The topological mechanism of phage lambda integrase

Bacteriophage lambda integrase (Int) is a versatile site-specific recombina se. In concert with other proteins, it mediates phage integration into and excision out of the bacterial chromosome. Int recombines intramolecular sit es in inverse or direct orientation or sites on separate DNA molecules. Thi s wide spectrum of Int-mediated reactions has, however, hindered our unders tanding of the topology of Int recombination. By systematically analyzing t he topology of Int reaction products and using a mathematical method called tangles, we deduce a unified model for Int recombination. We find that, ev en in the absence of (-) supercoiling, all Int reactions are chiral, produc ing one of two possible enantiomers of each product. We propose that this c hirality reflects a right-handed DNA crossing within or between recombinati on sites in the synaptic complex that favors formation of right-handed Holl iday junction intermediates. We demonstrate that the change in linking numb er associated with excisive inversion with relaxed DNA is equally +2 and -2 , reflecting two different substrates with different topology but the same chirality. Additionally, we deduce that integrative Int recombination diffe rs from excisive recombination only by additional plectonemic (-) DNA cross ings in the synaptic complex: two with supercoiled substrates and one with relaxed substrates. The generality of our results is indicated by our findi ng that two other members of the integrase superfamily of recombinases, Flp of yeast and Cre of phage beta 1, show the same intrinsic chirality as lam bda Int. (C) 1999 Academic Press.