Compilation and analysis of sigma(54)-dependent promoter sequences

Nucleic Acids Res. 1999 Nov 15;27(22):4305-13. doi: 10.1093/nar/27.22.4305.

Abstract

Promoters recognized by the RNA-polymerase with the alternative sigma factor sigma(54) (Esigma54) are unique in having conserved positions around -24 and -12 nucleotides upstream from the transcriptional start site, instead of the typical -35 and -10 boxes. Here we compile 186 -24/-12 promoter sequences reported in the literature and generate an updated and extended consensus sequence. The use of the extended consensus increases the probability of identifying genuine -24/-12 promoters. The effect of several reported mutations at the -24/-12 elements on RNA-polymerase binding and promoter strength is discussed in the light of the updated consensus.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Bacteria / genetics*
  • Base Sequence
  • Consensus Sequence
  • Conserved Sequence
  • DNA, Bacterial / analysis
  • DNA, Bacterial / genetics*
  • DNA, Bacterial / metabolism
  • DNA-Binding Proteins*
  • DNA-Directed RNA Polymerases / metabolism*
  • Databases, Factual
  • Molecular Sequence Data
  • Mutation
  • Promoter Regions, Genetic / genetics*
  • Promoter Regions, Genetic / physiology
  • RNA Polymerase Sigma 54
  • Sequence Homology, Nucleic Acid
  • Sigma Factor / metabolism*
  • Transcription, Genetic

Substances

  • DNA, Bacterial
  • DNA-Binding Proteins
  • Sigma Factor
  • DNA-Directed RNA Polymerases
  • RNA Polymerase Sigma 54