Chapter 25 : Mechanisms of DNA Transposition

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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 ( ).

Citation: Hickman A, Dyda F. 2015. Mechanisms of DNA Transposition, p 531-553. In Craig N, Chandler M, Gellert M, Lambowitz A, Rice P, Sandmeyer S (ed), Mobile DNA III. ASM Press, Washington, DC. doi: 10.1128/microbiolspec.MDNA3-0034-2014
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Figure 1

Basic chemical reactions catalyzed by DNA transposases. (A) An RNase H-like active site, based on structures of PFV intasomes ( ). The green DNA represents the cleaved dinucleotide, and orange is the target strand. Spheres indicate bound metal ions. (B) HUH nuclease active site acting on single-stranded DNA (based on PDB ID 2X06 of IS TnpA). Shown is the reaction that occurs at the transposon Left End (LE). After cleavage, the DNA flanking the LE (black) remains in the active site; upon exchange of α-helices between the two active sites of the dimeric transposase, the cleaved LE moves to the other monomer where it is joined to the cleaved RE to form a circular excised transposon (not shown). At the same time, the flanking DNA from the RE of the transposon switches active sites (as shown here in black) and subsequent joining results in a sealed donor backbone. (C) DNA cleavage catalyzed by a serine recombinase. The active serine is surrounded by many Arg residues. Upon 180° rotation of one dimer within a tetramer, one strand rotates out of the active site (green) while another rotates in (orange). (D) DNA cleavage catalyzed by a tyrosine recombinase. Crucial residues within the active site include a conserved RHR triad (for details, see also ( )).

Citation: Hickman A, Dyda F. 2015. Mechanisms of DNA Transposition, p 531-553. In Craig N, Chandler M, Gellert M, Lambowitz A, Rice P, Sandmeyer S (ed), Mobile DNA III. ASM Press, Washington, DC. doi: 10.1128/microbiolspec.MDNA3-0034-2014
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Figure 2

Proposed pathway for transposon circle integration into target DNA catalyzed by a serine transposase. At the top, a tetrameric assembly is shown bringing together the abutted Left End (LE; orange) and Right End (RE; red) of an excised circular transposon with a target DNA (green). The reactions in the dashed box show how four cleavage reactions in which each active site serine becomes covalently attached to one strand of DNA, followed by a 180 degree rotation of the left-most dimer, leads to a re-organization of the strands. Resolution of the four covalent intermediates results in an integrated transposon.

Citation: Hickman A, Dyda F. 2015. Mechanisms of DNA Transposition, p 531-553. In Craig N, Chandler M, Gellert M, Lambowitz A, Rice P, Sandmeyer S (ed), Mobile DNA III. ASM Press, Washington, DC. doi: 10.1128/microbiolspec.MDNA3-0034-2014
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Figure 3

Pathway of conjugative transposition. Whether catalyzed by a serine or a tyrosine transposase, excision results in a circular intermediate in which the transposon ends are abutted. Only one of the strands of this intermediate is transferred to the recipient cell, and replication (new strands shown in blue) regenerates the double-stranded form in both cells.

Citation: Hickman A, Dyda F. 2015. Mechanisms of DNA Transposition, p 531-553. In Craig N, Chandler M, Gellert M, Lambowitz A, Rice P, Sandmeyer S (ed), Mobile DNA III. ASM Press, Washington, DC. doi: 10.1128/microbiolspec.MDNA3-0034-2014
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Figure 4

Proposed pathways of excision and integration by tyrosine transposases. (A) Transposon excision. (B) Transposon integration.

Citation: Hickman A, Dyda F. 2015. Mechanisms of DNA Transposition, p 531-553. In Craig N, Chandler M, Gellert M, Lambowitz A, Rice P, Sandmeyer S (ed), Mobile DNA III. ASM Press, Washington, DC. doi: 10.1128/microbiolspec.MDNA3-0034-2014
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Figure 5

Transposition pathways for RNase H-like transposases. Arrows indicate sites of strand cleavage and the black dots indicate 3′-OH groups. Many pathways converge on essentially the same form of the excised transposon (highlighted with grey boxes). This linear intermediate is then integrated into target DNA as shown in (f). Target site duplications (TSDs) are generated when the cell repairs the gaps introduced by staggered strand transfer reactions. Adapted from ( ).

Citation: Hickman A, Dyda F. 2015. Mechanisms of DNA Transposition, p 531-553. In Craig N, Chandler M, Gellert M, Lambowitz A, Rice P, Sandmeyer S (ed), Mobile DNA III. ASM Press, Washington, DC. doi: 10.1128/microbiolspec.MDNA3-0034-2014
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Figure 6

Transpososome structures for the RNase H-like DNA transposases. Cartoon representations of five transpososomes containing RNase H-like catalytic domains determined by X-ray crystallography. In all images, the catalytically active protomers acting on the two transposon ends are colored in orange and green, with the green catalytic domain acting on the DNA end shown in blue and the orange domain acting on the DNA end in red. Where target DNA is present, it is shown in grey. Inactive protomers (MuA, PFV IN and Hermes) are colored purple and magenta. The following PDB codes were used: (A) Tn, 1MUH; (B) PFV IN, 4E7J; (C) Mos1, 3HOT; (D) MuA, 4FCY; (E) Hermes, 4D1Q.

Citation: Hickman A, Dyda F. 2015. Mechanisms of DNA Transposition, p 531-553. In Craig N, Chandler M, Gellert M, Lambowitz A, Rice P, Sandmeyer S (ed), Mobile DNA III. ASM Press, Washington, DC. doi: 10.1128/microbiolspec.MDNA3-0034-2014
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Figure 7

Transpososome of the HUH transposase TnpA of IS, modelled as binding one Left End (LE; red) and one Right End (RE; blue). The PDB codes 2VJV and 2VJU were used. The inset shows the step of the reaction in the strand transfer and reset model for IS transposition (see He , this volume) to which the structure corresponds; note that the RE flank has not yet been observed crystallographically.

Citation: Hickman A, Dyda F. 2015. Mechanisms of DNA Transposition, p 531-553. In Craig N, Chandler M, Gellert M, Lambowitz A, Rice P, Sandmeyer S (ed), Mobile DNA III. ASM Press, Washington, DC. doi: 10.1128/microbiolspec.MDNA3-0034-2014
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Table 1

Examples of proteins containing the four types of nuclease catalytic domains found in DNA transposases and other enzymes that rearrange DNA

Citation: Hickman A, Dyda F. 2015. Mechanisms of DNA Transposition, p 531-553. In Craig N, Chandler M, Gellert M, Lambowitz A, Rice P, Sandmeyer S (ed), Mobile DNA III. ASM Press, Washington, DC. doi: 10.1128/microbiolspec.MDNA3-0034-2014

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