Cooperativity in long-range gene regulation by the λ CI repressor

Effective repression of cI transcription from P-RM by the bacteriophage gimel CI repressor requires binding sites (O-L) located 2.4 kb from the promoter. A CI tetramer bound to O(L)1.O(L)2 interacts with a tetramer bound near PRM (O(R)1.O(R)2), looping the intervening DNA. We previously proposed that in this CI octamer:DNA complex, the distant O(L)3 operator and the weak O(R)3 operator overlapping P-RM are juxtaposed so that a CI dimer at O(L)3 can cooperate with a CI dimer binding to O(R)3. Here we show that O(L)3 is necessary for effective repression of P-RM and that the repressor at O(L)3 appears to interact specifically with the repressor at O(R)3. The O(L)3-CI-O(R)3 interaction involves the same CI interface used for short-range dimer-dimer interactions and does not occur without the other four operators. The long-range interactions were incorporated into a physicochemical model, allowing estimation of the long-range interaction energies and showing the lysogenic state to be ideally poised for CI negative autoregulation. The results establish the X system as a powerful tool for examining long-range gene regulatory interactions in vivo.