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. 2005 Jul 7;33(12):e105. doi: 10.1093/nar/gni106

Figure 3.

Figure 3

Homologous recombination in the heteromolecular and mixed homo-heteromolecular systems. Light and thicker lines represent viral genomic RNAs and nascent recombinant RNA, respectively. WtRNA1 is red (the recombinationally active sequence RAS1s which it contains is additionally boxed), wtRNA2 is black and modified RNA3 is blue. When inserted into RNA3, the wtRNA1-derived RAS1s sequence is also shown as a red box. The portion of the RNA3 recombinant synthesized on wtRNA1 is red and the fragment synthesized on RNA3 is blue. The black dot symbolizes the ΔXho mutation present in MatH-RNA3. RF, recombination frequency. (A) Heteromolecular system (MH-BMV). The presence of two RAS1s sequences in the MH-BMV mutant (one in wtRNA1 and one in MagH-RNA3) creates an opportunity for homologous recombination events between two different segments of the viral genome. However, during MH-BMV infection recombinants were not identified (RF = 0%). (B) Mixed system (MatH-BMV). Three identical RAS1s sequences are located in the MatH-BMV genome, two in MatH-RNA3 and one in wtRNA1. The recombination frequency observed during infection with MatH-BMV was 85%. Among the identified recombinants 80% did not have the ΔXho marker, and 20% had the ΔXho marker. (C) Putative scenario of RAS1-mediated homologous recombination in the heteromolecular system. BMV replicase starts nascent strand synthesis at the 3′ end of wtRNA1 is paused within the RAS1s sequence and then switches to the identical region located in MagH-RNA3. (D) Putative scenarios of RAS1-mediated homologous recombination in the mixed system. The presence of three identical RAS1s sequences in the MatH-BMV genome (3′RAS1s and 5′RAS1s sequences in MatH-RNA3 and RAS1s in wtRNA1) caused several scenarios of homologous recombination to be possible. BMV polymerase can initiate nascent strand synthesis at the 3′ end of wtRNA1 and then switch to 3′ or 5′RAS1s located in MatH-RNA3 (intermolecular wtRNA1/MatH-RNA3 crossover). Crossovers between 3′RAS1s and 5′RAS1s of two MatH-RNA3 molecules (intermolecular) and between two RAS1s sequences of the same MatH-RNA3 molecule (intramolecular) can also occur.