Development of RNA polymerase-promoter contacts during open complex formation

We have charted the movements of E σ 32 RNA polymerase at the heat-shock promoter P groE throughout open complex formation, using hydroxyl radical footprinting. In combination with methylation protection and DNase I experiments, these data suggest the following model for open complex formation. E σ 32 initially anchors itself in the upstream region of the promoter forming the first closed complex, RP C1; in this complex the enzyme makes backbone contacts in the −35 region of the promoter that are maintained throughout open complex formation. An isomerization follows resulting in a second closed complex, RP C2; in this complex the enzyme makes base-specific and backbone contacts in the −10 region that are almost identical to those found in the open complex. Thus, at the groE promoter, upstream contacts are established in RP c1 and downstream contacts in RP c2. A similar pattern of backbone contacts was obtained for E σ 32 bound in the open complex at two additional heat-shock promoters, suggesting that the overall topology of holoenzyme in the open complex is similar regardless of sequence variations in the promoter.