Mode of promoter recognition by the Escherichia coli RNA polymerase holoenzyme containing the sigma S subunit: identification of the recognition sequence of the fic promoter.

Transcription of a number of genes during stationary phase in Escherichia coli requires the alternative sigma factor sigma S, encoded by the rpoS gene. No consensus sequence for the promoters recognized by the RNA polymerase holoenzyme containing the sigma S subunit (E sigma S) is known. To identify the E sigma S recognition sequence, we analysed the promoter region of the fic gene, whose expression depends on E sigma S both in vivo and in vitro. By random mutagenesis, we isolated a large number of the fic promoter mutants that had defective promoter activities in an rpoS+ strain. All such mutants contained alterations within the -10 region, TATACT, whereas no mutant was isolated with alterations in the -35 region. Based on further analyses including scanning mutagenesis and DNase I footprinting assays of the fic promoter region, and in vitro transcription assays, we conclude that the -10 hexamer is essential to transcription initiation from the fic promoter by E sigma S.