Control of Cre recombination by regulatory elements from Xer recombination systems

<jats:title>Summary</jats:title><jats:p>Site‐specific recombination by the Cre recombinase takes place at a simple DNA site (<jats:italic>loxP</jats:italic>), requires no additional proteins and gives topologically simple recombination products. In contrast, <jats:italic>cer</jats:italic> and <jats:italic>psi</jats:italic> sites for Xer recombination contain ≈ 150 bp of accessory sequences, require accessory proteins PepA, ArgR and ArcA, and the products are specifically linked to form a four‐noded catenane. Here, we use hybrid sites consisting of accessory sequences of <jats:italic>cer</jats:italic> or <jats:italic>psi</jats:italic> fused to <jats:italic>loxP</jats:italic> to probe the function of accessory proteins in site‐specific recombination. We show that PepA instructs Cre to produce four‐noded catenane, but is not required for recombination at these hybrid sites. Mutants of Cre that require PepA and accessory sequences for efficient recombination were selected. PepA‐dependent Cre gave products with a specific topology and displayed resolution selectivity. Our results reveal that PepA acts autonomously in the synapsis of <jats:italic>psi</jats:italic> and <jats:italic>cer</jats:italic> accessory sequences and is the main architectural element responsible for intertwining accessory site DNA. We suggest that accessory proteins can activate recombinases simply by synapsing the regulatory DNA sequences, thus bringing the recombination sites together with a specific geometry. This may occur without the need for protein–protein interactions between accessory proteins and the recombinases.</jats:p>