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Chapter 18 : Tn Transposition

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Abstract:

This chapter presents an overall view of the structure of Tn, and enables the reader to study the mechanism behind the Tn transposition process by using the available genetics, biochemistry, and molecular structures as guides. Later, the regulation of Tn transposition referring to both transposon functions and host functions are discussed. Finally, the use of the Tn system as a practical tool are also discussed. There are three surprising aspects to the structure. The first surprise is the great complexity of the protein-DNA contacts. The second is that protein-DNA contacts and not protein-protein contacts provide most of the interactions stabilizing the complex. The final surprise is the clarity with which the structure correlates with the hairpin-cleavage mechanism. Tn propagates within cells and it is obviously important that the host cells survive for the propagation to be successful. However, transposition itself is likely to be a deleterious event both in terms of the double end breaks left behind in donor DNA and in terms of target genes suffering insertion mutations. Recently we have learned that the same basic technology has been successfully applied to and . The basic approach involved injecting a preformed transposition complex into the insect preblastoderm and finding animals that expressed the Tn-encoded function (GFP) among the progeny.

Citation: Reznikoff W. 2002. Tn Transposition, p 403-422. In Craig N, Craigie R, Gellert M, Lambowitz A (ed), Mobile DNA II. ASM Press, Washington, DC. doi: 10.1128/9781555817954.ch18

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Figures

Image of Figure 1.
Figure 1.

Tnstructure. (A) Tn. Two nearly identical insertion sequences (ISL and ISR) bracket three genes that encode resistance to kanamycin, bleomycin, and streptomycin. ISR encodes two proteins that play important roles in Tntransposition: the transposase (Tnp) and the inhibitor of transposition (Inh). Both proteins are read in the same reading frame, but Inh is initiated 56 residues downstream of Tnp. ISL encodes two inactive truncated versions of these proteins (P3 and P4) because of an ochre codon 26 residues from the C terminus. The sites that define the ends of the transposable elements and at which Tnp acts are 19-bp sequences called OE (outside end) and IE (inside end) ( Fig. 1D ). For Tntransposition, Tnp acts at two OE sequences (see Fig. 2 ). For IStransposition, Tnp acts at one OE and one IE. (B) Schematic of Tnp primary structure. The locations of critical active-site residues are indicated with Xs. These include the DDE motif, the YREK signature sequence found in ISfamily transposases, and K330. K330 is found in retroviral integrases and is similar to R found in other ISfamily transposases. The black boxes marked with Cs locate domains involved in OE contacts. The open boxes marked with Ts locate domains involved in OE contacts; TH is the hairpin clamp contacts and TA is the active-site contacts. The shaded box is the location of the Tnp-Tnp dimer interface. Upward facing marks indicate hyperactive mutations. Downward facing marks are defective mutations caused by dimerization failure. (C) Tnp and Inh regulatory elements. The mRNAs that encode Tnp and Inh are programmed by two overlapping promoters. Two Dam methylation sites overlap the Tnp promoter −10 region. (D) End sequences. The nontransferred strands are presented for OE and IE with position 1 (5′) on the left. In addition, a hyperactive end sequence called the mosaic end (ME) is shown. The seven positions at which OE and IE differ are indicated in bold. The bold letters in the ME sequence indicate positions at which it has an OE-specific base in place of an IE base. Also shown are sites specific for host proteins: DnaA, Dam, and Fis.

Citation: Reznikoff W. 2002. Tn Transposition, p 403-422. In Craig N, Craigie R, Gellert M, Lambowitz A (ed), Mobile DNA II. ASM Press, Washington, DC. doi: 10.1128/9781555817954.ch18
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Image of Figure 2.
Figure 2.

Tntransposes via a cut-and-paste conservative mechanism. Monomeric Tnp binds to the end sequences. Dimerization of Tnp and formation of Tnp-DNA contacts lead to formation of the synapse. Tnp (in the presence of Mg) cleaves the transposon DNA free from the donor backbone DNA through a three-step reaction.

