TRT, a Vertebrate and ProtozoanTc1-Like Transposon: Current Activity and Horizontal Transfer

Abstract

We report a Danio rerio transposon named DrTRT, for D. rerio Transposon Related to Tc1. The complete sequence of the DrTRT transposon is 1,563 base pairs (bp) in length, and its transposase putatively encodes a 338-amino acid protein that harbors a DD37E motif in its catalytic domain. We present evidence based on searches of publicly available genomes that TRT elements commonly occur in vertebrates and protozoa. Phylogenetic and functional domain comparisons confirm that TRT constitutes a new subfamily within the Tc1 family. Hallmark features of having no premature termination codons within the transposase, the presence of all expected functional domains, and its occurrence in the bony fish transcriptome suggest that TRT might have current or recent activity in these species. Further analysis showed that the activity of TRT elements in these species might have arisen about between 4 and 19 Ma. Interestingly, our results also implied that the widespread distribution of TRT among fishes, frog, and snakes is the result of multiple independent HT events, probably from bony fishes to snakes or frog. Finally, the mechanisms underlying horizontal transfer of TRT elements are discussed.

Evolution of pogo, a separate superfamily of IS630-Tc1-mariner transposons, revealing recurrent domestication events in vertebrates

“…S1). Then, 19 representative IS630 transposase sequences including the 11 clades, Tc1/mariner transposase families identified previously [ 21 – 23 , 26 , 42 – 47 ], and Zator transposases, which were defined as a superfamily close to ITm group [ 28 ], were combined with all identified pogo transposases to infer a phylogenetic tree by using maximum likelihood methods with the IQ-TREE program [ 48 ]. The resulting tree shows that although pogo , Tc1/mariner (including DD34E/ Tc1 , DD35E/ TR , DD36E/ IC , DD34D/ mariner , DD37D/ maT , DD37E/ TRT , DD37D, DD39D, and DD41D), Zator , and DD34E/ Gambol transposases are sister clades, they formed four distinct highly supported monophyletic clades, with 74, 99, 92, and 100% bootstrap supports for pogo , Zator , Tc1/mariner , and DD34E/ Gambol clades respectively (Fig.…”

“…The bacteria IS256 transposase was used as outgroup. Then, the representative sequences of IS630 transposases from each clade and other unclassified sequences, Tc1/mariner known families transposases [ 21 – 23 , 26 , 42 – 47 ], and Zatror transposases [ 28 ] were jointed with the pogo transposases to infer the phylogenetic tree based on the multiple amino acid alignment of the conserved DDE domain by using the maximum likelihood method within IQ-TREE [ 48 ]. The best-fit model was selected by ModelFinder embedded in IQ-TREE [ 48 ], and the reliability of maximum likelihood trees was estimated by using the ultrafast bootstrap approach with 1000 replicates.…”

“…S2 for an uncollapsed tree). Transposase sequences of DD36E/IC, DD35E/TR, DD37E/TRT are from the references [22,23,42]. GenBank access numbers of other reference elements are included in Additional file 2: Fig.…”

“…Different organizations of transposase domains, which were screened by using hmmscan [50], across the families and clades of pogo transposons were also observed. Significant variability was observed in the numbers of amino acids between the last two residues of the catalytic domain (DDE) of transposase for the families of Tigger (DD29- This number was highly conserved in most other Tc1/ mariner families [26,38,42], while almost all Passer and Fot/Fot-like transposons were characterized by DD35D, and all Mover transposons by DD36D. Only four Fot-like transposons in Ichthyosporea are characterized by a DD36D domain.…”

Why did theTc1-like elements of mollusks acquired the spliceosomal introns?

“…The classification of ITm elements is based on phylogenetic analysis and, until recently, it was well correlated with structural features (the length of peptide chain between the second and the third amino acid residues of the catalytic DDE/D triad (Tellier et al 2015). However, the recent studies have identified, at least, four different groups of ITm elements with DD37E signature: mosquito (Shao and Tu 2001), TRT (Zhang et al 2016a), L18 and L31 (Puzakov et al 2018). Thus, the families of ITm elements cannot be accurately distinguished by the spacer size of DDE/D domains.…”