The large bat Helitron DNA transposase forms a compact monomeric assembly that buries and protects its covalently bound 5′-transposon end

Košek, Dalibor; Grabundžija, Ivana; Lei, Haotian; Bilić, Ilija; Wang, Huaibin; Jin, Yukun; Peaslee, Graham F.; Hickman, A.B.; Dyda, Fred

doi:10.1016/j.molcel.2021.07.028

Cited by 21 publications

(18 citation statements)

References 106 publications

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“…In addition, despite their inverted orientation, the 3D topology of these motifs in relaxases and RCR proteins is essentially the same ( Chandler et al 2013 ). Interestingly, the cryo-EM structure of the RepHel in complex with the Helitron 5′-end ssDNA was solved only recently, revealing an even higher degree of organizational similarity with relaxases, particularly with TraI ( Kosek et al 2021 ). As mentioned by the authors, the structural similarity between these two classes of proteins does not imply a close evolutionary relationship, which is also supported by our results and previous studies involving the Rep domain ( Heringer and Kuhn 2018 ; Kazlauskas et al 2019 ).…”

Section: Discussionmentioning

confidence: 99%

“…Indeed, it has been shown that a mutation in the Walker A motif from Hel domains causes Helitrons to lose their transposition activity in cells ( Grabundzija et al 2016 ). In addition, the RepHel cryo-EM structure reveals a considerable interface between the catalytic portion of Rep and the Hel domain, suggesting that they act in conjunction to unwind dsDNA and generate sufficient ssDNA to allow strand cleavage as transposition starts ( Kosek et al 2021 ). Thus, it is conceivable that a Hel domain also favored the invasion and colonization of eukaryotic genomes by Helitrons , which would explain their pervasiveness in this domain of life that lacks other groups of RC TEs.…”

Section: Discussionmentioning

confidence: 99%

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Pif1 Helicases and the Evidence for a Prokaryotic Origin of Helitrons

Heringer

Kuhn

2021

Molecular Biology and Evolution

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Helitrons are the only group of rolling-circle transposons that encode a transposase with a helicase domain (Hel), which belongs to the Pif1 family. Because Pif1 helicases are important components of eukaryotic genomes, it has been suggested that Hel domains probably originated after a host eukaryotic Pif1 gene was captured by a Helitron ancestor. However, the few analyses exploring the evolution of Helitron transposases (RepHel) have focused on its Rep domain, which is also present in other mobile genetic elements. Here, we used phylogenetic and non-metric multidimensional scaling analyses to investigate the relationship between Hel domains and Pif1-like helicases from a variety of organisms. Our results reveal that Hel domains are only distantly related to genomic helicases from eukaryotes and prokaryotes, and thus are unlikely to have originated from a captured Pif1 gene. Based on this evidence, and on recent studies indicating that Rep domains are more closely related to rolling-circle plasmids and phages, we suggest that Helitrons are descendants of a RepHel-encoding prokaryotic plasmid element that invaded eukaryotic genomes before the radiation of its major groups. We discuss how a Pif1-like helicase domain might have favored the transposition of Helitrons in eukaryotes beyond simply unwinding DNA intermediates. Finally, we demonstrate that some examples in the literature describing genomic helicases from eukaryotes actually consist of Hel domains from Helitrons, a finding that underscores how transposons can hamper the analysis of eukaryotic genes. This investigation also revealed that two groups of land plants appear to have lost genomic Pif1 helicases independently.

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Section: Discussionmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

Pif1 Helicases and the Evidence for a Prokaryotic Origin of Helitrons

Heringer

Kuhn

2021

Molecular Biology and Evolution

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“…The motifs are located on the expected secondary structural elements in the Replitron-1 transposase predicted structure: motif I and II on the first and third b-strand, respectively, and motif III on the third a-helix (Figure 1C, Figure 2, Figure S1). The conserved Glu upstream of motif II may represent the third metal-binding ligand, analogous to similarly located Glu residues in the Reps of the CRESS-DNA virus PCV2 (Tompkins et al 2021), the Helitron Helraiser (Kosek et al 2021) and the parvovirus AAV-5 (Hickman et al 2002). Amino acids are coloured according to their conservation and physicochemical properties as per ClustalX default settings (Larkin et al 2007).…”

