Conservative Site-specific Recombination and Phase Variation

Site-specific recombination is a type of genetic exchange where specialized enzymes called site-specific recombinases catalyze the movement of DNA sections between defined sites that share some sequence homology.

When movements such as these occur, the regions to be exchanged are typically flanked by a pair of symmetric sequences comprised of double-stranded DNA of around 20 to 30 base-pairs long.

The specialized enzymes called recombinases that bind to these sequences can belong to Serine or Tyrosine recombinase families. The families have either a serine or a tyrosine residue at the active site of the enzyme and employ distinct mechanisms.

In the case of serine recombinase, the subunits first specifically bind to their novel recognition sequences, forming a synaptic complex. Then, the active site serine attacks the phosphodiester DNA backbone at the center of these sequences creating break-points known as crossover sites.

Next, serine recombinases will cut all involved DNA helices before strand exchange proceeds.

In contrast, Tyrosine recombinases bind in the same manner, but cut and join one strand of the DNA duplex at a time. The Tyrosine residue then covalently bonds with the 3’ end of the cleaved strand while the free 5’ hydroxyl groups attack the protein-DNA bond, forming a Holliday junction intermediate.

This complex pattern is the first crossover event. Then, when the remaining DNA strands are cleaved and exchanged by the recombinase subunits in the second event, the Holliday junction is resolved to the recombinant products.

There are three potential outcomes of recombination events like these. 

The first is integration, in which a circular DNA molecule gets inserted into a second, linear DNA.

When both the sites are on the same DNA molecule the second outcome might be excision, where the part of the DNA cut out is simply removed, free to integrate elsewhere in the genome. 

In the third scenario, if the incision sites are in opposite orientations inversion can occur - where the section of DNA is removed and then re-integrated in the opposite orientation.

A well-studied example of this phenomenon is the site-specific inversion of a chromosomal segment of the bacterium Salmonella, which allows it to produce two different types of the protein flagellin depending on the environment, and this process is called Phase variation.