RNA DETERMINANTS OF JUNCTION SITE SELECTION IN RNA VIRUS RECOMBINANTSAND DEFECTIVE INTERFERING RNAS

RNA recombination plays an important role in the diversification and e volution of RNA viruses. Most of these events are believed to be media ted by an actively copying viral replicase switching from a donor temp late to an acceptor template, where it resumes synthesis. In addition, intramolecular replicase-mediated events (i.e., rearrangements) can l ead to the generation of replicable deleted forms of a viral genome, t ermed defective interfering (DI) RNAs. To gain further insight into th e recombination process, the effect of various primary and secondary s tructures on recombination site selection in vivo was examined using p lant RNA tombusviruses. The effect of sequence identity and complement arity on deletion events that generate DI RNAs was also investigated. Our results suggest that (1) 5' termini and strong hairpin structures in donor templates represent preferred sites for recombination, (2) ju nction sites in acceptor templates do not occur in double-stranded reg ions, (3) nucleotide homology can shift donor and acceptor recombinati on sites closer to regions of identity and, (4) both sequence identity and complementarity can direct deletion sites in Di RNAs. These resul ts further define RNA determinants of tombusvirus RNA recombination an d rearrangement.