DNA stretching by bacterial initiators promotes replication origin opening

Nature. 2011 Oct 2;478(7368):209-13. doi: 10.1038/nature10455.

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.

Publication types

  • Research Support, N.I.H., Extramural

MeSH terms

  • AT Rich Sequence
  • Adenosine Triphosphatases / metabolism
  • Adenosine Triphosphate / metabolism
  • Bacteria / enzymology
  • Bacteria / genetics
  • Bacterial Proteins / chemistry
  • Bacterial Proteins / metabolism*
  • Biocatalysis
  • Crystallography, X-Ray
  • 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
  • Models, Molecular
  • Molecular Conformation
  • Multienzyme Complexes / metabolism
  • Nucleic Acid Conformation*
  • Nucleic Acid Denaturation
  • Rec A Recombinases / chemistry
  • Replication Origin* / genetics
  • Substrate Specificity

Substances

  • Bacterial Proteins
  • DNA, Bacterial
  • DNA, Single-Stranded
  • DNA-Binding Proteins
  • DnaA protein, Bacteria
  • Multienzyme Complexes
  • Adenosine Triphosphate
  • DNA synthesome
  • Rec A Recombinases
  • DNA-Directed DNA Polymerase
  • Adenosine Triphosphatases

Associated data

  • PDB/3R8F