DNA binding in high salt: analysing the salt dependence of replication protein A3 from the halophile Haloferax volcanii

Archaea. 2012:2012:719092. doi: 10.1155/2012/719092. Epub 2012 Sep 3.

Abstract

Halophilic archaea maintain intracellular salt concentrations close to saturation to survive in high-salt environments and their cellular processes have adapted to function under these conditions. Little is known regarding halophilic adaptation of the DNA processing machinery, particularly intriguing since protein-DNA interactions are classically salt sensitive. To investigate such adaptation, we characterised the DNA-binding capabilities of recombinant RPA3 from Haloferax volcanii (HvRPA3). Under physiological salt conditions (3 M KCl), HvRPA3 is monomeric, binding 18 nucleotide ssDNA with nanomolar affinity, demonstrating that RPAs containing the single OB-fold/zinc finger architecture bind with broadly comparable affinity to two OB-fold/zinc finger RPAs. Reducing the salt concentration to 1 M KCl induces dimerisation of the protein, which retains its ability to bind DNA. On circular ssDNA, two concentration-dependent binding modes are observed. Conventionally, increased salt concentration adversely affects DNA binding but HvRPA3 does not bind DNA in 0.2 M KCl, although multimerisation may occlude the binding site. The single N-terminal OB-fold is competent to bind DNA in the absence of the C-terminal zinc finger, albeit with reduced affinity. This study represents the first quantitative characterisation of DNA binding in a halophilic protein in extreme salt concentrations.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Adaptation, Biological*
  • Archaeal Proteins / chemistry*
  • Archaeal Proteins / genetics
  • Binding Sites
  • Chromatography, Gel / methods
  • DNA Replication
  • DNA, Archaeal / chemistry*
  • DNA, Single-Stranded / chemistry
  • DNA-Binding Proteins / chemistry*
  • DNA-Binding Proteins / genetics
  • Electrophoresis, Polyacrylamide Gel
  • Haloferax volcanii / chemistry*
  • Haloferax volcanii / genetics
  • Potassium Chloride / chemistry
  • Protein Multimerization
  • Recombinant Proteins / chemistry
  • Recombinant Proteins / genetics
  • Species Specificity
  • Trace Elements / chemistry
  • Zinc Fingers

Substances

  • Archaeal Proteins
  • DNA, Archaeal
  • DNA, Single-Stranded
  • DNA-Binding Proteins
  • Recombinant Proteins
  • Trace Elements
  • Potassium Chloride