dumas et al. (1987), J. Biomol. Struct. Dyn. 263, 652-657). Base substitutions in the loop that crosses the shallow groove of the pseudoknot structure resulted, however, in an unexpected decrease in the rate of cleavage, probably due to conformational changes in the substrates. Studies on other tRNA-like structures revealed an important role in the reaction with RNase P for both the nucleotide at the 3' side of the loop that spans the deep groove and the nucleotide at position 4, which correspond to positions--1 and 73, respectively, in tRNA precursors.

Biologically active transcripts of alfalfa mosaic virus RNA3

Transcripts of the bicistronic RNA3 of alfalfa mosaic virus were synthesized using the in vitro T7 run-off transcription system. Synthetic RNA3 containing one additional G nucleotide at the 5' end were found to be infectious when coinoculated with RNA1 and RNA2 and coat protein.

Susceptibility to virus infection of transgenic tobacco plants expressing structural and nonstructural genes of tobacco rattle virus

Tobacco plants were transformed with the coat protein (CP) genes and several nonstructural genes of tobacco rattle virus (TRV) strains PLB and TCM. Accumulation of RNA transcripts from the integrated viral genes was detectable in all types of transformants. Plants expressing CP were resistant to infection with virions of the homologous strain but susceptible to infection with RNA of the homologous strain or nucleoprotein of the heterologous strain. No resistance was detectable in plants transformed with the nonstructural 13K and 16K genes of strain PLB, or with the 29K gene that is unique to RNA-2 of strain TCM. When protoplasts from plants expressing TCM-CP were inoculated with TCM virions, there was a normal production of genomic RNAs and CP but the synthesis of mRNA and protein corresponding to the 16K gene was selectively defective. Because this defect was not observed when protoplasts from plants expressing PLB-CP were inoculated with PLB virions, it probably plays no role in the coat protein-mediated protection observed in transgenic plants.