Ginger DNA transposons in eukaryotes and their evolutionary relationships with long terminal repeat retrotransposons

<p>Abstract</p> <p>Background</p> <p>In eukaryotes, long terminal repeat (LTR) retrotransposons such as <it>Copia, BEL </it>and <it>Gypsy </it>integrate their DNA copies into the host genome using a particular type of DDE transposase called integrase (INT). The <it>Gypsy </it>INT-like transposase is also conserved in the <it>Polinton/Maverick </it>self-synthesizing DNA transposons and in the 'cut and paste' DNA transposons known as <it>TDD-4 </it>and <it>TDD-5</it>. Moreover, it is known that INT is similar to bacterial transposases that belong to the IS<it>3</it>, IS<it>481</it>, IS<it>30 </it>and IS<it>630 </it>families. It has been suggested that LTR retrotransposons evolved from a non-LTR retrotransposon fused with a DNA transposon in early eukaryotes. In this paper we analyze a diverse superfamily of eukaryotic cut and paste DNA transposons coding for INT-like transposase and discuss their evolutionary relationship to LTR retrotransposons.</p> <p>Results</p> <p>A new diverse eukaryotic superfamily of DNA transposons, named <it>Ginger </it>(for '<it>Gypsy </it>INteGrasE Related') DNA transposons is defined and analyzed. Analogously to the IS<it>3 </it>and IS<it>481 </it>bacterial transposons, the <it>Ginger </it>termini resemble those of the <it>Gypsy </it>LTR retrotransposons. Currently, <it>Ginger </it>transposons can be divided into two distinct groups named <it>Ginger1 </it>and <it>Ginger2/Tdd</it>. Elements from the <it>Ginger1 </it>group are characterized by approximately 40 to 270 base pair (bp) terminal inverted repeats (TIRs), and are flanked by CCGG-specific or CCGT-specific target site duplication (TSD) sequences. The <it>Ginger1</it>-encoded transposases contain an approximate 400 amino acid N-terminal portion sharing high amino acid identity to the entire <it>Gypsy</it>-encoded integrases, including the YPYY motif, zinc finger, DDE domain, and, importantly, the GPY/F motif, a hallmark of <it>Gypsy </it>and endogenous retrovirus (ERV) integrases. <it>Ginger1 </it>transposases also contain additional C-terminal domains: ovarian tumor (OTU)-like protease domain or Ulp1 protease domain. In vertebrate genomes, at least two host genes, which were previously thought to be derived from the <it>Gypsy </it>integrases, apparently have evolved from the <it>Ginger1 </it>transposase genes. We also introduce a second <it>Ginger </it>group, designated <it>Ginger2/Tdd</it>, which includes the previously reported DNA transposon <it>TDD-4</it>.</p> <p>Conclusions</p> <p>The <it>Ginger </it>superfamily represents eukaryotic DNA transposons closely related to LTR retrotransposons. <it>Ginger </it>elements provide new insights into the evolution of transposable elements and certain transposable element (TE)-derived genes.</p

Small and Medium-Sized Enterprises as a Driver of Innovative Development of the Russian Fuel and Energy Complex

The urgency of the studied problem is caused by the fact that international sanctions led to a number of bans in the oil and gas industry, and there is the necessity to create the role of small and medium-sized innovative enterprises. In this regard, this article is aimed at identifying the positive and negative aspects of these enterprises, as well as their significance in the development of the oil and gas service segment. Keywords: fuel and energy complex, innovative enterprises, international sanctions, import substitution, territorial clusters JEL Classifications: O13, P18, M2

RAG1 Core and V(D)J Recombination Signal Sequences Were Derived from Transib Transposons

The V(D)J recombination reaction in jawed vertebrates is catalyzed by the RAG1 and RAG2 proteins, which are believed to have emerged approximately 500 million years ago from transposon-encoded proteins. Yet no transposase sequence similar to RAG1 or RAG2 has been found. Here we show that the approximately 600-amino acid “core” region of RAG1 required for its catalytic activity is significantly similar to the transposase encoded by DNA transposons that belong to the Transib superfamily. This superfamily was discovered recently based on computational analysis of the fruit fly and African malaria mosquito genomes. Transib transposons also are present in the genomes of sea urchin, yellow fever mosquito, silkworm, dog hookworm, hydra, and soybean rust. We demonstrate that recombination signal sequences (RSSs) were derived from terminal inverted repeats of an ancient Transib transposon. Furthermore, the critical DDE catalytic triad of RAG1 is shared with the Transib transposase as part of conserved motifs. We also studied several divergent proteins encoded by the sea urchin and lancelet genomes that are 25%−30% identical to the RAG1 N-terminal domain and the RAG1 core. Our results provide the first direct evidence linking RAG1 and RSSs to a specific superfamily of DNA transposons and indicate that the V(D)J machinery evolved from transposons. We propose that only the RAG1 core was derived from the Transib transposase, whereas the N-terminal domain was assembled from separate proteins of unknown function that may still be active in sea urchin, lancelet, hydra, and starlet sea anemone. We also suggest that the RAG2 protein was not encoded by ancient Transib transposons but emerged in jawed vertebrates as a counterpart of RAG1 necessary for the V(D)J recombination reaction

