FIGURE 6.

Model of DnaA box R1-mediated stabilization of IHF binding at oriC. Our findings suggest that, specifically at the stage of replication initiation, a secondary IBS (termed IBS2 in this study; sky-blue bar) overlaps with DnaA box R1, providing a new possible role for DnaA box R1 (black arrowhead). First, IHF binds to either a known IBS (IBS1; blue bar) or IBS2. When IHF binds to IBS2, DnaA cannot bind to R1; thus we hypothesize that even though oriC IBS2–IHF binding is relatively unstable, it plays a supportive role in stabilizing overall IHF binding at oriC by preventing free diffusion of IHF dissociated from oriC and promoting re-binding to oriC. When IHF binds to IBS1 with higher affinity and bends DNA, ATP–DnaA can form higher-order oligomers to initiate replication from oriC. In the initiation complex, IHF binding and bending at IBS1 is further stabilized by an ATP–DnaA oligomer, which is formed by interaction between ATP–DnaA molecules bound at R1 and another DnaA box R5 (gray arrowhead).