Genetic Recombination in Brome Mosaic Virus: The Role of Intergenic Region in Junction Site Selection

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ABSTRACTThe long-term goal of this project is to understand the mechanism(s) of genetic recombination in RNA viruses. By using brome mosaic bromovirus (BMV) as a model RNA virus, mechanistic differences between homologous and nonhomologous events at the RNA and protein levels have been previously reported. These studies have suggested a copy choice mechanism, where the BMV replicase complex has changed among the RNA templates during RNA replication. To define the role of signal sequences during the junction sites selection and thus to determine the conditions leading to the efficient recombination hot spots, this project focuses on the multifunctional intergenic region in BMV RNA3. Frequent homologous exchanges between molecules of BMV RNA3 within the intergenic hot spot have been recently confirmed experimentally. One goal of this project is to map the recombinationally active sequences inside the intergenic region, by using molecular genetics approaches. Its second goal is to determine how these sequences relate to each other in order to direct the junction sites efficiently. Specific aims to achieve the above research goals include studies of the role of a subgenomic promoter in recombination, including 1) the core region; 2) the polyA tract; 3) enhancing sequences; and 4) secondary structures. This novel experimental approach will help us obtain new data regarding the mechanism(s) of homologous RNA recombination. This, in turn, will provide information concerning the control of recombination activities in RNA viruses. The results of this model research will be applicable to a variety of RNA viruses that utilize intergenic (subgenomic) promoter sequences.