Phage-encoded Serine Integrases and Other Large Serine Recombinases

Conservative site-specific recombination systems are ubiquitous in bacteria, where they play important roles in the horizontal transfer of genetic information, genome stability, and the control of gene expression. The outcomes of site-specific recombination are DNA integration, DNA excision (sometimes referred to as resolution), and DNA inversion. The systems comprise a recombinase, the sequence specific DNA substrates, and any accessory factors that are required for control. There are two evolutionarily and mechanistically different families of site-specific recombinases, the tyrosine and serine recombinases (1). All types of recombination outcomes are mediated by recombinases from both families. In the serine recombinase family there is a clear division between the resolvase/invertases and the enzymes that mediate integration/excision. The resolvase/invertases are approximately 180 to 200 amino acid proteins and are increasingly referred to as the small serine recombinases. The (pro)phage-encoded serine integrases, the transposases, such as those from clostridial ICE elements, Tn4451 and Tn5397, and the recombinases from the staphylococcal cassette chromosomes (SCC) elements are between 400 and 700 amino acids and are collectively known as the large serine recombinases (LSRs) (2). The first LSRs to be studied in in vitro recombination systems were the integrases from the Streptomyces phage, ɸC31 (3) and mycobacteriophage Bxb1 (4). Understanding the mechanism of the LSRs, however, was greatly hindered by the lack of structural information. In a breakthrough paper, Rutherford et al. published the structure of the large C-terminal domain (CTD) of a serine integrase bound to one half site of one substrate (5). This work has led to a step change in our understanding of the mechanism of the serine integrases (6, 7).