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

Strategic Directions for Increasing the Share of Renewable Energy Sources in the Structure of Energy Consumption

In recent decades, the European energy sector is transforming due to the growing demand for electricity and increased requirements for ensuring the continuity of supply. In the European Union, almost 50% of energy consumption is provided through energy imports. One of the main conditions for the continuity of supply is the diversification of their sources, considered as an important prerequisite for energy security. The EU government has serious hopes for the development of alternative energy and believes that in the future "green" energy will play a significant role in the structure of energy consumption. The object of this study is renewable energy sources. The subject of the research is the problems of increasing the share of renewable energy sources in the structure of energy consumption. Keywords: electric power industry, alternative energy, the electricity consumers. JEL Classifications: K32, O13, P4

Defeat and intensity of dental caries of first-graders in Krasnoyarsk depend on the level of dental care at schools

To study the infestation and intensity of dental caries of first-graders depending on the level of dental care at school, has been viewed 239 children at school entry and at the end of the first class. Dental examination performed by standard methods. It is concluded that despite the almost identical results children caries at school entry, after the first class statistically significant excess of the indicator at school, where there is no dentist, as compared to school where he is

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

Eastern Vector of Russian State Policy Development for Ensuring Energy Security

This article is dedicated to the current problem of forming the Eastern vector of oil and gas policy within new energy policy and modern circumstances. The main goal of the work is to study the energy relations between Russia and the countries of the Asia-Pacific region, namely China. Using the analysis method, authors have highlighted the threats and possibilities of the influence of the current situation in the fuel and energy complex on Russia's energy security. Analysis of the existing situation on the global energy market has revealed that deepening and expansion of partnerships in economic and energy sphere with China are of interest to Russia as a Eurasian state. The basis for a partnership is a cooperation, based on China's demand for natural resources, while Russia will benefit from using effective innovation models of modernisation. Keywords: Asia-Pacific Region, Energy Sphere, Oil and Gas Policy, Raw Material Resource Potential, Energy Security, Energy Dialogue. JEL Classifications: P48, Q40

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

Integration of Small and Middle-Sized Enterprises into Large Energy Corporations as a Factor of Business Sustainability

Small businesses are traditionally the driver of the economic growth in the conditions of market economy, so in the modern circumstances this thesis is seen as an axiom not requiring additional argumentation. Moreover, the role of small and middle-sized businesses in the acceleration in the rates of economic grows currently increases. The economic recession triggered by the sanctions as well as by the international collapse in oil prices, to an even greater degree actualized the task of searching the ways and methods of the Russian economy potential activation including more active and rational use of the most important nonmaterial resource of market economy that is business initiative. Keywords: Enterprises, small and middle-sized business, energy complex JEL Classifications: L53; M14; O1

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

Expansion and Evolution of the X-Linked Testis Specific Multigene Families in the melanogaster Species Subgroup

The testis specific X-linked genes whose evolution is traced here in the melanogaster species subgroup are thought to undergo fast rate of diversification. The CK2ßtes and NACβtes gene families encode the diverged regulatory β-subunits of protein kinase CK2 and the homologs of β-subunit of nascent peptide associated complex, respectively. We annotated the CK2βtes-like genes related to CK2ßtes family in the D. simulans and D. sechellia genomes. The ancestor CK2βtes-like genes preserved in D. simulans and D. sechellia are considered to be intermediates in the emergence of the D. melanogaster specific Stellate genes related to the CK2ßtes family. The CK2ßtes-like genes are more similar to the unique autosomal CK2ßtes gene than to Stellates, taking into account their peculiarities of polymorphism. The formation of a variant the CK2ßtes gene Stellate in D. melanogaster as a result of illegitimate recombination between a NACßtes promoter and a distinct polymorphic variant of CK2ßtes-like ancestor copy was traced. We found a close nonrandom proximity between the dispersed defective copies of DINE-1 transposons, the members of Helitron family, and the CK2βtes and NACβtes genes, suggesting an involvement of DINE-1 elements in duplication and amplification of these genes