IS481EU Shows a New Connection between Eukaryotic and Prokaryotic DNA Transposons

SIMPLE SUMMARY: Transposable elements (TEs) are genetic parasites that mobilize themselves from one locus to another in the host genome. DDD/E transposase gene is the most abundant gene in nature and its protein product catalyzes DNA transposition. The IS481 family is a group of prokaryotic TEs that encode a DDD/E transposase. Here, we report a group of eukaryotic TEs that shows close affinity to some of the prokaryotic IS481 family members, and designate them IS481EU. IS481EU was found in palabasalids including Trichomonas vaginalis. Although most TEs with DDD/E transposase generate direct repeats of fixed or similar lengths (target site duplications, TSDs) at both ends of insertion, IS481EU generates TSDs of discrete lengths (~4 bps, ~15 bps, or ~25 bps). The unique characteristics of IS481EU in protein sequences and the distribution of TSD lengths support its placement as a new superfamily of eukaryotic DNA transposons. The transmission of prokaryotic IS481 to a eukaryotic lineage likely resulted in the birth of IS481EU, and may have contributed to lineage-specific evolutionary trajectories. ABSTRACT: DDD/E transposase gene is the most abundant gene in nature and many DNA transposons in all three domains of life use it for their transposition. A substantial number of eukaryotic DNA transposons show similarity to prokaryotic insertion sequences (ISs). The presence of IS481-like DNA transposons was indicated in the genome of Trichomonas vaginalis. Here, we surveyed IS481-like eukaryotic sequences using a bioinformatics approach and report a group of eukaryotic IS481-like DNA transposons, designated IS481EU, from parabasalids including T. vaginalis. The lengths of target site duplications (TSDs) of IS481EU are around 4 bps, around 15 bps, or around 25 bps, and strikingly, these discrete lengths of TSDs can be observed even in a single IS481EU family. Phylogenetic analysis indicated the close relationships of IS481EU with some of the prokaryotic IS481 family members. IS481EU was not well separated from IS3EU/GingerRoot in the phylogenetic analysis, but was distinct from other eukaryotic DNA transposons including Ginger1 and Ginger2. The unique characteristics of IS481EU in protein sequences and the distribution of TSD lengths support its placement as a new superfamily of eukaryotic DNA transposons.