σ factor selectivity of Escherichia coli RNA polymerase:: role for CRP, IHF and Lrp transcription factors

osmY is a stationary phase-induced and osmotically regulated gene in Escherichia coli that requires the stationary phase RNA polymerase (E sigma(S)) for in vivo expression. We show here that the major RNA polymerase, E sigma(70), also transcribes osmY in vitro and, depending on genetic background, even in vivo. The cAMP receptor protein (CRP) bound to cAMP, the leucine-responsive regulatory protein (Lrp) and the integration host factor (IHF) inhibit transcription initiation at the osmY promoter, The binding site for CRP is centred at -12.5 from the transcription start site, whereas Lrp covers the whole promoter region, The site for IHF maps in the -90 region. By mobility shift assay, permanganate reactivity and in vitro transcription experiments, we show that repression is much stronger with E sigma(70) than with E sigma(S) holoenzyme. We conclude that CRP, Lrp and IHF inhibit open complex formation more efficiently with E sigma(70) than with E sigma(S). This different ability of the two holoenzymes to interact productively with promoters once assembled in complex nucleoprotein structures may be a crucial factor in generating sigma(S) selectivity in vivo.