Genes VII

In addition to the "simple" intermolecular transposition that results in insertion at a new site, transposons promote other types of DNA rearrangements. Some of these events are consequences of the relationship between the multiple copies of the transposon. Others represent alternative outcomes of the transposition mechanism, and they leave clues about the nature of the underlying events.

Rearrangements of host DNA may result when a transposon inserts a copy at a second site near its original location. Host systems may undertake reciprocal recombination between the two copies of the transposon; the consequences are determined by whether the repeats are the same or in inverted orientation.

Figure 15.8 illustrates the general rule that recombination between any pair of direct repeats will delete the material between them. The intervening region is excised as a circle of DNA (which is lost from the cell); the chromosome retains a single copy of the direct repeat. A recombination between the directly repeated IS1 modules of the composite transposon Tn9 would replace the transposon with a single IS1 module.

Deletion of sequences adjacent to a transposon could therefore result from a two-stage process; transposition generates a direct repeat of a transposon, and recombination occurs between the repeats. However, the majority of deletions that arise in the vicinity of transposons probably result from a variation in the pathway followed in the transposition event itself.

Figure 15.9 depicts the consequences of a reciprocal recombination between a pair of inverted repeats. The region between the repeats becomes inverted; the repeats themselves remain available to sponsor further inversions. A composite transposon whose modules are inverted is a stable component of the genome, although the direction of the central region with regard to the modules could be inverted by recombination.

Excision is not supported by transposons themselves, but may occur when bacterial enzymes recognize homologous regions in the transposons. This is important because the loss of a transposon may restore function at the site of insertion. Precise excision requires removal of the transposon plus one copy of the duplicated sequence. This is rare; it occurs at a frequency of ~10 ^V6 for Tn5 and ~10 ^V9 for Tn10. It probably involves a recombination between the 9 bp duplicated target sites.

Imprecise excision leaves a remnant of the transposon. Although the remnant may be sufficient to prevent reactivation of the target gene, it may be insufficient to cause polar effects in adjacent genes, so that a change of phenotype occurs. Imprecise excision occurs at a frequency of ~10 ^V6 for Tn10. It involves recombination between sequences of 24 bp in the IS10 modules; these sequences are inverted repeats, but since the IS10 modules themselves are inverted, they form direct repeats in Tn10.

The greater frequency of imprecise excision compared with precise excision probably reflects the increase in the length of the direct repeats (24 bp as opposed to 9 bp). Neither type of excision relies on transposon-coded functions, but the mechanism is not known. Excision is RecA-independent and could occur by some cellular mechanism that generates spontaneous deletions between closely spaced repeated sequences.