Pokey, a New DNA Transposon in Daphnia (Cladocera: Crustacea)

Abstract

We report the complete sequence of two representatives of the transposable element, Pokey, isolated from the ribosomal DNA of the cladoceran, Daphnia pulicaria. We describe the general features of this element, which confirms its classification as a DNA transposon. We show that Pokey is similar to piggyBac and, as such, is a member of the TTAA-specific family of elements. Pokey is putatively autonomous, possessing an open reading frame that encodes a putative protein with similarity to piggyBac's transposase, in addition to putative proteins from Drosophila and human LOOPER elements, and several human proteins of unknown function. We show that these proteins all contain amino acid motifs that are perhaps conserved for similar functions. We demonstrate that Pokey is carrying several regions of similarity to Daphnia pulex IGS sequences, likely the result of some sort of recombination event with the host genome. Pokey inserts into a conserved region of the large subunit ribosomal RNA gene known to contain other arthropod elements, suggesting that this location is a hot spot for insertional activity. However, Pokey is unique in that it is the only DNA transposon yet known to insert into this region, as other such insertions are non-LTR retrotransposons. It is now clear that this "ecological niche" has been effectively exploited by both retrotransposons and DNA transposons.

Diverse DNA transposons in rotifers of the class Bdelloidea

“…5 Top, which is published as supporting information on the PNAS web site). This finding may be interpreted as evidence of Avmar1 insertion preference for a specific target site in a multicopy sequence, which is unusual for DNA TEs, but not unprecedented (19,27). Alternatively, a copy of Avmar1 may have been inserted into another TE with a higher proliferative potential, leading to preferential amplification of this copy within a larger transposable unit.…”

“…The element AvPB1, which contains two frameshifts and only one TIR, was identifed in A. vaga in the course of UFW from Avmar1. Identification of TTAA in the target allowed us to deduce a putative TIR, which begins with a characteristic CCC, as do many other piggyBac TIRs (19) (Fig. 2D).…”

“…However, the use of this TIR sequence, together with the TTAA target, as a PCR primer yielded only a weak and diffuse band, and sequencing of cloned amplicons revealed two defective (one frameshift and two stop codons in each) copies of a related (60% amino acid identity) family, designated AvPB2, which are 97% identical and share an intron in the TPase ORF. A conserved Cys 5 -His-Cys 2 motif at the C terminus of the TPase and the preceding bipartite NLS (19,37) are detectable in AvPB1 and AvPB2, as is the putative DDD catalytic triad, which can be described as DE (77)DN(97)D (2)D. Moreover, a highly conserved tryptophan with adjacent basic residues, a motif essential for base flipping during hairpin formation and resolution in Tn5 and possibly in hAT and in RAG recombinase (35,40), is found between the catalytic domain and the Cys-rich motif (Fig. 1B), indicating that a hairpin intermediate may be formed during piggyBac transposition.…”

piggyBacTransposon

“…Analyses of these genome sequences revealed a number of piggyBac-like repetitive sequences. Furthermore, the full-length transposase-coding sequence of the Pokey element was isolated in 2002 and showed a clear similarity to T. ni piggyBac transposase (21). Thus far, piggyBac-like sequences have been found in the genomes of a wide range of organisms including fungi, plants, insects, crustaceans, urochordates, amphibians, fishes, and mammals (22).…”

Two families of non-LTR retrotransposons, Syrinx and Daphne, from the Darwinulid ostracod, Darwinula stevensoni

“…Little information, however, is available regarding genome structure and TE content in crustaceans. Scarce reports of crustacean TEs include such host species as an isopod and horseshoe crab (rDNA-specific non-LTR retrotransposon R2; Burke et al, 1999), waterflea (rDNA-specific DNA transposon Pokey from the piggyBac superfamily; Penton et al, 2002), and hydrothermal crab (mariner-like DNA transposon Bytmar1, Halaimia-Toumi et al, 2004; they also mention jockey-like gag and CR1-like RT fragments).Thus, the vast majority of crustacean TEs remains unexplored.…”