Topological nuts and bolts

Geometry of site alignment during int family recombination: antiparallel synapsis by the Flp recombinase

The Flp site-specific recombinase functions in the copy number amplification of the yeast 2 microm plasmid. The recombination reaction is catalyzed by four monomers of Flp bound to two separate, but identical, recombination sites (FRT sites) and occurs in two sequential pairs of strand exchanges. The relative orientation of the two recombination sites during synapsis was examined. Topoisomerase relaxation and nick ligation were used to detect topological nodes introduced by the synapse prior to the chemical steps of recombination. A single negative supercoil was found to be trapped by Flp in substrates with inverted FRT sites whereas no trapped supercoils were observed with direct repeats. The topology of products resulting from Flp-mediated recombination adjacent to a well characterised synapse, that of Tn3 resolvase/res, was analyzed. The deletion and inversion reactions yielded the four noded catenane and the three noded knot, respectively, as the simplest and the most abundant products. The linking number change introduced by the Flp-mediated inversion reaction was determined to be +/-2. The most parsimonious explanation of these results is that Flp aligns its recombination sites with antiparallel geometry. The majority of synapses appear to occur without entrapment of additional random plectonemic DNA supercoils between the sites and no additional crossings are introduced as a result of the chemical steps of recombination.

The integrase family of recombinase: organization and function of the active site

The integrase family of site-specific recombinases (also called the tyrosine recombinases) mediate a wide range of biological outcomes by the sequential exchange of two pairs of DNA strands at defined phosphodiester positions. The reaction produces a recombinant arrangement of the DNA sequences flanking the cross-over region. The crystal structures of four integrase family members have revealed very similar three-dimensional protein folds that belie the large diversity in amino acid sequences among them. The active sites are similar in organization to those seen in structures of eukaryotic type IB topoisomerases, and conservation of catalytic mechanism is expected. The crystal structures, combined with previous biochemical knowledge, allow the refinement of models for recombination and the assignment of catalytic function to the active site residues. However, each system has its own peculiarities, and the exact sequence of events that allows the reaction to proceed from the first exchange reaction to the second is still unclear for at least some family members.