The Ty1 LTR-retrotransposon of budding yeast, Saccharomyces cerevisiae

Ty1 elements have a structure that is analogous to simple retroviruses, but they lack an envelope gene (Fig. 1) (1). The most highly characterized Ty1 element is Ty1-H3, which was isolated following its retrotransposition into plasmid DNA (2). Nucleotide coordinates provided in this review specifically refer to Ty1-H3, unless otherwise noted. Ty1 is 5918 base pairs (bp) in length with 334 bp direct repeats, or long-terminal repeats (LTRs), at each end. Ty1 LTRs, like that of most LTR-retrotransposons and retroviruses, have the dinucleotide inverted repeat, 5'-TG...CA-3' at their termini, and are composed of three distinct domains-U3, R, and U5. These domains are defined by their position in the major sense-strand transcript expressed from Ty1 DNA. The 38-nucleotide U5 region and 240-nucleotide U3 region are unique to the 5' and 3' end of the Ty1 RNA, respectively, while the R region of 56 nucleotides is repeated at both ends of the processed transcript. Functional Ty1 elements encode two partially overlapping open reading frames: GAG (historically known as TYA) and POL (TYB). The last three nucleotides of the R region of the 5' LTR encode the first codon of GAG. The GAG ORF encodes a single functional protein with capsid and nucleic acid chaperone functions. The POL ORF is in the +1 frame relative to GAG and overlaps the last 38 base pairs of GAG. POL encodes three proteins with catalytic activity: protease (PR), integrase (IN), and reverse transcriptase/RNase H (RT/RH).