title: DNA stretching by bacterial initiators promotes replication origin opening.
abstract: Many replication initiators form higher-order oligomers that process host replication 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 proposed to assist in single-stranded DNA formation during origin melting. Here we show crystallographically and in solution that the ATP-dependent assembly of Aquifex aeolicus 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 opens replication origins by a direct ATP-dependent stretching mechanism. Comparative studies reveal notable commonalities between the approach used by DnaA to engage DNA substrates and other, nucleic-acid-dependent, AAA+ systems.
authors.affiliation: Biophysics Graduate Group, University of California, Berkeley, Berkeley, California 94720, USA.
authors.forename: Karl E
authors.initials: KE
authors.lastname: Duderstadt
authors.forename: Kevin
authors.initials: K
authors.lastname: Chuang
authors.forename: James M
authors.initials: JM
authors.lastname: Berger
mesh_terms: D020856:AT Rich Sequence; D000251:Adenosine Triphosphatases / Q000378:metabolism; D000255:Adenosine Triphosphate / Q000378:metabolism; D001419:Bacteria / Q000201:enzymology / Q000235:genetics; D001426:Bacterial Proteins / Q000737:chemistry / Q000378:metabolism*; D055162:Biocatalysis; D018360:Crystallography, X-Ray; D004261:DNA Replication; D004269:DNA, Bacterial / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism*; D004277:DNA, Single-Stranded / Q000737:chemistry / Q000235:genetics / Q000378:metabolism; D004268:DNA-Binding Proteins / Q000737:chemistry / Q000378:metabolism*; D004259:DNA-Directed DNA Polymerase / Q000378:metabolism; D008958:Models, Molecular; D008968:Molecular Conformation; D009097:Multienzyme Complexes / Q000378:metabolism; D009690:Nucleic Acid Conformation; D009691:Nucleic Acid Denaturation; D011938:Rec A Recombinases / Q000737:chemistry; D018741:Replication Origin / Q000235:genetics; D013379:Substrate Specificity; D000099272:Replisomes
chemical_list: D000251:Adenosine Triphosphatases; D000255:Adenosine Triphosphate; D001426:Bacterial Proteins; D004269:DNA, Bacterial; D004277:DNA, Single-Stranded; D004268:DNA-Binding Proteins; D004259:DNA-Directed DNA Polymerase; D009097:Multienzyme Complexes; D011938:Rec A Recombinases; D000099272:Replisomes; C066312:DnaA protein, Bacteria