FIG. 4.

RNAP at p_R interferes with open complex formation at p_RM for the wild-type (a and b) but not the D10 (c) interpromoter distance. The α subunits of RNAP are shown in white, with the N-terminal domains anchored to the β and β′ subunits of the RNAP (gray and striped regions) and the CTDs and the flexible linkers jutting away from RNAP. The p_RM promoter is on the left, and p_R is on the right. The sequences of the −10 and −35 regions are indicated for the nontemplate strand of each promoter. The spacer DNAs between the −10 and the −35 regions are shown as devoid of contacts with RNAP. (a) The −35 regions of p_R and p_RM are separated by 13 pdb. Within seconds of the addition of RNAP, an open complex forms at the p_R promoter. Proposed upstream contacts of the α-CTDs of the RNAP are shown. (b) Subsequent interaction of RNAP with p_RM in the presence of an RNAP at p_R. The RNAP at p_R obstructs upstream access by the α-CTDs of the RNAP at p_RM. (c) The −35 regions of p_R and p_RM are separated by 2 bp. This closer-in arrangement allows the spacer DNAs of p_R and p_RM to be contacted by the α-CTDs of the RNAP at the other promoter, facilitating open complex formation at p_RM despite the presence of an RNAP at p_R.