排序方式: 共有5条查询结果,搜索用时 15 毫秒
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Supriya Khedkar Georgy Smyshlyaev Ivica Letunic Oleksandr
M Maistrenko Luis
Pedro Coelho Askarbek Orakov Sofia K Forslund Falk Hildebrand Mechthild Luetge Thomas S B Schmidt Orsolya Barabas Peer Bork 《Nucleic acids research》2022,50(6):3155
Prokaryotic Mobile Genetic Elements (MGEs) such as transposons, integrons, phages and plasmids, play important roles in prokaryotic evolution and in the dispersal of cargo functions like antibiotic resistance. However, each of these MGE types is usually annotated and analysed individually, hampering a global understanding of phylogenetic and environmental patterns of MGE dispersal. We thus developed a computational framework that captures diverse MGE types, their cargos and MGE-mediated horizontal transfer events, using recombinases as ubiquitous MGE marker genes and pangenome information for MGE boundary estimation. Applied to ∼84k genomes with habitat annotation, we mapped 2.8 million MGE-specific recombinases to six operational MGE types, which together contain on average 13% of all the genes in a genome. Transposable elements (TEs) dominated across all taxa (∼1.7 million occurrences), outnumbering phages and phage-like elements (<0.4 million). We recorded numerous MGE-mediated horizontal transfer events across diverse phyla and habitats involving all MGE types, disentangled and quantified the extent of hitchhiking of TEs (17%) and integrons (63%) with other MGE categories, and established TEs as dominant carriers of antibiotic resistance genes. We integrated all these findings into a resource (proMGE.embl.de), which should facilitate future studies on the large mobile part of genomes and its horizontal dispersal. 相似文献
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Novikova O Mayorov V Smyshlyaev G Fursov M Adkison L Pisarenko O Blinov A 《The Plant journal : for cell and molecular biology》2008,56(4):562-574
Retrotransposons are the major component of plant genomes. Chromodomain-containing Gypsy long terminal repeat (LTR) retrotransposons are widely distributed in eukaryotes. Four distinct clades of chromodomain-containing Gypsy retroelements are known from the vascular plants: Reina, CRM, Galadriel and Tekay. At the same time, almost nothing is known about the repertoire of LTR retrotransposons in bryophyte genomes. We have combined a search of chromodomain-containing Gypsy retroelements in Physcomitrella genomic sequences and an experimental investigation of diverse moss species. The computer-based mining of the chromodomain-containing LTR retrotransposons allowed us to describe four different elements from Physcomitrella. Four novel clades were identified that are evolutionarily distinct from the chromodomain-containing Gypsy LTR retrotransposons of other plants. 相似文献
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Kanazhevskaya L. Y. Smyshlyaev D. A. Alekseeva I. V. Fedorova O. S. 《Russian Journal of Bioorganic Chemistry》2019,45(6):630-640
Russian Journal of Bioorganic Chemistry - Fe2+/2-ketoglutarate-dependent DNA-dioxygenase AlkB from Escherichia coli is able to restore the native structure of alkylated DNA bases. The enzymatic... 相似文献
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Thomas Bock Wei-Hua Chen Alessandro Ori Nayab Malik Noella Silva-Martin Jaime Huerta-Cepas Sean T. Powell Panagiotis L. Kastritis Georgy Smyshlyaev Ivana Vonkova Joanna Kirkpatrick Tobias Doerks Leo Nesme Jochen Ba?ler Martin Kos Ed Hurt Teresa Carlomagno Anne-Claude Gavin Orsolya Barabas Christoph W. Müller Vera van?Noort Martin Beck Peer Bork 《Nucleic acids research》2014,42(22):13525-13533
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Mobile genetic elements (MGEs) sequester and mobilize antibiotic resistance genes across bacterial genomes. Efficient and reliable identification of such elements is necessary to follow resistance spreading. However, automated tools for MGE identification are missing. Tyrosine recombinase (YR) proteins drive MGE mobilization and could provide markers for MGE detection, but they constitute a diverse family also involved in housekeeping functions. Here, we conducted a comprehensive survey of YRs from bacterial, archaeal, and phage genomes and developed a sequence‐based classification system that dissects the characteristics of MGE‐borne YRs. We revealed that MGE‐related YRs evolved from non‐mobile YRs by acquisition of a regulatory arm‐binding domain that is essential for their mobility function. Based on these results, we further identified numerous unknown MGEs. This work provides a resource for comparative analysis and functional annotation of YRs and aids the development of computational tools for MGE annotation. Additionally, we reveal how YRs adapted to drive gene transfer across species and provide a tool to better characterize antibiotic resistance dissemination. 相似文献
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