Open reading frames of turnip crinkle virus involved in satellite symptom expression and incompatibility with Arabidopsis thaliana ecotype Dijon

Analysis in vivo of turnip crinkle virus satellite RNA C variants with mutations in the 3'-terminal minus-strand promoter

Turnip crinkle virus and its associated RNA, sat-RNA C, share similar, but not identical hairpins near their 3' ends and terminate with CCUGCCC-OH, which forms a single-stranded tail. With an in vitro transcription system containing partially purified TCV RdRp, the 3'-terminal 29 bases making up the hairpin and single-stranded tail were previously demonstrated to be required for transcription, and alterations in the stem, but not the loop, could affect template activity (C. Song and A. E. Simon, 1995, J. Mol. Biol. 254, 6-14). We have now analyzed sat-RNA C mutants in the 3' hairpin for ability to accumulate in vivo. While active templates in vitro were able to accumulate in vivo, some very weak templates in vitro were also able to accumulate in vivo without reversion or second-site alterations. Computer models of hairpin structure indicated that biologically active promoters could have hairpins less stable than wild type, with loops of variable length and sequence, and without a need for a 6-base single-stranded tail. In addition, transcripts containing compensatory exchanges in the upper stem region that had limited activity in vitro were biologically active in vivo, indicating that positioning of specific bases in the stem is not required to produce an active minus-strand promoter.

Cauliflower Mosaic Virus Isolate NY8153 Breaks Resistance in Arabidopsis Ecotype En-2

ABSTRACT Arabidopsis thaliana ecotype En-2 was previously shown to be resistant to cauliflower mosaic caulimovirus (CaMV) isolate CM4-184. In this study, En-2 plants were screened with eight other isolates of CaMV to identify viruses capable of overcoming resistance and to determine if the mechanism of resistance was the same for each virus. En-2 resistance to most CaMV isolates was mediated by the same mechanism, i.e., preventing virus long-distance movement. One CaMV isolate, NY8153, was found that produced a severe systemic infection on En-2 plants. In addition, the CM1841 isolate was able to spread systemically through En-2 plants, to a limited extent, without producing visible symptoms. These data indicate that the resistance shown by En-2 plants is not an all-or-none phenomenon. En-2 plants were susceptible to turnip mosaic potyvirus, suggesting that resistance is specific to CaMV.

Analysis of the two subgenomic RNA promoters for turnip crinkle virus in vivo and in vitro

Infection of plants or protoplasts with turnip crinkle virus (TCV), a monopartite RNA virus, results in the synthesis of the genomic RNA and two subgenomic (sg) RNAs. The transcription start site for the 1.45-kb sgRNA was previously mapped to position 2606 (J. C. Carrington, T. J. Morris, P. G. Stockley, and S. C. Harrison, (1987). J. Mol. Biol. 194, 265-276) corresponding to position 2607 in the TCVms isolate and the start site for the 1.7-kb sgRNA has now been mapped to position 2333 in TCVms. A 96-base sequence (90 bases upstream and 6 bases downstream) encompassing the transcription start site for the 1.45-kb sgRNA was sufficient for full promoter activity. Similarly, a 94-base sequence (90 bases upstream and 4 bases downstream) encompassing the start site was required for full activity of the 1.7-kb sgRNA promoter. The 1.45-kb sgRNA promoter, but not the 1.7-kb sgRNA promoter, was able to direct synthesis of a nontemplate RNA in vitro using partially purified TCV RNA-dependent RNA polymerase. Computer generated secondary structures for the two sgRNA promoters revealed an extensive hairpin just upstream from the transcription start site. Comparisons of corresponding sequences from related viruses indicates higher sequence conservation for the 1.45-kb sgRNA promoter compared with the 1.7-kb sgRNA promoter, despite the latter's location within the RNA-dependent RNA polymerase open reading frame.

A novel 3'-end repair mechanism in an RNA virus

Many positive-stranded RNA viruses contain short, single-stranded 3' ends that are vulnerable to degradation by host cellular RNases. Therefore, the existence of a 3'-end repair mechanism (analogous to cellular telomerases) must be required and/or advantageous for RNA viruses. Accordingly, we provide evidence suggesting that deletions of up to 6 nt from the 3' end of satellite (sat-) RNA C (a small parasitic RNA associated with turnip crinkle carmovirus) are repaired to the wild-type sequence in vivo and in vitro. The novel 3'-end repair mechanism involves the production of 4-8 nt oligoribonucleotides by abortive synthesis by the viral replicase using the 3' end of the viral genomic RNA as template. Based on our in vitro results, we postulate that the oligoribonucleotides are able to prime synthesis of wild-type negative-strand sat-RNA C in a reaction that does not require base pairing of the oligoribonucleotides to the mutant, positive-strand RNA template. The discovery of a 3'-end repair mechanism opens up new strategies for interfering with viral infections.