Site-Specific Recombination Occurs at Specific DNA Sequences in the Target DNA
Conservative site-specific recombination (CSSR) is responsible for many reactions in which a defined segment of DNA is rearranged. A key feature of these reactions is that the segment of DNA that will be moved carries specific short sequence elements, called recombination sites, where DNA exchange occurs. An example of this type of recombination is the integration of the phage X genome into the bacteria] chromosome (Figure 11-2 and Chapter 21).
During X integration, recombination always occurs at exactly the same nucleotide sequence within two recombination sites, one on the phage DNA, and the other on the bacterial DNA. Recombination sites
FIGURE 11-2 Integration of the X genome into the chromosome of the host cell. DNA exchange occurs specifically between the recombination sites on the two DNA molecules. The relative lengths of the A and cellular chromosomes are not shown to scale.
phage recombination site bacterial-re combination ate phage recombination site bacterial-re combination ate
Conservative Site-Spticip'c Reconxbinatitifi carry two clashes of sequence elements; sequences specifically bound by the recombinases, and sequences where DNA cleavage and rejoining occur. Recombination sites are often quite short, 20 bp or so, although they may be much longer and carry additional sequences bound by proteins. Examples of the more complex recombination sites are discussed when we consider specific recombination reactions.
CSSR can generate three different types of DNA rearrangements (Figure 11-3): (1) insertion of a segment of UNA into a specific site (as occurs during phage X UNA integration); (2) deletion of a DNA segment; or (3) inversion of a DNA segment. Whether recombination results in DNA insertion, deletion, or inversion depends on the organization of the recombination recognition sites on the DNA molecule or molecules that participate in recombination.
To understand how the organization of recombination sites determines the type of DNA rearrangement, we must louk at the sequence elements within the recombination sites in more detail (Figure 11-4). Each recombination site is organized as a pair of recombinase recognition sequences, positioned symmetrically. These recognition sequences flank a central short asymmetric sequence, known as the crossover region, where DNA cleavage and rejoining occurs.
Because the crossover region is asymmetric, a given recombination site always has a defined polarity. The orientation of two sites present on a single DNA molecule will be related to each other either in an inverted repeat or a direct repeat manner. Recombination between a pair oi inverted sites will invert the DNA segment between the two sites (Figure lt-3, right panel}. En contrast, recombination using the identical mechanism but uccuring between sites organized as direct repeats deletes the DNA segment between the two sites. Finally, insertion specifically occurs when recombination sites on two different molecules are brought together lor DNA exchange. Examples of each of these three types of rearrangements will be considered below, after a general discussion of the recombinases.
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FIGURE 11-3 Three types of CSSR recombination. In each ease, it is the ted segment of ONA that is moved or rearranged during recombinat>on. a B, X, and V denote genes that lie within the different segments of DNA itie darter red end blue boxes are the recombinase recognition sequences and the black arrows are the crossover regions. These sequence elements together form (he recombination sites
FIGURE 11-4 Structures involved in C5SR- The pair of symmetric recombinase récognition sequences flank the crossover region wftere recombination occurs The submits of the recombinase bind these recognition sites. Notice that the sequence of the crossover region is not palindromic, resulting in an intrinsic asymmetry to the recombination sites. (Source: Fran Craig N. et al. 2002. Mobile DNA II. p.4,iVÊ 2002 ASM Press)
1 r recombinase recognition sequences crossover region
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