Dual regulation of open-complex formation and promoter clearance by Arc explains a novel repressor to activator switch

In studies of variants of the P-ant promoter of bacteriophage P22, the Arc protein was found not only to slow the rate at which RNA polymerase forms open complexes but also to accelerate the rate at which the enzyme clears the promoter, These dual activities permit Are, bound at a single operator subsite, to act as an activator or as a repressor of different promoter variants, For example, Arc activates a P-ant variant for which promoter clearance is rate limiting in the presence and absence of Are but represses a closely related variant for which open-complex formation becomes rate limiting in the presence of Are. The acceleration of promoter clearance by Arc requires occupancy of the operator subsite proximal to the -35 region and is diminished when Are bears a mutation in Arg-23, a residue that makes a DNA-backbone contact in the operator complex.