RNA recombination in turnip crinkle virus: its role in formation of chimeric RNAs, multimers, and in 3′-end repair

RNA recombination is well documented for an increasing number of viruses and it is thought to have affected viral evolution and adaptation. However, molecular mechanisms mediating crossover events have been studied in only a few viral systems due to difficulties such as the low frequency of the event, and the scattered distribution of junction sites. Therefore, the uniquely high recombination frequency and nonrandom crossover site distribution for recombination among turnip crinkle carmovirus (TCV) RNAs make TCV an excellent model recombination system. Characterization of large numbers of junction sites between two species of TCV satellite RNAs and between the TCV genomic RNA and one of the satellite RNAs revealed for the first time the role of specific sequences and structures in recombination. Also, recombination was found to play a role in formation of novel chimeric RNAs, multimeric forms of satellite RNAs as well in 3′ end repair of mutated satellite RNAs. A replicase-driven template-switching model is presented to explain many common features occurring during recombination in TCV infections.