FLP protein of 2 μ circle plasmid of yeast induces multiple bends in the FLP recognition target site

Abstract

The FLP recombinase of the 2 mu plasmid of Saccharomyces cerevisiae binds to a target containing three 13 base-pair symmetry elements called a, b and c. The symmetry elements b and c are in direct orientation while the a element is in inverted orientation with respect to b and c on the opposite side of an eight base-pair core region. Each symmetry element acts as a binding site for the FLP protein. The FLP protein can form three different complexes with the FLP recognition target (FRT site) according to the number of elements within the site that are occupied by the FLP protein. Binding of FLP to the FRT site induces DNA bending. We have measured the angles of bends caused by the binding of the FLP protein to full and partial FRT sites. We find that FLP induces three types of bend in the FRT-containing DNA. The type I bend is approximately 60 degrees and results from a molecule of FLP bound to one symmetry element. The type II bend is greater than 144 degrees and results from FLP molecules bound to symmetry elements a and b. The type III bend is approximately 65 degrees and results from FLP proteins bound to symmetry elements b and c. Certain FLP proteins that are defective in recombination can generate the type I and type III bends but are impaired in their ability to induce the type II bend. We discuss the role of bending in FLP-mediated recombination.