DNA stretching by bacterial initiators promotes replication origin opening

• Published in: Nature (London) Vol. 478; no. 7368; pp. 209 - 213
• Main Authors: Duderstadt, Karl E., Chuang, Kevin, Berger, James M.
• Format: Journal Article
• Language: English
• Published: London Nature Publishing Group UK 13-10-2011; Nature Publishing Group
• Subjects: 631/337/151; 631/45/535; Adenosine Triphosphatases - metabolism; Adenosine Triphosphate - metabolism; Amino acids; AT Rich Sequence; ATP; Bacteria; Bacteria - enzymology; Bacteria - genetics; Bacterial Proteins - chemistry; Bacterial Proteins - metabolism; Bacteriology; Biocatalysis; Biological and medical sciences; Comparative studies; Crystal structure; Crystallography, X-Ray; Data collection; Deoxyribonucleic acid; DNA; DNA Replication; DNA, Bacterial - chemistry; DNA, Bacterial - genetics; DNA, Bacterial - metabolism; DNA, Single-Stranded - chemistry; DNA, Single-Stranded - genetics; DNA, Single-Stranded - metabolism; DNA-Binding Proteins - chemistry; DNA-Binding Proteins - metabolism; DNA-Directed DNA Polymerase - metabolism; E coli; Fundamental and applied biological sciences. Psychology; Genetics; Humanities and Social Sciences; Microbiology; Models, Molecular; Molecular Conformation; multidisciplinary; Multienzyme Complexes - metabolism; Nucleic Acid Conformation; Nucleic Acid Denaturation; Nucleic acids; Proteins; Rec A Recombinases - chemistry; Replication Origin - genetics; Science; Science (multidisciplinary); Substrate Specificity; Replication origin; Bacteria; Replication; DNA; Stretching
• ISSN: 0028-0836; 1476-4687; 1476-4687
• DOI: 10.1038/nature10455

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.
DNA initiation at a stretch
DNA replication initiates locations known as origins. One feature of bacterial origins is an AT-rich sequence known as a DNA unwinding element (DUE) that is melted to allow assembly of the replisome. DnaA is an AAA+ ATPase involved in the initiation of replication. Although it was thought that the energy of ATP hydrolysis was used to disrupt base pairing of the DUE, Berger and colleagues now show that the ATPase activity of DnaA helps it to assemble as a spiral filament that opens and extends single-stranded DNA. Although this extension of DNA by a filament is surprisingly similar to the early steps in homologous pairing by RecA protein, the DNA stretched by DnaA is inaccessible to base pairing with a complementary strand.