Phantom, a New Subclass ofMutatorDNA Transposons Found in Insect Viruses and Widely Distributed in Animals

Abstract

Transposons of the Mutator (Mu) superfamily have been shown to play a critical role in the evolution of plant genomes. However, the identification of Mutator transposons in other eukaryotes has been quite limited. Here we describe a previously uncharacterized group of DNA transposons designated Phantom identified in the genomes of a wide range of eukaryotic taxa, including many animals, and provide evidence for its inclusion within the Mutator superfamily. Interestingly three Phantom proteins were also identified in two insect viruses and phylogenetic analysis suggests horizontal movement from insect to virus, providing a new line of evidence for the role of viruses in the horizontal transfer of DNA transposons in animals. Many of the Phantom transposases are predicted to harbor a FLYWCH domain in the amino terminus, which displays a WRKY-GCM1 fold characteristic of the DNA binding domain (DBD) of Mutator transposases and of several transcription factors. While some Phantom elements have terminal inverted repeats similar in length and structure to Mutator elements, some display subterminal inverted repeats (sub-TIRs) and others have more complex termini reminiscent of so-called Foldback (FB) transposons. The structural plasticity of Phantom and the distant relationship of its encoded protein to known transposases may have impeded the discovery of this group of transposons and it suggests that structure in itself is not a reliable character for transposon classification.

Striking structural dynamism and nucleotide sequence variation of the transposon Galileo in the genome of Drosophila mojavensis

“…This would be in agreement with the statement that any region generated by duplication can thereafter be duplicated [42,43]. Furthermore, the tandem repeats in the TIR or in subterminal regions of transposons have been proposed to harbor secondary binding sites for the transposase [30,44-46]. In our case, Galileo elements also present these tandem repeats (subfamilies G and F [23,24]) and they contain secondary binding sites at least in Dbuz\GalileoG (Marzo M, Liu D, Ruiz A and Chalmers R, submitted).…”

“…The TIR length dynamics, along with the chimeric origin observed among Galileo copies is in agreement with an important dynamic DNA exchange of sequences and recombination [43,47,48]. Thus, this would explain why different non-related class II transposons present subfamilies with long TIRs and why TIR length is not a reliable feature for transposon classification [30,44,46,49]. …”

Selective Acquisition and Retention of Genomic Sequences by Pack-Mutator-Like Elements Based on Guanine-Cytosine Content and the Breadth of Expression

“…Since the initial discovery of Mu1 and MuDR in maize (Robertson, 1978;Robertson et al, 1989), similar elements were later identified from the maize genome and subsequently in other organisms including plants, animals, and fungi, where they are referred to as Mutator-like elements (MULEs; Yu et al, 2000;Lisch et al, 2001;Chalvet et al, 2003;Jiang et al, 2004;Holligan et al, 2006;Marquez and Pritham, 2010). MULEs are typically characterized by an 8-to 11-bp target site duplication (TSD) flanking the element, with 9-bp TSD as the most frequent form.…”

Structures, Functions, and Evolutionary Histories of DNA-Binding Domains of Plant-Specific Transcription Factors

“…The group clearly contains the DBDs of transposases, such as animal phantom transposase (Marquez and Pritham, 2010). The DBD motif of phantom is a FLYWCH Zn-binding domain.…”