| Summary: | <p>Abstract</p> <p>Background</p> <p>"Domestication" of transposable elements (TEs) led to evolutionary breakthroughs such as the origin of telomerase and the vertebrate adaptive immune system. These breakthroughs were accomplished by the adaptation of molecular functions essential for TEs, such as reverse transcription, DNA cutting and ligation or DNA binding. <it>Cryptons </it>represent a unique class of DNA transposons using tyrosine recombinase (YR) to cut and rejoin the recombining DNA molecules. <it>Cryptons </it>were originally identified in fungi and later in the sea anemone, sea urchin and insects.</p> <p>Results</p> <p>Herein we report new <it>Cryptons </it>from animals, fungi, oomycetes and diatom, as well as widely conserved genes derived from ancient <it>Crypton </it>domestication events. Phylogenetic analysis based on the YR sequences supports four deep divisions of <it>Crypton </it>elements. We found that the domain of unknown function 3504 (DUF3504) in eukaryotes is derived from <it>Crypton </it>YR. DUF3504 is similar to YR but lacks most of the residues of the catalytic tetrad (R-H-R-Y). Genes containing the DUF3504 domain are potassium channel tetramerization domain containing 1 (<it>KCTD1</it>), <it>KIAA1958</it>, zinc finger MYM type 2 (<it>ZMYM2</it>), <it>ZMYM3</it>, <it>ZMYM4</it>, glutamine-rich protein 1 (<it>QRICH1</it>) and "without children" (<it>WOC</it>). The <it>DUF3504 </it>genes are highly conserved and are found in almost all jawed vertebrates. The sequence, domain structure, intron positions and synteny blocks support the view that <it>ZMYM2</it>, <it>ZMYM3</it>, <it>ZMYM4</it>, and possibly <it>QRICH1</it>, were derived from <it>WOC </it>through two rounds of genome duplication in early vertebrate evolution. <it>WOC </it>is observed widely among bilaterians. There could be four independent events of <it>Crypton </it>domestication, and one of them, generating <it>WOC</it>/<it>ZMYM</it>, predated the birth of bilaterian animals. This is the third-oldest domestication event known to date, following the domestication generating telomerase reverse transcriptase (<it>TERT</it>) and <it>Prp8</it>. Many <it>Crypton</it>-derived genes are transcriptional regulators with additional DNA-binding domains, and the acquisition of the DUF3504 domain could have added new regulatory pathways via protein-DNA or protein-protein interactions.</p> <p>Conclusions</p> <p><it>Cryptons </it>have contributed to animal evolution through domestication of their YR sequences. The DUF3504 domains are domesticated YRs of animal <it>Crypton </it>elements.</p>
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