Hiker, a new family of DNA transposons encoding transposases with DD35E motifs, displays a distinct phylogenetic relationship with most known DNA transposon families of IS630-Tc1-mariner (ITm).

DNA transposons play a crucial role in determining the size and structure of eukaryotic genomes. In this study, a new family of IS630-Tc1-mariner (ITm) DNA transposons, named Hiker (HK), was identified. HK is characterized by a DD35E catalytic domain and is distinct from all previously known families of the ITm group. Phylogenetic analyses showed that DD35E/Hiker forms a monophyletic clade with DD34E/Gambol, indicating that they may represent a separate superfamily of ITm. A total of 178 Hiker species were identified, with 170 found mainly in Actinopterygii, one in Chondrichthyes, six in Anura and one in Mollusca. Gambol (GM), on the other hand, are found in invertebrates, with 18 in Arthropoda and one in Platyhelminthes. Hiker transposons have a total length ranging from 2.14 to 3.67 kb and contain a single open reading frame that encodes a protein of approximately 370 amino acids (range 311-413 aa). They are flanked by short terminal inverted repeats (TIRs) of 16-30 base pairs and two base pair (TA) target-site duplications. In contrast, most transposons of the Gambol family have a total length of 1.35-5.96 kb, encode a transposase protein of approximately 350 amino acids (range 306-374 aa), and are flanked by TIRs that range from 32 to 1097 bp in length. Both Hiker and Gambol transposases have several conserved motifs, including helix-turn-helix (HTH) motifs and a DDE domain. Our study observed multiple amplification waves and repeated horizontal transfer (HT) events of HK transposons in vertebrate genomes, indicating their role in diversifying and shaping the genomes of Actinopterygii, Chondrichthyes, and Anura. Conversely, GM transposons showed few Horizontal transfer events. According to cell-based transposition assays, most HK transposons are likely inactive due to the truncated DNA binding domains of their transposases. We present an updated classification of the ITm group based on these findings, which will enhance the understanding of both the evolution of ITm transposons and that of their hosts.

maT and mosquito transposons in cnidarians: evolutionary history and intraspecific differences.

Transposable elements exert a significant effect on the size and structure of eukaryotic genomes. Tc1/mariner superfamily elements represent the widely distributed and highly variable group of DNA transposons. Tc1/mariner elements include TLE/DD34-38E, MLE/DD34D, maT/DD37D, Visitor/DD41D, Guest/DD39D, mosquito/DD37E, and L18/DD37E families, all of which are well or less scarcely studied. However, more detailed research into the patterns of prevalence and diversity of Tc1/mariner transposons enables one to better understand the coevolution of the TEs and the eukaryotic genomes. We performed a detailed analysis of the maT/DD37D family in Cnidaria. The study of 77 genomic assemblies demonstrated that maT transposons are found in a limited number of cnidarian species belonging to classes Cubozoa (1 species), Hydrozoa (3 species) и Scyphozoa (5 species) only. The identified TEs were classified into 5 clades, with the representatives from Pelagiidae (class Scyphozoa) forming a separate clade of maT transposons, which has never been described previously. The potentially functional copies of maT transposons were identified in the hydrae. The phylogenetic analysis and the studies of distribution among the taxons and the evolutionary dynamics of the elements suggest that maT transposons of the cnidarians are the descendants of several independent invasion events occurring at different periods of time. We also established that the TEs of mosquito/DD37E family are found in Hydridae (class Hydrozoa) only. A comparison of maT and mosquito prevalence in two genomic assemblies of Hydra viridissima revealed obvious differences, thus demonstrating that each individual organism might carry a unique mobilome pattern. The results of the presented research make us better understand the diversity and evolution of Tc1/mariner transposons and their effect on the eukaryotic genomes.

The IS630/Tc1/mariner transposons in three ctenophore genomes.