The amphioxus genome and the evolution of the chordate karyotype

Lancelets ('amphioxus') are the modern survivors of an ancient chordate lineage, with a fossil record dating back to the Cambrian period. Here we describe the structure and gene content of the highly polymorphic approx520-megabase genome of the Florida lancelet Branchiostoma floridae, and analyse it in the context of chordate evolution. Whole-genome comparisons illuminate the murky relationships among the three chordate groups (tunicates, lancelets and vertebrates), and allow not only reconstruction of the gene complement of the last common chordate ancestor but also partial reconstruction of its genomic organization, as well as a description of two genome-wide duplications and subsequent reorganizations in the vertebrate lineage. These genome-scale events shaped the vertebrate genome and provided additional genetic variation for exploitation during vertebrate evolution

The \u3cem\u3eChlamydomonas\u3c/em\u3e Genome Reveals the Evolution of Key Animal and Plant Functions

Chlamydomonas reinhardtii is a unicellular green alga whose lineage diverged from land plants over 1 billion years ago. It is a model system for studying chloroplast-based photosynthesis, as well as the structure, assembly, and function of eukaryotic flagella (cilia), which were inherited from the common ancestor of plants and animals, but lost in land plants. We sequenced the ∼120-megabase nuclear genome of Chlamydomonas and performed comparative phylogenomic analyses, identifying genes encoding uncharacterized proteins that are likely associated with the function and biogenesis of chloroplasts or eukaryotic flagella. Analyses of the Chlamydomonas genome advance our understanding of the ancestral eukaryotic cell, reveal previously unknown genes associated with photosynthetic and flagellar functions, and establish links between ciliopathy and the composition and function of flagella

Modeling the asymmetric evolution of a mouse and rat-specific microRNA gene cluster intron 10 of the Sfmbt2 gene

<p>Abstract</p> <p>Background</p> <p>The total number of miRNA genes in a genome, expression of which is responsible for the miRNA repertoire of an organism, is not precisely known. Moreover, the question of how new miRNA genes arise during evolution is incompletely understood. Recent data in humans and opossum indicate that retrotranspons of the class of short interspersed nuclear elements have contributed to the growth of microRNA gene clusters.</p> <p>Method</p> <p>We studied a large miRNA gene cluster in intron 10 of the mouse Sfmbt2 gene using bioinformatic tools.</p> <p>Results</p> <p>Mice and rats are unique to harbor a 55-65 Kb DNA sequence in intron 10 of the Sfmbt2 gene. This intronic region is rich in regularly repeated B1 retrotransposons together with inverted self-complementary CA/TG microsatellites. The smallest repeats unit, called MSHORT1 in the mouse, was duplicated 9 times in a tandem head-to-tail array to form 2.5 Kb MLONG1 units. The center of the mouse miRNA gene cluster consists of 13 copies of MLONG1. BLAST analysis of MSHORT1 in the mouse shows that the repeat unit is unique for intron 10 of the Sfmbt2 gene and suggest a dual phase model for growth of the miRNA gene cluster: arrangment of 10 MSHORT1 units into MLONG1 and further duplication of 13 head-to-tail MLONG1 units in the center of the miRNA gene cluster. Rats have a similar arrangment of repeat units in intron 10 of the Sfmbt2 gene. The discrepancy between 65 miRNA genes in the mouse cluster as compared to only 1 miRNA gene in the corresponding rat repeat cluster is ascribed to sequence differences between MSHORT1 and RSHORT1 that result in lateral-shifted, less-stable miRNA precursor hairpins for RSHORT1.</p> <p>Conclusion</p> <p>Our data provides new evidence for the emerging concept that lineage-specific retroposons have played an important role in the birth of new miRNA genes during evolution. The large difference in the number of miRNA genes in two closely related species (65 versus 1, mice versus rats) indicates that this species-specific evolution can be a rapid process.</p