Escherichia coli low-copy-number plasmid R1 centromere parC forms a U-shaped complex with its binding protein ParR

Nucleic Acids Res. 2008 Feb;36(2):607-15. doi: 10.1093/nar/gkm672. Epub 2007 Dec 3.

Abstract

The Escherichia coli low-copy-number plasmid R1 contains a segregation machinery composed of parC, ParR and parM. The R1 centromere-like site parC contains two separate sets of repeats. By atomic force microscopy (AFM) we show here that ParR molecules bind to each of the 5-fold repeated iterons separately with the intervening sequence unbound by ParR. The two ParR protein complexes on parC do not complex with each other. ParR binds with a stoichiometry of about one ParR dimer per each single iteron. The measured DNA fragment lengths agreed with B-form DNA and each of the two parC 5-fold interon DNA stretches adopts a linear path in its complex with ParR. However, the overall parC/ParR complex with both iteron repeats bound by ParR forms an overall U-shaped structure: the DNA folds back on itself nearly completely, including an angle of approximately 150 degrees . Analysing linear DNA fragments, we never observed dimerized ParR complexes on one parC DNA molecule (intramolecular) nor a dimerization between ParR complexes bound to two different parC DNA molecules (intermolecular). This bacterial segrosome is compared to other bacterial segregation complexes. We speculate that partition complexes might have a similar overall structural organization and, at least in part, common functional properties.

MeSH terms

  • Bacterial Proteins / metabolism*
  • Bacterial Proteins / ultrastructure
  • Binding Sites
  • Centromere / chemistry
  • DNA, Bacterial / chemistry
  • DNA, Bacterial / ultrastructure*
  • Escherichia coli / genetics*
  • Escherichia coli Proteins / metabolism*
  • Escherichia coli Proteins / ultrastructure
  • Microscopy, Atomic Force
  • Nucleic Acid Conformation
  • Plasmids / genetics*
  • Repetitive Sequences, Nucleic Acid
  • Repressor Proteins / metabolism*
  • Repressor Proteins / ultrastructure

Substances

  • Bacterial Proteins
  • DNA, Bacterial
  • Escherichia coli Proteins
  • ParR protein, E coli
  • ParR protein, bacteria
  • Repressor Proteins