DNA Recombination:- Transposable Genetic Elements Move from One Location to Another
We now consider the third general type of recombination system: recombination that allows the movement of transposable elements, or transposons. These segments of DNA, found in virtually all cells, move, or “jump,” from one place on a chromosome (the donor site) to another on the same or a different chromosome (the target site). DNA sequence homology is not usu ally required for this movement, called transposition; the new location is determined more or less randomly. Insertion of a transposon in an essential gene could kill the cell, so transposition is tightly regulated and usually very infrequent. Transposons are perhaps the simplest of molecular parasites, adapted to replicate passively within the chromosomes of host cells. In some cases, they carry genes that are useful to the host cell, and thus exist in a kind of symbiosis with the host. Bacteria have two classes of transposons. Insertion sequences (simple transposons) contain only the sequences required for transposition and the genes for proteins (transposases) that promote the process. Complex transposons contain one or more genes in addition to those needed for transposition. These extra genes might, for example, confer resistance to antibiotics and thus enhance the survival chances of the host cell. The spread of antibiotic-resistance elements among disease-causing bacterial populations that is rendering some antibiotics ineffectual is mediated in part by transposition. Bacterial transposons vary in structure, but most have short repeated sequences at each end that serve as binding sites for the transposase. When transposition occurs, a short sequence at the target site (5 to 10 bp) is duplicated to form an additional short repeated sequence that flanks each end of the inserted transposon (Fig. 1). These duplicated segments result from the cutting mechanism used to insert a transposon into the DNA at a new location. There are two general pathways for transposition in bacteria. In direct or simple transposition (Fig. 2, left), cuts on each side of the transposon excise it, and the transposon moves to a new location. This leaves a double-strand break in the donor DNA that must be repaired. At the target site, a staggered cut is made (as in Fig. 2), the transposon is inserted into the break, and DNA replication fills in the gaps to duplicate the target site sequence. In replicative transposition (Fig. 2, right), the entire transposon is replicated, leaving a copy behind at the donor location. A cointegrate is an intermediate in this process, consisting of the donor region covalently linked to DNA at the target site. Two complete copies of the transposon are present in the cointegrate, both having the same relative orientation in the DNA. In some well-characterized transposons, the cointegrate intermediate is converted to products by site-specific recombination, in which specialized recombinases promote the required deletion reaction.
Eukaryotes also have transposons, structurally similar to bacterial transposons, and some use similar trans position mechanisms. In other cases, however, the mechanism of transposition appears to involve an RNA intermediate. Evolution of these transposons is inter twined with the evolution of certain classes of RNA viruses. Both are described in the next chapter.
FIGURE 1 Duplication of the DNA sequence at a target site when a transposon is inserted. The duplicated sequences are shown in red. These sequences are generally only a few base pairs long, so their size (compared with that of a typical transposon) is greatly ex aggerated in this drawing.
FIGURE 2 Two general pathways for transposition: direct (simple) and replicative. 1 The DNA is first cleaved on each side of the transposon, at the sites indicated by arrows. 2 The liberated 3 hydroxyl groups at the ends of the transposon act as nucleophiles in a direct attack on phosphodiester bonds in the target DNA. The target phosphodiester bonds are staggered (not directly across from each other) in the two DNA strands. 3 The transposon is now linked to the target DNA. In direct transposition, replication fills in gaps at each end. In replicative transposition, the entire transposon is replicated to create a cointegrate intermediate. 4 The cointegrate is often resolved later, with the aid of a separate site-specific recombination system. The cleaved host DNA left behind after direct transposition is either repaired by DNA end-joining or degraded (not shown). The latter outcome can be lethal to an organism.
