DNA sequence requirements for hobo transposable element transposition in Drosophila melanogaster

Kim, Yu Jung; Hice, Robert H.; O’Brochta, David A.; Atkinson, Peter W.

doi:10.1007/s10709-011-9600-2

Cited by 12 publications

(10 citation statements)

References 53 publications

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“…One notable feature of hAT transposon ends are multiple copies of short 5-6 bp subterminal sequences, apparently haphazardly arrayed in both orientations without evident periodicity (Kunze and Starlinger, 1989; Kim et al, 2011; Liu and Crawford, 1998; Liu et al, 2001; Urasaki et al, 2006). Accumulating data indicates that hAT transposases recognize their transposon tips in a bipartite manner, with weaker transposase binding to the TIRs and stronger binding by an N-terminal domain to these subterminal repeat sequences (Kunze and Starlinger, 1989; Becker and Kunze, 1997; Mack and Crawford, 2001; Urasaki et al, 2006; Kahlon et al, 2011; Kim et al, 2011).…”

Section: Resultsmentioning

confidence: 99%

“…Accumulating data indicates that hAT transposases recognize their transposon tips in a bipartite manner, with weaker transposase binding to the TIRs and stronger binding by an N-terminal domain to these subterminal repeat sequences (Kunze and Starlinger, 1989; Becker and Kunze, 1997; Mack and Crawford, 2001; Urasaki et al, 2006; Kahlon et al, 2011; Kim et al, 2011). …”

Section: Resultsmentioning

confidence: 99%

“…A 5’-GTGGC repeat has been previously identified within Hermes ends where one repeat on each end overlaps with the TIR, and it has been proposed that some of these repeats are likely important for DNA binding (Kim et al, 2011). There are seven repeats within Hermes (Figure 6A), and the location of the outermost repeat on each end, defined here as 13 bp encompassing the GTGGC repeat and designated “LE_1” (bp 13-25 from the tip of LE) and “RE_1” (bp 13-25 from the RE tip), taken in light of the structure, suggests that these are bound by the BED-finger domain: Hermes79-612 does not interact with the TIR after bp 11, and if TIR DNA were extended towards the center of the octamer, the BED domains would likely encounter DNA subterminal to the TIRs.…”

Section: Resultsmentioning

confidence: 99%

“…For hobo , whose transposase is 55% identical in sequence to Hermes, in vivo transposition requires at least 140 bp of its LE and 65 bp of RE (Kim et al, 2011). To establish if Hermes also has an end length requirement, we tested transposition in vivo as a function of transposon length (Table S4).…”

Section: Resultsmentioning

confidence: 99%

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Structural Basis of hAT Transposon End Recognition by Hermes, an Octameric DNA Transposase from Musca domestica

Hickman

Ewis

et al. 2014

Cell

131

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SUMMARY Hermes is a member of the hAT transposon superfamily which has active representatives, including McClintock's archetypal Ac mobile genetic element, in many eukaryotic species. The crystal structure of the Hermes transposase-DNA complex reveals that Hermes forms an octameric ring organized as a tetramer of dimers. While isolated dimers are active in vitro for all the chemical steps of transposition, only octamers are active in vivo. The octamer can provide not only multiple specific DNA-binding domains to recognize repeated subterminal sequences within the transposon ends, which are important for activity, but also multiple non-specific DNA binding surfaces for target capture. The unusual assembly explains the basis of bipartite DNA recognition at hAT transposon ends, provides a rationale for transposon end asymmetry, and suggests how the avidity provided by multiple sites of interaction could allow a transposase to locate its transposon ends amidst a sea of chromosomal DNA.

