Integrases

Integrases are enzymes that catalyze site-specific recombination between defined DNA sequences, enabling the integration or excision of DNA segments within genomes. They are a subset of recombinases that recognize short attachment sites, such as attP, attB, attL, and attR in phage-bacterium systems, and they play a central role in viral lysogeny and horizontal gene transfer. The two major families are tyrosine recombinases and serine recombinases. Tyrosine integrases include the bacteriophage lambda integrase (Int) and require accessory proteins to control reaction direction (e.g., excision vs integration). Serine integrases, such as Bxb1, phiC31, and related enzymes, typically catalyze recombination via a concerted four-strand exchange and are often unidirectional, frequently not requiring host cofactors for activity in engineered contexts.

Mechanistically, tyrosine integrases perform recombination through sequential cleavage and exchange of DNA strands using a catalytic tyrosine, with directionality influenced by auxiliary factors such as excisionase or host DNA-bending proteins. Serine integrases cut all four DNA termini simultaneously, form covalent protein-DNA intermediates, and rejoin ends to complete the exchange; many operate in a predominantly irreversible, site-specific manner, especially in heterologous systems.

In nature, integrases mediate the integration of phage genomes into bacterial chromosomes during lysogeny and can excise when lytic cycles are induced. In biotechnology and medicine, they are harnessed to insert transgenes into predefined genomic loci, reducing position effects and improving stability. PhiC31 and Bxb1 integrases are widely used for mammalian genome engineering; lambda integrase has been employed in prokaryotic systems and specialized workflows to couple integration with controlled excision.

Limitations include restricted target site availability, potential off-target recombination, and delivery challenges for therapeutic applications. Ongoing research aims to expand att-site repertoires, improve specificity and efficiency, and combine integrases with other genome-editing tools for precise, safe genome modification.