Opposed actions of regulatory proteins, DnaA and IciA, in opening the replication origin of Escherichia coli.

The opening of the three tandem 13-mers (iterons) in the replication origin (oriC) of Escherichia coli by DnaA protein, assisted by protein HU or IHF (Hwang, D. S., and Kornberg, A. (1992) J. Biol. Chem. 267, 23083-23086), represents an essential early stage in the initiation of chromosomal replication (Bramhill, D., and Kornberg, A. (1988) Cell 54, 915-918). We now show by mutational alterations of the 13-mer region that oriC function, both in vitro and in vivo, requires AT-richness in the left 13-mer and sequence specificity in the middle and right 13-mers. Interactions of DnaA protein with the middle and right 13-mers are crucial for the opening of the region. Binding of the protein to the top strand of the 13-mers appeared to maintain single-strandedness in the bottom strand. IciA protein, the inhibitor of initiation, binds the three 13-mers and blocks the opening of the region. The degrees of inhibition by IciA protein of 13-mer opening and of oriC plasmid replication observed with mutant forms of the 13-mers could be correlated with the binding affinity of IciA protein. Whereas the binding of IciA protein to the 13-mers did not affect the binding of DnaA protein to its four 9-mers boxes, interaction of DnaA protein with the 13-mers was blocked. The selective interactions of DnaA and IciA proteins with the 13-mer region appear to be components of the on/off switch that controls initiation of E. coli chromosomal replication.