DNA stretching by bacterial initiators promotes replication origin melting

Many replication initiators form higher-order oligomers that process host origins to promote replisome formation. In addition to dedicated duplex DNA-binding domains, cellular initiators possess AAA+ (ATPases Associated with various cellular Activities) elements that drive functions ranging from protein assembly to origin recognition. In bacteria, the AAA+ domain of the initiator DnaA has been suggested to bind single-stranded DNA formed during origin melting. Here we show crystallographically and in solution that the ATP-dependent assembly of DnaA into a spiral oligomer creates a continuous surface that allows successive AAA+ domains to bind and extend single-stranded DNA segments. The mechanism of binding is unexpectedly similar to that of RecA, a homologous recombination factor, but it differs in that DnaA promotes a nucleic acid conformation that prevents pairing of a complementary strand. These findings, combined with strand-displacement assays, indicate that DnaA melts replication origins by a direct ATP-dependent stretching mechanism. Comparative studies reveal remarkable commonalities between the approach used by DnaA to engage DNA substrates and other, nucleic acid-dependent AAA+ systems.