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Chapter 9 : Insertion Sequences and Transposons

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Abstract:

Transposable elements (TEs) have been defined as DNA sequences able to insert at many sites in the genome. At present there are about 500 TEs identified in many different bacterial species. Most insertion sequence (IS) elements and transposons were discovered after their transposition into genes of interest. In bacteria the relative juxtapositions of genes are not necessarily important because most will be involved in producing tows-acting factors, which are able to fulfill their function irrespective of their location or arrangement in the genome. Nonreplicative (or "cut-and-paste") transposons are excised from the donor site by double-strand breaks and inserted at the target site without the duplication of the transposon sequences (e.g., IS10 and IS50). Some bacteriophages are also considered to group with the replicative transposons because they use transposition to replicate during the lytic phase of their life cycles. It should be noted that the transposons in the portable-homology rearrangements are no longer flanked by the same direct repeats of target sequences as they were before the rearrangements. Usually composite transposons have their IS elements in the inverted-repeat configuration so that homologous recombination only causes the inversion of the markers within the transposon. Conjugative transposons harbor within the same sequence the cellular (transposition) and the intercellular (conjugation) mobilities. In the few experiments where selection has been maintained for many generations, IS elements have been found to have a major effect on the genetic structure of the population.

Citation: Chalmers R, Blot M. 1999. Insertion Sequences and Transposons, p 151-169. In Charlebois R (ed), Organization of the Prokaryotic Genome. ASM Press, Washington, DC. doi: 10.1128/9781555818180.ch9

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Figures

Image of FIGURE 1
FIGURE 1

Mechanism of nonreplicative transposition. The DNA components of the reactions are all shown, but supercoiling and the protein components have been omitted for clarity. Markers A and B are in the transposon; C and D are in the flanking donor DNA, which is lost; X and Y are in the target DNA. Symbols: half boxes, transposon ends; solid and shaded circles, 5′ phosphate groups; solid and shaded triangles, 3′ hydroxyl groups; half arrows, direct repeats of target sequences.

Citation: Chalmers R, Blot M. 1999. Insertion Sequences and Transposons, p 151-169. In Charlebois R (ed), Organization of the Prokaryotic Genome. ASM Press, Washington, DC. doi: 10.1128/9781555818180.ch9
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Image of FIGURE 2
FIGURE 2

Mechanism of replicative transposition. The transposon and donor (AB and CD, respectively) are fused with the target molecule, XY, to form a Shapiro intermediate, which is converted to a cointegrate by replication. Symbols: half boxes, transposon ends; shaded circles, 5′ phosphate groups; solid and shaded triangles, 3′ hydroxyl groups; half arrows, direct repeats of target sequences.

Citation: Chalmers R, Blot M. 1999. Insertion Sequences and Transposons, p 151-169. In Charlebois R (ed), Organization of the Prokaryotic Genome. ASM Press, Washington, DC. doi: 10.1128/9781555818180.ch9
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Image of FIGURE 3
FIGURE 3

Transposons as regions of portable homology. Transposons are represented as rectangles, with arrows indicating the relative orientations of the insertions. Homologous recombination between insertions in the direct-repeat configuration deletes one copy of the transposon and the markers in between. Recombination between inverted repeats causes inversion of one copy of the transposon and the markers in between.

Citation: Chalmers R, Blot M. 1999. Insertion Sequences and Transposons, p 151-169. In Charlebois R (ed), Organization of the Prokaryotic Genome. ASM Press, Washington, DC. doi: 10.1128/9781555818180.ch9
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Image of FIGURE 4
FIGURE 4

Precise and nearly precise excision. (Middle) A transposon insertion is shown as a rectangle flanked by 5-bp direct repeats of target site duplications. (Top) Precise excision restores the locus to wild type by the deletion of the transposon and one of the 5-bp target site repeats. (Bottom) Nearly precise excision leaves behind remnants of the transposon and both of the target duplications. Nearly precise excision can go on to give precise excisions.

Citation: Chalmers R, Blot M. 1999. Insertion Sequences and Transposons, p 151-169. In Charlebois R (ed), Organization of the Prokaryotic Genome. ASM Press, Washington, DC. doi: 10.1128/9781555818180.ch9
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Image of FIGURE 5
FIGURE 5

Intramolecular replicative transposition. The ends of the transposon are represented as interrupted half boxes on either side of transposon markers AB. An arbitrary target site is located between CD and EF. Following strand transfer, replication of the transposon sequences results in deletions and inversions. Symbols: half boxes, transposon ends; circles, 5′ phosphate groups; triangles, 3′ hydroxyl groups.

Citation: Chalmers R, Blot M. 1999. Insertion Sequences and Transposons, p 151-169. In Charlebois R (ed), Organization of the Prokaryotic Genome. ASM Press, Washington, DC. doi: 10.1128/9781555818180.ch9
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Image of FIGURE 6
FIGURE 6

Inside-out transposition, dimer donors, and cryptic ends. (A) The IS elements on the left (L) and right (R) of a composite transposon are represented as rectangles, with arrows indicating their relative orientations. The transposon carries the unique sequences XYZ, and an arbitrary target site is located between markers DEF and GHI. During inside-out transposition, the innermost pair of ends from the IS elements are cleaved and transferred to the target site. The cleavage step always deletes the transposon sequences XYZ. Strand transfer produces either deletions or inversions, depending on the orientation of the target. A target site on a different DNA molecule would produce a replicon fusion (not shown). (B) A replicon with a single IS element will have multiple ends available if it exists as a dimer. If opposite ends of the sister IS elements are used for transposition, cleavage will delete half of the dimer and yield an intermediate, almost identical to inside-out transposition. Strand transfer will likewise produce deletions, inversions, and replicon fusions (not shown). (С) A cryptic transposon end (half box) may be present in the correct location and orientation with respect to one of the transposon ends.

Citation: Chalmers R, Blot M. 1999. Insertion Sequences and Transposons, p 151-169. In Charlebois R (ed), Organization of the Prokaryotic Genome. ASM Press, Washington, DC. doi: 10.1128/9781555818180.ch9
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Image of FIGURE 7
FIGURE 7

Bimolecular synapsis. Transposon ends are represented as open and solid half boxes to distinguish the left and right ends, respectively. An arbitrary intramolecular target site is illustrated, flanked by markers ABC and DEF. After the transposon sequences have been duplicated by the passage of a replication fork, transposase cleaves at the opposite ends of each of the sister elements. If the target site is on a different DNA molecule, the strand transfer product is a cointegrate (left side of figure). If the target site is intramolecular, the products are replicative deletions or replicative inversions, depending on the relative orientations of the ends and the target site. Open circle, potential target site; solid circle, actual target site used.

Citation: Chalmers R, Blot M. 1999. Insertion Sequences and Transposons, p 151-169. In Charlebois R (ed), Organization of the Prokaryotic Genome. ASM Press, Washington, DC. doi: 10.1128/9781555818180.ch9
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