Section: Replitron Transposases Feature An Undescribed Rep Huh Endonu...mentioning

confidence: 99%

“…The “RepHel” transposases of Helitrons feature a Y2 Rep domain fused to a superfamily 1 helicase, and often feature accessory domains (Thomas and Pritham 2015). Experimental characterisations of Helraiser , a reconstructed active Helitron, have established a model of their rolling circle transposition mechanism, which results in an increase in copy number upon transposition (Grabundzija et al 2016; Grabundzija et al 2018; Kosek et al 2021). Finally, IS 91 (Y2 Rep) and IS CR (Y1 Rep) are phylogenetically related insertion sequences that are thought to be mobilised via a rolling circle mechanism similar to that of Helitrons (Mendiola et al 1994; Garcillán-Barcia et al 2002), although they lack a helicase domain.…”

Section: Introductionmentioning

confidence: 99%

Replitrons: a new group of eukaryotic transposons encoding HUH endonuclease

Craig

2022

Preprint

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HUH endonucleases of the Rep (replication protein) class mediate the replication of highly diverse plasmids and viral genomes across all domains of life. Reps also function as transposases, and three evolutionarily independent groups of transposable elements (TEs) mobilised by Reps have been described: the prokaryotic insertion sequences IS200/IS605and IS91/ISCR, and the eukaryotic Helitrons. Here I present Replitrons, a new group of eukaryotic transposons encoding Rep HUH endonuclease. Replitron transposases feature Rep with one catalytic Tyr (Y1) as their only recognised domain, contrasting with Helitron transposases that feature Rep with two Tyr (Y2) and a fused helicase domain (i.e. RepHel). Protein clustering found no link between Replitron transposases and described Rep transposases, and instead recovered a weak association with Reps of circular Rep-encoding single stranded (CRESS) DNA viruses and their related plasmids (pCRESS). The predicted tertiary structure of the transposase ofReplitron-1, the founding member of the group that is active in the green algaChlamydomonas reinhardtii, closely resembles that of CRESS-DNA viruses and other HUH endonucleases. Replitrons are present in at least three eukaryotic supergroups and reach high copy numbers in non-seed plant genomes. Replitron DNA sequences generally feature short direct repeats at, or potentially near, their termini. Finally, I characterisecopy-and-paste de novoinsertions ofReplitron-1using long-read sequencing ofC. reinhardtiiexperimental lines. Overall, these results support an ancient and evolutionarily independent origin of Replitrons, in line with other major groups of eukaryotic TEs. This work substantially expands the known diversity of both transposons and HUH endonucleases in eukaryotes.

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“…The recruitment of male-specific lethal complex to the X chromosome in males increases transcription ( Muyle et al, 2021 ). It’s unclear whether Helitron regulates dosage compensation in other species, such as Helraiser (part of the Helitron family) present in the little brown bat, Myotis lucifugus ( Kosek et al, 2021 ), or in human cells ( Sandoval-Villegas et al, 2021 ). Supplementary to dosage compensation, TEs function as a chromatin remodeler in the mammalian X chromosome ( Chatterjee, 2017 ).…”

Section: Transposable Elements On Sex Chromosomesmentioning

confidence: 99%

The Role of Transposable Elements in Sexual Development

Chiang

DeRosa

Park

et al. 2022

Front. Behav. Neurosci.

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Up to 50% of most mammalian genomes are made up of transposable elements (TEs) that have the potential to mobilize around the genome. Despite this prevalence, research on TEs is only beginning to gain traction within the field of neuroscience. While TEs have long been regarded as “junk” or parasitic DNA, it has become evident that they are adaptive DNA and RNA regulatory elements. In addition to their vital role in normal development, TEs can also interact with steroid receptors, which are key elements to sexual development. In this review, we provide an overview of the involvement of TEs in processes related to sexual development- from TE activity in the germline to TE accumulation in sex chromosomes. Moreover, we highlight sex differences in TE activity and their regulation of genes related to sexual development. Finally, we speculate on the epigenetic mechanisms that may govern TEs’ role in sexual development. In this context, we emphasize the need to further the understanding of sexual development through the lens of TEs including in a variety of organs at different developmental stages, their molecular networks, and evolution.

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The large bat Helitron DNA transposase forms a compact monomeric assembly that buries and protects its covalently bound 5′-transposon end

Cited by 21 publications

References 106 publications

Pif1 Helicases and the Evidence for a Prokaryotic Origin of Helitrons

Pif1 Helicases and the Evidence for a Prokaryotic Origin of Helitrons

Replitrons: a new group of eukaryotic transposons encoding HUH endonuclease

The Role of Transposable Elements in Sexual Development

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