Transposable genetic elements are DNA fragments containing genes that do not have a fixed location in a genome but can move from place to place within the genome, albeit with low frequency.

Transposition occurs without benefit of DNA sequence homology, but the enzymes catalyzing transposition recognize short sequences of about a half dozen nucleotides.

Transposable elements have been demonstrated in many eukaryotes, including maize, Drosophila, yeast, and bacteria. Gene transposition in eukaryotic systems presents some strong similarities to and some distinct differences from transposition in bacteria. The first major distinction is that integration and excision are distinct processes in eukaryotes. Thus, the transposable element can be isolated in free form, often as a double-strand circular DNA. Second, replication of that DNA often involves the synthesis of an RNA intermediate. Both of these properties are seen in the retroviruses of vertebrates, perhaps the most widely studied class of eukaryotic transposable elements.

There are several distinctions between bacterial transposition and other recombinational mechanisms. They include the following

1. Transposition does not require extensive DNA sequence homology. Transposition occurs normally when RecA is absent from a host, suggesting that homologous recombination events are not involved.

2. DNA synthesis is involved in bacterial transposition. Transposition always involves duplication of the target site, the short sequence (3-12 base pairs) at which the transposable element is inserted. In many instances the transposable element is itself replicated, with one copy being deposited in the new sequence and one remaining in the donor sequence.

3. Transposable elements can restructure a host chromosome. A transposable element can move from one site to another within the same chromosome, producing two homologous sequences resident in the same chromosome. Depending on whether these sequences are oriented identically or in reverse, homologous recombination between them can yield a deletion or an inversion, as shown in Figure 25.34.

4. Transposable elements can inactivate any gene into which they move (where insertion interrupts the coding sequence). Alternatively, transposable elements can activate adjacent genes (where a promoter, or transcriptional activator, might be created next to the gene). Abortive transpositional events can cause deletions or inversions in the chromosome. Insertional inactivation of genes is useful for isolating mutants defective in specific functions and for mapping genes.

Three different classes of transposable elements in bacteria, with general structures are shown in Figure 25.35.

1. Class I elements; and

2. Class II elements; and

3. Class III elements.

Table 25.4 summarizes the properties of a number of transposons and insertion sequences. Each transposon (conventionally referred to with the abbreviation Tn) and IS inserts at a specific target sequence of five or nine base pairs in the examples shown. Insertion involves a duplication of that site, and it results in two copies of the target sequence, one on each side of the integrated element (Figure 25.36). It seems likely that this results from the action of transposase, which generates a staggered cut that brackets the target sequence. Attachment of the mobile element to each end results in gaps, which are then filled and ligated to generate the flanking direct repeats.

The transposable element never exists as free linear DNA. The currently favored model to explain how the ends of the element are generated to join with the ends of the staggered cut of the target sequence is shown in Figure 25.37. It involves the following steps:

1. The transposase introduces both the staggered cuts in the target site and a nick at each of the 3' ends of the element, precisely between the transposon sequence and the flanking direct repeat.

2. The free 5' ends in the recipient DNA target sequence are joined to the 3' ends of the element. Two outcomes are then possible.

3a. In simple transposition the joining is followed by cutting of the 5' ends of the transposon, also immediately adjacent to the flanking sequences. This gives a gapped structure like that shown in Figure 25.36, which can be filled and closed by DNA polymerase and ligase. In this form of transposition, only the target sequence is copied; the donor chromosome suffers a lethal double-strand break. Tn10 transposes by a conservative mechanism, with both original strands somehow transferred to the new location.

3b. The other process, replicative transposition, requires the enzyme resolvase, so it occurs only with class II and class III elements. The 3' ends of the target chromosome, after the first cutting and splicing, serve as replicative primers for copying both the gaps (Figure 25.37) and the two strands of the transposable element itself. Ligase action generates a cointegrate, a large circular structure containing both donor and target chromosomes with two freshly replicated copies of the transposable element. The other enzyme, resolvase, catalyzes site-specific recombination between the two elements, resulting in one copy of the transposable element inserted into each of the two chromosomes.