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Section: Resultsmentioning

confidence: 99%

Section: Resultsmentioning

confidence: 99%

Section: Resultsmentioning

confidence: 99%

Section: Resultsmentioning

confidence: 99%

See 2 more Smart Citations

Structural Basis of hAT Transposon End Recognition by Hermes, an Octameric DNA Transposase from Musca domestica

Hickman

Ewis

et al. 2014

Cell

131

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“…Among the eukaryotic transposons, the transposon ends of the Hermes transposon are typical of other hAT elements as its asymmetric ends are several hundred bp long and contain multiple apparently haphazardly arranged subterminal binding sites (91,116). The active form of Hermes is a ring-shaped octamer in which eight N-terminal site-specific DNA binding domains are available to interact with these interior sites while presenting the two transposon TIRs to the catalytic sites of one of the dimers of the octameric assembly (91; Figure 6E).…”

Section: How Do Transposases Synapse Their Two Transposon Ends?mentioning

confidence: 99%

Mechanisms of DNA Transposition

Hickman

Dyda

2015

Microbiol Spectr

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DNA transposases use a limited repertoire of structurally and mechanistically distinct nuclease domains to catalyze the DNA strand breaking and rejoining reactions that comprise DNA transposition. Here, we review the mechanisms of the four known types of transposition reactions catalyzed by (1) RNase H-like transposases (also known as DD(E/D) enzymes); (2) HUH single-stranded DNA transposases; (3) serine transposases; and (4) tyrosine transposases. The large body of accumulated biochemical and structural data, particularly for the RNase H-like transposases, has revealed not only the distinguishing features of each transposon family, but also some emerging themes that appear conserved across all families. The more-recently characterized single-stranded DNA transposases provide insight into how an ancient HUH domain fold has been adapted for transposition to accomplish excision and then site-specific integration. The serine and tyrosine transposases are structurally and mechanistically related to their cousins, the serine and tyrosine site-specific recombinases, but have to date been less intensively studied. These types of enzymes are particularly intriguing as in the context of site-specific recombination they require strict homology between recombining sites, yet for transposition can catalyze the joining of transposon ends to form an excised circle and then integration into a genomic site with much relaxed sequence specificity.In this chapter, we provide an overview of the fundamental concepts of DNA transposition mechanisms. Our aim is to emphasize basic themes and, in this effort, we will focus on specific illustrative cases rather than attempt an exhaustive review of the literature. We hope that the selected references will point the curious reader towards the landmark studies in the field as well as some of the most exciting recent results. We also direct the reader to other recent reviews (1-3).DNA transposases are enyzmes that move discrete segments of DNA called transposons from one location in the genome (often called the donor site) to a new site without using RNA intermediates. DNA transposases are usually encoded by the mobile element itself (in which case they are "autonomous" transposons). However, some transposons are missing a self-encoded transposase yet have ends that can be recognized by a transposase encoded somewhere else in the genome, and thus are "non-autonomous" (Siguier et al., this volume). Although logic suggests that all DNA transposons are moved by transposases, the term was originally reserved for those enzymes that do not require significant regions of homology between any part of the transposon and the sites to which they are moved, the so-called target (or insertion or integration) sites. As biology is not always neat and tidy, transposases can exhibit a spectrum of homology requirements and vagaries of terminology have arisen such that certain transposases are sometimes referred to as "resolvases" or by the generic term "recombinases".From a mechanistic perspective, t...

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General survey of hAT transposon superfamily with highlight on hobo element in Drosophila

et al. 2012

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The hAT transposons, very abundant in all kingdoms, have a common evolutionary origin probably predating the plant-fungi-animal divergence. In this paper we present their general characteristics. Members of this superfamily belong to Class II transposable elements. hAT elements share transposase, short terminal inverted repeats and eight base-pairs duplication of genomic target. We focus on hAT elements in Drosophila, especially hobo. Its distribution, dynamics and impact on genome restructuring in laboratory strains as well as in natural populations are reported. Finally, the evolutionary history of hAT elements, their domestication and use as transgenic tools are discussed.

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DNA sequence requirements for hobo transposable element transposition in Drosophila melanogaster

Cited by 12 publications

References 53 publications

Structural Basis of hAT Transposon End Recognition by Hermes, an Octameric DNA Transposase from Musca domestica

Structural Basis of hAT Transposon End Recognition by Hermes, an Octameric DNA Transposase from Musca domestica

Mechanisms of DNA Transposition

General survey of hAT transposon superfamily with highlight on hobo element in Drosophila

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