Endonuclease domain of the Drosophila melanogaster R2 non-LTR retrotransposon and related retroelements: a new model for transposition

Муха, Д. В.; Pasyukova, Elena G.; Kapelinskaya, T. V.; Kagramanova, A. S.

doi:10.3389/fgene.2013.00063

Cited by 8 publications

(12 citation statements)

References 86 publications

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“…An article by Mukha et al . was published reporting this similarity using the Drosophila melanogaster R2 element as a query sequence, corroborating our work-in-progress ( 32 ).…”

Section: Introductionsupporting

confidence: 86%

Endonuclease domain of non-LTR retrotransposons: loss-of-function mutants and modeling of the R2Bm endonuclease

et al. 2016

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Non-LTR retrotransposons are an important class of mobile elements that insert into host DNA by target-primed reverse transcription (TPRT). Non-LTR retrotransposons must bind to their mRNA, recognize and cleave their target DNA, and perform TPRT at the site of DNA cleavage. As DNA binding and cleavage are such central parts of the integration reaction, a better understanding of the endonuclease encoded by non-LTR retrotransposons is needed. This paper explores the R2 endonuclease domain from Bombyx mori using in vitro studies and in silico modeling. Mutations in conserved sequences located across the putative PD-(D/E)XK endonuclease domain reduced DNA cleavage, DNA binding and TPRT. A mutation at the beginning of the first α-helix of the modeled endonuclease obliterated DNA cleavage and greatly reduced DNA binding. It also reduced TPRT when tested on pre-cleaved DNA substrates. The catalytic K was located to a non-canonical position within the second α-helix. A mutation located after the fourth β-strand reduced DNA binding and cleavage. The motifs that showed impaired activity form an extensive basic region. The R2 biochemical and structural data are compared and contrasted with that of two other well characterized PD-(D/E)XK endonucleases, restriction endonucleases and archaeal Holliday junction resolvases.

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“…An article by Mukha et al . was published reporting this similarity using the Drosophila melanogaster R2 element as a query sequence, corroborating our work-in-progress ( 32 ).…”

Section: Introductionsupporting

confidence: 86%

Endonuclease domain of non-LTR retrotransposons: loss-of-function mutants and modeling of the R2Bm endonuclease

et al. 2016

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“…Transposable elements (TEs) of the R series are non-LTR elements known to specifically insert in the 28S (R1, R2, R4, R5, R6, R9, and RT families) or into the 18S (R7 and R8 families) ribosomal genes (Kojima et al, 2006;Gladyshev & Arkhipova, 2009). R2 is the most studied non-LTR TE and it was used as a model to decipher the non-LTR mechanism of mobilization and reintegration, that appears also mediated by recombination (Eickbush, 2002;Fujimoto et al, 2004;Mukha et al, 2013).…”

Section: Introductionmentioning

confidence: 99%

Obligatory parthenogenesis and TE load: Bacillus stick insects and the R2 non‐LTR retrotransposon

et al. 2016

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Transposable elements (TEs) are selfish genetic elements whose self-replication is contrasted by the host genome. In this context, host reproductive strategies are predicted to impact on both TEs load and activity. The presence and insertion distribution of the non-LTR retrotransposon R2 was here studied in populations of the strictly bisexual Bacillus grandii maretimi and of the obligatory parthenogenetic Bacillus atticus atticus. Furthermore, data were also obtained from the offspring of selected B. a. atticus females. At the population level, the gonochoric B. g. maretimi showed a significantly higher R2 load than the obligatory parthenogenetic B. a. atticus. The comparison with bisexual and unisexual Bacillus rossius populations showed that their values were higher than those recorded for B. a. atticus and similar, or even higher, than those of B. g. maretimi. Consistently, an R2 load reduction is scored in B. a. atticus offspring even if with a great variance. On the whole, data here produced indicate that in the obligatory unisexual B. a. atticus R2 is active and that mechanisms of molecular turnover are effective. Furthermore, progeny analyses show that, at variance of the facultative parthenogenetic B. rossius, the R2 activity is held at a lower rate. Modeling parental-offspring inheritance, suggests that in B. a. atticus recombination plays a major role in eliminating insertions rather than selection, as previously suggested for unisexual B. rossius progeny, even if in both cases a high variance is observed. In addition to this, mechanisms of R2 silencing or chances of clonal selection cannot be ruled out.

