Mobile genetic elements have the inherent potential to shape the genomes of their hosts. The retroelements, which include the retrotransposons and retroviruses, are a particularly abundant class of mobile elements. The site of retroelement insertion in the host genome is largely determined by the element-encoded protein integrase (IN). Research presented here addresses three aspects of IN from the retrotransposon Ty5: the function of a conserved domain (GKGY) in the IN C-terminus, the role of IN post-translational modification in targeted integration, and the origin of the Ty5 targeting mechanism.;Sequence analysis of a conserved domain (GKGY) found in the C-termini of all retrotransposons of the Ty1/copia family revealed two variant forms of this motif: the 'classic' motif found in most Ty1/ copia elements including Ty5, and a variant form characteristic of the retrotransposon Ty1 and closely related orthologues. Point mutations in the GKGY domains of both Ty1 and Ty5 resulted in greatly decreased transposition and low or undetectable levels of IN and reverse transcriptase (RT). Gag levels in all mutants were comparable to wild type, although less efficient processing of Gag and Pol was observed in Ty1. Lower levels of IN and RT were not due solely to low levels of polyprotein, as analysis of Ty1 protease mutants revealed only a modest decrease in polyprotein compared to wild type. These data collectively indicate that after processing of the polyprotein by protease, the GKGY motif has a role in forming a stable complex between IN and RT and/or in mediating their proper folding.;Ty5 IN encodes a short targeting domain (TD) at the very C-terminus that interacts with the heterochromatin protein Sir4. The TD/Sir4 interaction is responsible for Ty5's preference to integrate into heterochromatin. Ty5 TD is phosphorylated at serine 1095, and using surface plasmon resonance, the TD/Sir4 interaction was shown to be dependent on the phospho-serine at position 1095. Mutations preventing phosphorylation of this residue disrupt the ability of TD to target Ty5 integration in vivo. Exposure of yeast cells to environmental stresses decreased TD phosphorylation, indicating an active role for the host cell in determining Ty5 target specificity in response to environmental signals. Together, v these results are the first to show direct involvement of the host cell in regulating target site selection of a transposable element.;The hypothesis was tested that the TD/Sir4 interaction imitates an interaction between a host protein and Sir4. Initially deletion analyses were used to define the N- and C-terminal boundaries of Sir4 that interact with IN. Multiple Sir4 missense mutants were also generated that failed to interact with IN. Using an assay that measures Ty5 targeting to sites to which the mutant Sir4 proteins are tethered, most mutants did not target Ty5 integration. With the IN-interacting domain of Sir4 characterized, we tested the hypothesis that IN imitates a host protein by identifying Sir4-interactors through a genome-wide yeast two hybrid screen. The interaction profiles between Sir4 and candidate proteins were compared to the Sir4/IN interaction profile. Esc1 was found to have the same Sir4 N- and C-terminal interaction boundaries as IN and failed to interact with the majority of Sir4 mutants. Esc1 through its interaction with Sir4 partitions DNA to daughter cells. The interaction of Sir4 with a small 34 amino acid region of Esc1 (aa 1440-1473) correlated with the ability to reliably partition DNA. A conserved 13 amino acid domain was found within this region, which along with a smaller 9 amino acid fragment, were shown to interact with Sir4 and to nucleate silent chromatin, a feature shared by IN and the TD. The functional equivalence of the TD and the 13 amino acid domain of Esc1 was demonstrated by exchanging these respective motifs to create chimeric IN and Esc1 proteins that maintained the ability to target integration and partition DNA, respectively. As with TD, mass spectrometry analysis of Esc1 (aa 1440-1473) revealed that this short domain is a phosphoprotein. These studies indicate that Ty5 imitates a conserved region of the host protein Esc1 in order to interact with Sir4 and target integration to heterochromatic regions. These data also suggest that like the IN/Sir4 interaction, the interaction between Sir4 and Esc1 and the in vivo ability to partition DNA depends upon a small conserved region in the Esc1 C-terminus that is phosphorylated.