Over the past year, we have made progress in the following areas. Ty1 copy number dynamics has been studied by reintroducing active elements into a Ty-less strain where resident elements had been lost by long terminal repeat (LTR-LTR) recombination. Repopulated strains exhibit alterations in chromosome size that are associated with Ty1 insertions, but do not become genetically isolated. The rates of element gain and loss under genetic and environmental conditions known to affect Ty1 retrotransposition have been determined using genetically tagged reference elements. Ty1 gain and loss ratios obtained under different conditions suggest that copy number oscillates over time by altering the rate of retrotransposition, resulting in the diverse copy numbers observed in Saccharomyces. On a broader scale, our results suggest that the gain and loss of LTR-retrotransposons can be highly dynamic and has the potential to remodel genomes over short evolutionary time periods. In collaboration with Dr. Dwight V. Nissley (SAIC, Frederick MD), we have shown that hybrid elements composed of Ty1 and the reverse transcriptase gene from HIV-1 are useful tools for detecting, monitoring, and isolating drug-resistant reverse transcriptases in budding yeast. This sensitive phenotypic assay detects drug-resistant variants in clinical samples when the variants comprise as little as 0.3 to 1.0% of the virus population. Furthermore, our assay can detect of both known and novel reverse transcriptase variants and should be useful in studies of the evolution and clinical significance of minor drug-resistant variants.