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“…However, it should be remembered that the ecosystems in which TEs have co-evolved with their hosts as well as their strategy for invasion and maintenance are not the same as viruses, despite sharing some nuclear ecological niches with certain viruses (viruses may also serve as vectors of horizontal transfer for TEs). These nuclear ecological niches are likely the reason why TEs have evolved their own particular survival solutions, as exemplified by certain TE species with strict requirements for integration into host chromosomes (Tn7, Pokey, non-LTR retrotransposons; Mukha et al, 2013), or into non-conventional introns (Milanowski et al, 2013). Such features might have sped up TE evolution and their coevolution with host factor that drives the evolution of their transposition mechanism.…”

Section: A Universal Te Classification Systemmentioning

confidence: 98%

“…It would therefore be expected that these three types of TP-retrotransposons should be classified into three groups of unrelated TEs that use three transposition mechanisms with different origins (but having numerous convergent features). Recently, it has been highlighted that even within LINEs two types of endonucleases (EN) with different origins are encountered: AP and a nuclease similar to PD-(D/E)XK (Stoddard, 2005;Mukha et al, 2013). Within certain LINE species, such as the Dualen elements (Kojima and Fujiwara, 2005), the situation is even more complex since they encode both EN types.…”

Section: Critical Analysis Of the Curcio And Derbyshire Proposalmentioning

confidence: 98%

A survey of transposable element classification systems – A call for a fundamental update to meet the challenge of their diversity and complexity

Piégu

Bire

Arensburger

et al. 2015

Molecular Phylogenetics and Evolution

138

132

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The increase of publicly available sequencing data has allowed for rapid progress in our understanding of genome composition. As new information becomes available we should constantly be updating and reanalyzing existing and newly acquired data. In this report we focus on transposable elements (TEs) which make up a significant portion of nearly all sequenced genomes. Our ability to accurately identify and classify these sequences is critical to understanding their impact on host genomes. At the same time, as we demonstrate in this report, problems with existing classification schemes have led to significant misunderstandings of the evolution of both TE sequences and their host genomes. In a pioneering publication Finnegan (1989) proposed classifying all TE sequences into two classes based on transposition mechanisms and structural features: the retrotransposons (class I) and the DNA transposons (class II). We have retraced how ideas regarding TE classification and annotation in both prokaryotic and eukaryotic scientific communities have changed over time. This has led us to observe that: (1) a number of TEs have convergent structural features and/or transposition mechanisms that have led to misleading conclusions regarding their classification, (2) the evolution of TEs is similar to that of viruses by having several unrelated origins, (3) there might be at least 8 classes and 12 orders of TEs including 10 novel orders. In an effort to address these classification issues we propose: (1) the outline of a universal TE classification, (2) a set of methods and classification rules that could be used by all scientific communities involved in the study of TEs, and (3) a 5-year schedule for the establishment of an International Committee for Taxonomy of Transposable Elements (ICTTE).

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Endonuclease domain of the Drosophila melanogaster R2 non-LTR retrotransposon and related retroelements: a new model for transposition

Cited by 8 publications

References 86 publications

Endonuclease domain of non-LTR retrotransposons: loss-of-function mutants and modeling of the R2Bm endonuclease

Endonuclease domain of non-LTR retrotransposons: loss-of-function mutants and modeling of the R2Bm endonuclease

Obligatory parthenogenesis and TE load: Bacillus stick insects and the R2 non‐LTR retrotransposon

A survey of transposable element classification systems – A call for a fundamental update to meet the challenge of their diversity and complexity

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