DETERMINANTS OF SELECTIVITY IN XER SITE-SPECIFIC RECOMBINATION

A remarkable property of some DNA-binding proteins that can interact w ith and pair distant DNA segments is that they mediate their biologica l function only when their binding sites are arranged in a specific co nfiguration. Xer site-specific recombination at natural plasmid recomb ination sites (e.g., cer in ColE1) is preferentially intramolecular, c onverting dimers to monomers. In contrast, Xer recombination at the Es cherichia coli chromosomal site dif can occur intermolecularly and int ramolecularly. Recombination at both types of site requires the cooper ative interactions of two related recombinases, XerC and XerD, with a 30-bp recombination core site. The dif core site is sufficient for rec ombination when XerC and XerD are present, whereas recombination at pl asmid sites requires similar to 200 bp of adjacent accessory sequences and accessory proteins. These accessory factors ensure that recombina tion is intramolecular. Here we use a model system to show that select ivity for intramolecular recombination, and the consequent requirement for accessory factors, can arise by increasing the spacing between Xe rC- and XerD-binding sites from 6 to 8 bp. This reduces the affinity o f the recombinases for the core site and changes the geometry of the r ecombinase/DNA complex. These changes are correlated with altered inte ractions of the recombinases with the core site and a reduced efficien cy of XerC-mediated cleavage. We propose that the accessory sequences and proteins compensate for these changes and provide a nucleoprotein structure of fixed geometry that can only form and function effectivel y on circular molecules containing directly repeated sites.