The 3′-terminal sequence of a wound tumor virus transcript can influence conformational and functional properties associated with the 5′-terminus

We recently reported the presence of segment-specific inverted repeats within the terminal regions of wound tumor virus genomic segments (1. V. Anzola, Z. Xu, T. Asamizu, and D. L. Nuss, 1987, Proc. Natl. Acad. Sci. USA, 84, 8301–8305). This report describes a series of experiments designed to investigate potential intramolecular interactions involving the 5′- and 3′-terminal domains of wound tumor virus transcripts. A series of transcription vectors were constructed which allowed the synthesis of an exact copy of the transcript corresponding to genomic segment S8 and four analogs that differed from the authentic sequence only at the immediate 3′-terminus. Modifications designed to extend or alter the 3′-terminal inverted repeat altered the in vitro translational efficiency of the transcript and the sensitivity of phosphodiester bonds within the immediate 5′-terminal domain to digestion by nuclease T1. These results were consistent with computer-assisted secondary structure analyses of the complete nucleotide sequence of transcripts corresponding to six genomic segments which predicted intramolecular interactions involving the terminal inverted repeats. Potential roles of the terminal domains in expression, sorting and packaging of a segmented RNA genome are considered.