Transposable elements (TEs) exert a significant effect on the structure and functioning of the genomes and also serve as a source of the new genes. The study of the TE diversity and evolution in different taxa is indispensable for the fundamental understanding of their roles in the genomes. IS630/Tc1/mariner (ITm) transposable elements represent the most prevalent and diverse group of DNA transposons. In this work, we studied the diversity, evolutionary dynamics and the phylogenetic relationships of the ITm transposons found in three ctenophore species: Mnemiopsis leidyi, Pleurobrachia bachei, Beroe ovata. We identified 29 ITm transposons, seven of which possess the terminal inverted repeats (TIRs) and an intact transposase, and, thus, are, presumably, active. Four other ITm transposons have the features of domesticated TEs. According to the results of the phylogenetic analysis, the ITm transposons of the ctenophores represent five groups - MLE/DD34D, TLE/DD34-38E, mosquito/DD37E, Visiror/DD41D and pogo/DDxD. Pogo/DDxD superfamily turnes out to be the most diverse and prevalent, since it accounts for more than 40% of the TEs identified. The data obtained in this research will fill the gap of knowledge of the diversity and evolution of the ITm transposons in the multicellular genomes and will lay the ground for the study of the TE effects on the evolution of the ctenophores.

Newly Discovered AqE Gene is Highly Conserved in Non-tetrapod Vertebrates.

Studying the diversity of energy production pathways is important for understanding the evolutionary relationships between metabolic pathways and their biochemical precursors. The lactate/malate dehydrogenase (LDH/MDH) superfamily has been a model system for structural and functional evolution for a long time. Recently, the type-2 family of LDH/MDH (or LDH2/MDH2 oxidoreductase) has been identified. The LDH2/MDH2 oxidoreductase family is now known to have functionally more diverse enzymes than the LDH/MDH superfamily. In channel catfish, the gene encoding the LDH2/MDH2 oxidoreductase has been found (and was provisionally termed AqE). Homologs of this enzyme are predominantly present in organisms living in an aquatic environment. In this work, we studied the AqE gene distribution among non-tetrapod vertebrates. It was found that the AqE gene is present in the genomes of bony and cartilaginous fish and in the genomes of hagfishes and lampreys. In addition, it has been confirmed that in representatives of Cypriniformes, the AqE gene has been lost. AqE in representatives of Salmoniformes underwent significant deletions, which most likely led to its pseudogenization. In most orders of non-Tetrapoda vertebrates, the AqE gene remains highly conserved, suggesting that the AqE gene in aquatic vertebrates is an essential gene and undergoes rigorous selection. The AqE gene has the highest sequence similarity with the archaeal ComC gene that encodes sulfolactate dehydrogenase (SLDH). Based on the similarity of substrates, the enzyme encoded by the AqE gene is likely involved in the malate-aspartate shuttle mechanism or the biosynthesis of the energy coenzyme M equivalent.

Dominant manifestation of pluripotency in embryonic stem cell hybrids with various numbers of somatic chromosomes.

Developmental potential was assessed in 8 intra-specific and 20 inter-specific hybrid clones obtained by fusion of embryonic stem (ES) cells with either splenocytes or fetal fibroblasts. Number of chromosomes derived from ES cells in these hybrid clones was stable while contribution of somatic partner varied from single chromosomes to complete complement. This allowed us to compare pluripotency of the hybrid cells with various numbers of somatic chromosomes. Three criteria were used for the assessment: (i) expression of Oct-4 and Nanog genes; (ii) analyses of teratomas generated by subcutaneous injections of the tested cells into immunodeficient mice; (iii) contribution of the hybrid cells in chimeras generated by injection of the tested cells into C57BL blastocysts. All tested hybrid clones showed expression of Oct-4 and Nanog at level comparable to ES cells. Histological and immunofluorescent analyses demonstrated that most teratomas formed from the hybrid cells with different number of somatic chromosomes contained derivatives of three embryonic layers. Tested hybrid clones make similar contribution in various tissues of chimeras in spite of significant differences in the number of somatic chromosomes they contained. The data indicate that pluripotency is manifested as a dominant trait in the ES hybrid cells and does not depend substantially on the number of somatic chromosomes. The latter suggests that the developmental potential derived from ES cells is maintained in ES-somatic cell hybrids by cis-manner and is rather resistant to trans-acting factors emitted from the somatic one.