Coupled energetics of λ cro repressor self-assembly and site-specific DNA operator binding II:: Cooperative interactions of cro dimers

The bacteriophage lambda relies on interactions of the cI and cro repressors which self assemble and bind the two operators (O-R and O-L) of the phage genome to control the lysogenic to lytic switch. While the self assembly and OR binding of cI have been investigated in detail, a more complete understanding of gene regulation by phage lambda also requires detailed knowledge of the role of cro repressor as it dimerizes and binds at O-R sites. Since dimerization and operator binding are coupled processes, a full elucidation of the regulatory energetics in this system requires that the equilibrium constants for dimerization and cooperative binding be determined. The dimerization constant for cro has been measured as a prelude to these binding studies. Here, the energetics of cro binding to O-R, are evaluated using quantitative DNaseI footprint titration techniques. Binding data for wild-type and modified O-R site combinations have been simultaneously analyzed in concert with the dimerization energetics to obtain both the intrinsic and cooperative DNA binding energies for cro with the three O-R ,sites. Binding of cro dimers is strongest to O(R)3, then O(R)1 and lastly, O(R)2. Adjacently bound repressors exhibit positive cooperativity ranging from -0.6 to -1.0 kcal/mol. Implications of these, newly resolved, energetics are discussed in the framework of a dynamic model for gene regulation. This characterization of the DNA-binding properties of cro repressor establishes the foundation on which the system can be explored for other, more complex, regulatory elements such as cI-cro cooperativity. (C) 2000 Academic Press.