Reactivation of DnaA by DNA sequence-specific nucleotide exchange in vitro

In Escherichia coli, ATP-bound DnaA protein can initiate chromosomal replication. After initiation, DnaA-ATP is hydrolyzed by interactions with a complex containing a replicase subunit to yield the inactive ADP-DnaA. However, the mechanisms which regenerate ATP-DnaA from ADP-DnaA are not well understood. We report here that a 70-bp DNA segment promotes exchange of the DnaA-bound nucleotide in a sequence-specific manner, thus reactivating the initiation function of DnaA in vitro. This segment contains a typical DnaA-binding 9-mer motif, the DnaA box, and two DnaA box-like sequences. The presence and precise composition of these three motifs are required for the DnaA-reactivating activity, which suggests that a highly ordered complex which includes multimeric DnaA molecules is formed for isomerization of DnaA. We named this DNA segment DARS, for DnaA-reactivating sequence. The role of DARS in regulation of DnaA function in vivo is discussed.