Tomato spotted wilt virus S-segment mRNAs have overlapping 3′-ends containing a predicted stem-loop structure and conserved sequence motif

The Tomato spotted wilt virus ambisense M- and S-RNA segments contain an A/U-rich intergenic region predicted to form a stable hairpin structure. The site of transcription termination of S-segment encoded N and NSs mRNAs synthesised in an in vitro transcription system was roughly mapped to the 3′-end of the intergenic hairpin, i.e. position 1568–1574 for N and position 1852–1839 for NSs, as determined by RT-PCR cloning and size estimation on Northern blots. This suggests that these viral transcripts contain a predicted stem-loop structure at their 3′-end. The potential involvement of the 3′-end structure in transcription termination is discussed.