The EMBO Journal vol.9 no.6 pp.1709-1715, 1990

Recombination between satellite RNAs of turnip crinkle virus

Pamela J.Cascone*, Clifford D.Carpenter#, Xiao Hua Li* and Anne E.Simon*,#

*Program in Molecular and Cellular Biology and #Department of Plant Pathology, University of Massachusetts, Amherst, MA Ol003, USA

Turnip crinkle virus (TCV) is associated with satellite (sat) RNAs (sat-RNA D, sat-RNA F), defective interfering (DI RNAs (DI RNA G, DI1 RNA), and one RNA with properties of both sat-RNAs and DI RNAs (sat-RNA C). When plants were inoculated with TCV, sat-RNA D and in vitro sat-RNA C transcripts containing non-viable mutations in the 5' domain, recombinant sat-RNAs were recovered. These recombinants were composed of sat-RNA D at the 5' end and sat-RNA C sequences at the 3' end. Analysis of 20 independent recombination junctions revealed that unequal crossing-over had occurred in planta in a region of sequence similarity between the two sat-RNAs which resulted in the duplication of 3 -- 16 nucleotides. Thirty percent of the sat-RNA recombinants also had one to three additional nucleotides inserted at the crossover junctions which did not correspond to either sat-RNA C or sat-RNA D sequence. The right side of the recombination junctions always began with one of three consecutive nucleotides of sat-RNA C. Based on the similarity between this sequence of sat-RNA C, the right side junction of DI RNA G and the 5' end of TCV, as well as the sequence similarity between right side junctions of DI1 RNA and sat-RNA C and the 5' end of the sat-RNAs, a replicase-driven copy choice mechanism is proposed. The replicase, while replicating viral or sub- viral minus strands, can dissociate from the template along with the nascent plus strand and reinitiate synthesis at one of two internal replicase recognition sequences on the same or different template thus generating recombinant sat-RNAs or DI RNAs.