H-NS cooperative binding to high-affinity sites in a regulatory element results in transcriptional silencing

Nat Struct Mol Biol. 2007 May;14(5):441-8. doi: 10.1038/nsmb1233. Epub 2007 Apr 15.


H-NS is a protein of the bacterial nucleoid involved in DNA compaction and transcription regulation. In vivo, H-NS selectively silences specific genes of the bacterial chromosome. However, many studies have concluded that H-NS binds sequence-independently to DNA, leaving the molecular basis for its selectivity unexplained. We show that the negative regulatory element (NRE) of the supercoiling-sensitive Escherichia coliproU gene contains two identical high-affinity binding sites for H-NS. Cooperative binding of H-NS is abrogated by changes in DNA superhelical density and temperature. We further demonstrate that the high-affinity sites nucleate cooperative binding and establish a nucleoprotein structure required for silencing. Mutations in these sites result in loss of repression by H-NS. In this model, silencing at proU, and by inference at other genes directly regulated by H-NS, is tightly controlled by the cooperativity between bound H-NS molecules.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Bacterial Proteins / metabolism*
  • Binding Sites
  • DNA-Binding Proteins / metabolism*
  • Gene Expression Regulation, Bacterial
  • Gene Silencing*
  • Mutation / physiology
  • Protein Binding
  • Regulatory Elements, Transcriptional*
  • Transcription, Genetic


  • Bacterial Proteins
  • DNA-Binding Proteins
  • H-NS protein, bacteria