Protein Interactions Involved in tRNA Gene-Specific Integration of Dictyostelium discoideum Non-Long Terminal Repeat Retrotransposon TRE5-A

Abstract

Mobile genetic elements that reside in gene-dense genomes face the problem of avoiding devastating insertional mutagenesis of genes in their host cell genomes. To meet this challenge, some Saccharomyces cerevisiae long terminal repeat (LTR) retrotransposons have evolved targeted integration at safe sites in the immediate vicinity of tRNA genes. Integration of yeast Ty3 is mediated by interactions of retrotransposon protein with the tRNA gene-specific transcription factor IIIB (TFIIIB). In the genome of the social amoeba Dictyostelium discoideum, the non-LTR retrotransposon TRE5-A integrates ϳ48 bp upstream of tRNA genes, yet little is known about how the retrotransposon identifies integration sites. Here, we show direct protein interactions of the TRE5-A ORF1 protein with subunits of TFIIIB, suggesting that ORF1p is a component of the TRE5-A preintegration complex that determines integration sites. Our results demonstrate that evolution has put forth similar solutions to prevent damage of diverse, compact genomes by different classes of mobile elements.

A Superfamily of DNA Transposons Targeting Multicopy Small RNA Genes

“…This type of target specificity is observed in TRE5-A non-LTR retrotransposons from Dictyostelium discoideum and Tf1 LTR retrotransposons from Schizosaccharomyces pombe [18], [19]. Although these retrotransposons target specific types of sequences such as tRNA genes or RNA polymerase II promoters, they are not inserted at specific positions inside of their targets, but at a distance close to the targets.…”

Dynamic interactions between transposable elements and their hosts

“…For example, the Dictyostelium discoideum non-LTR retrotransposon DRE (also known as TRE-5A) preferentially inserts ~48bp upstream of tRNA genes, whereas the retrotransposon Tdd3 (also known as TRE-3A) inserts downstream of tRNA genes 29, 93 . Indeed, experimental evidence suggests that the TRE-5A ORF1-encoded protein directly interacts with subunits of TFIIIB to direct its integration to tRNA genes 94 .…”

In Vitro Targeting of Strand Transfer by the Ty3 Retroelement Integrase

“…For example, in Saccharomyces cerevisiae, the copia-like LTR retrotransposon Ty5 is targeted to heterochromatic DNA by interactions between the IN C-terminal domain and the Sir4 silencing protein (10 -11) and copia-like Ty1 and gypsy-like Ty3 LTR retrotransposons target the 5Ј-flanking regions of Pol III-transcribed genes (12)(13). In Dictystelium discoideum, the non-LTR retrotransposon TRE5 targets 5Ј-flanking regions of tRNA genes and the TRE5 ORF1 protein interacts with components of the Pol III transcription factor TFIIIB (14). The Schizosaccharomyces pombe gypsy-like Tf1 interacts with a subset of transcription factors to target RNA Pol II promoters (15).…”