Citation: Reznikoff W. 2002. Tn Transposition, p 403-422. In Craig N, Craigie R, Gellert M, Lambowitz A (ed), Mobile DNA II. ASM Press, Washington, DC. doi: 10.1128/9781555817954.ch18
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Image of Figure 3.
Figure 3.

Tnp-OE contacts. The structure data ( ) were used to generate a model for the Tnp-OE contacts. Residues in roman type represent contacts, and residues in italics represent contacts. Thick lines represent base-specific contacts in the major groove. Thin lines represent base-specific contacts in the minor groove. Dashed lines represent water-mediated interactions with bases. Phosphate interactions are also shown. This figure is based on the structure analysis by Douglas Davies and Scott Lovell.

Citation: Reznikoff W. 2002. Tn Transposition, p 403-422. In Craig N, Craigie R, Gellert M, Lambowitz A (ed), Mobile DNA II. ASM Press, Washington, DC. doi: 10.1128/9781555817954.ch18
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Image of Figure 4.
Figure 4.

Transposon-DBB cleavage and strand transfer. TnTnp catalyzes cleavage through a hairpin intermediate that involves three sequential phosphoryl transfer reactions. In the first step, the transposon-transferred strand-donor DNA junction is nicked. The released 3′-OH of the transferred strand then attacks the opposite strand to form a hairpin intermediate. The hairpin is then nicked. Strand transfer then follows after target capture. The attack of the 3′-OH groups during strand transfer is staggered 9 bp apart.

Citation: Reznikoff W. 2002. Tn Transposition, p 403-422. In Craig N, Craigie R, Gellert M, Lambowitz A (ed), Mobile DNA II. ASM Press, Washington, DC. doi: 10.1128/9781555817954.ch18
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Image of Figure 5.
Figure 5.

Intramolecular transposition yielding nested deletions. Intramolecular transposition events yield two types of products depending on the precise orientation of the strand transfer reaction: deletion circles or inversion circles. The generation of deletion circles can be used as a tool for generating nested deletion families. The generation of two such deletions is pictured. The generation of inversion circles is not shown. Both types of products are convenient templates for sequencing. In the case pictured, the transposon has been constructed to have a target sequence, an origin of replication, and a selectable marker. Only deletion products from one side (carrying the origin and the selectable marker) are inherited after transformation.

Citation: Reznikoff W. 2002. Tn Transposition, p 403-422. In Craig N, Craigie R, Gellert M, Lambowitz A (ed), Mobile DNA II. ASM Press, Washington, DC. doi: 10.1128/9781555817954.ch18
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Image of Figure 6.
Figure 6.

Electroporation of preformed transposon-Tnp complexes. Tnp forms stable synaptic complexes with precleaved transposon DNA in the absence of Mg. Electroporation of these complexes into target cells yields transposition events. This technology avoids the need to produce Tnp in the target cells.

Citation: Reznikoff W. 2002. Tn Transposition, p 403-422. In Craig N, Craigie R, Gellert M, Lambowitz A (ed), Mobile DNA II. ASM Press, Washington, DC. doi: 10.1128/9781555817954.ch18
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Image of Figure 7.
Figure 7.

Random gene fusion technology. Two sequential transposition events are used to generate a random library of X-Y and Y-X fusions. The initial transposon is defined at its ends by IE sequences. Inside each IE sequence is an OE sequence in inverted orientation. The first transposition event uses the IE-specific hyperactive transposase sC7v2.0 ( ) to make a library of inserts in gene X. The second transposition event uses the OE-specific hyperactive transposase EK-LP ( ) to transpose the X and X′ containing transposons into gene Y

Citation: Reznikoff W. 2002. Tn Transposition, p 403-422. In Craig N, Craigie R, Gellert M, Lambowitz A (ed), Mobile DNA II. ASM Press, Washington, DC. doi: 10.1128/9781555817954.ch18
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Tables

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Table 1.

Host functions and Tn transposition

Citation: Reznikoff W. 2002. Tn Transposition, p 403-422. In Craig N, Craigie R, Gellert M, Lambowitz A (ed), Mobile DNA II. ASM Press, Washington, DC. doi: 10.1128/9781555817954.ch18

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