Extensive DNA mimicry by the ArdA anti-restriction protein and its role in the spread of antibiotic resistance

Nucleic Acids Res. 2009 Aug;37(15):4887-97. doi: 10.1093/nar/gkp478. Epub 2009 Jun 8.

Abstract

The ardA gene, found in many prokaryotes including important pathogenic species, allows associated mobile genetic elements to evade the ubiquitous Type I DNA restriction systems and thereby assist the spread of resistance genes in bacterial populations. As such, ardA contributes to a major healthcare problem. We have solved the structure of the ArdA protein from the conjugative transposon Tn916 and find that it has a novel extremely elongated curved cylindrical structure with defined helical grooves. The high density of aspartate and glutamate residues on the surface follow a helical pattern and the whole protein mimics a 42-base pair stretch of B-form DNA making ArdA by far the largest DNA mimic known. Each monomer of this dimeric structure comprises three alpha-beta domains, each with a different fold. These domains have the same fold as previously determined proteins possessing entirely different functions. This DNA mimicry explains how ArdA can bind and inhibit the Type I restriction enzymes and we demonstrate that 6 different ardA from pathogenic bacteria can function in Escherichia coli hosting a range of different Type I restriction systems.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Amino Acid Sequence
  • Bacterial Proteins / chemistry*
  • Bacterial Proteins / genetics
  • Bacterial Proteins / metabolism
  • Crystallography, X-Ray
  • DNA / chemistry
  • DNA Restriction-Modification Enzymes / antagonists & inhibitors*
  • Deoxyribonucleases, Type I Site-Specific / antagonists & inhibitors
  • Dimerization
  • Drug Resistance, Bacterial / genetics
  • Genome, Bacterial
  • Models, Molecular
  • Molecular Mimicry*
  • Molecular Sequence Data
  • Protein Binding
  • Protein Structure, Tertiary
  • Sequence Homology, Amino Acid
  • Site-Specific DNA-Methyltransferase (Adenine-Specific) / chemistry

Substances

  • Bacterial Proteins
  • DNA Restriction-Modification Enzymes
  • DNA
  • DNA modification methylase EcoKI
  • Site-Specific DNA-Methyltransferase (Adenine-Specific)
  • Deoxyribonucleases, Type I Site-Specific