Crucial roles of both flanking sequences in silencing of the hilA promoter in Salmonella enterica

J Mol Biol. 2006 Mar 24;357(2):373-86. doi: 10.1016/j.jmb.2006.01.007. Epub 2006 Jan 19.


The hilA gene on the Salmonella enterica pathogenicity island-1 encodes the key transcriptional regulator of host cell invasion. Transcription of hilA is regulated by numerous physiological signals, including repression under low osmolarity conditions. To investigate the osmotic control of hilA transcription, promoter truncations that remove sequences flanking the hilA promoter were examined. Expression of the minimal hilA core promoter (-55 to +90, relative to the transcription start site) was 57-times higher than the intact promoter (-242 to +505) in the absence of osmotic stress. Both flanking sequences contributed to the strong silencing effect, which was greatly relieved by the simultaneous loss of the two nucleoid-structuring proteins, H-NS and Hha. Mobility-shift assays revealed the presence of binding sites for the H-NS and Hha proteins, both upstream and downstream of the promoter. Either flanking region depressed expression when it was placed downstream of the lacUV5 promoter, and this inhibition was increased when the other flanking sequence was present upstream of the promoter. These results show that the hilA promoter is highly active without other transcription regulators. Its high activity is strongly depressed in low osmolarity conditions by the nucleoid-structuring proteins H-NS and Hha, possibly by formation of a repressive DNA loop. The hilA activators, HilD and HilC appear to overcome effects of downstream silencing region and disrupt repressive DNA loop. Action of activators requires contact with RNA polymerase from their DNA binding site, centered at position -77, relative to the hilA transcription start site.

Publication types

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

MeSH terms

  • Bacterial Proteins / genetics*
  • Bacterial Proteins / metabolism
  • Base Sequence*
  • DNA-Binding Proteins / genetics
  • DNA-Binding Proteins / metabolism
  • Escherichia coli Proteins / metabolism
  • Gene Silencing*
  • Molecular Sequence Data
  • Osmolar Concentration
  • Promoter Regions, Genetic*
  • Salmonella typhimurium / genetics*
  • Trans-Activators / genetics*
  • Trans-Activators / metabolism
  • Transcription, Genetic


  • Bacterial Proteins
  • DNA-Binding Proteins
  • Escherichia coli Proteins
  • H-NS protein, bacteria
  • HilA protein, Salmonella
  • Trans-Activators
  • hha protein, E coli