Genetic Recombination in Phage

Genetic Recombination in Phage

Site-specific genetic recombination is very common method in phage for exchanging the genetic material. Unlike general recombination it is guided by a recombination enzyme that recognizes specific nucleotide sequences present on one or both of the recombining DNA molecules. Base-pairing between the recombining DNA molecules need not be involved, and even when it is, the heteroduplex joint that is formed is only a few base pairs long. By separating and joining double-stranded DNA molecules at specific sites, this type of recombination enables various types of mobile DNA sequences to move about within and between chromosomes.

Site-specific recombination was first discovered as the means by which a bacterial virus, bacteriophage lambda, moves its genome into and out of the E. coli chromosome. In its integrated state the virus is hidden in the bacterial chromosome and replicated as part of the host's DNA. When the virus enters a cell, a virus-encoded enzyme called lambda integrase is synthesized. This enzyme catalyzes a recombination process that begins when several molecules of the integrase protein bind tightly to a specific DNA sequence on the circular bacteriophage chromosome. The resulting DNA-protein complex can now bind to a related but different specific DNA sequence on the bacterial chromosome, bringing the bacterial and bacteriophage chromosomes close together. 

The integrase then catalyzes the required DNA cutting and resealing reactions, using a short region of sequence homology to form a tiny heteroduplex joint at the point of union. The integrase resembles a DNA topoisomerase in that it forms a reversible covalent linkage to DNA wherever it breaks a DNA chain. The same type of site-specific recombination mechanism can also be carried out in reverse by the lambda bacteriophage, enabling it to exit from its integration site in the E. coli chromosome in order to multiply rapidly within the bacterial cell. 

This excision reaction is catalyzed by a complex of the integrase enzyme (Figure) with a second bacteriophage protein, which is produced by the virus only when its host cell is stressed. If the sites recognized by such a recombination enzyme are flipped, the DNA between them will be inverted rather than excised (Figure ). Many other enzymes that catalyze site-specific recombination resemble lambda integrase in requiring a short region of identical DNA sequence on the two regions of DNA helix to be joined.

Because of this requirement, each enzyme in this class is fastidious with respect to the DNA sequences that it recombines, and it can be expected to catalyze one particular DNA joining event that is useful to the virus, plasmid, transposable element, or cell that contains it. These enzymes can be exploited as tools in transgenic animals to study the influence of specific genes on cell behavior.

Site-specific recombination enzymes that break and rejoin two DNA double helices at specific sequences on each DNA molecule often do so in a reversible way: as for lambda bacteriophage, the same enzyme system that joins two DNA molecules can take them apart again, precisely restoring the sequences of the two original DNA molecules. This type of recombination is therefore called conservative site-specific recombination to distinguish it from the mechanistically.