sigma 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 Escher ichia coil that requires the stationary phase RNA polymerase (E sigma(S)) f or in vivo expression. We show here that the major RNA polymerase, E sigma( 70), also transcribes osmY in vitro and, depending on genetic background, e ven ill vivo. The cAMP receptor protein (CRP) bound to cAMP, the leucine-re sponsive regulatory protein (Lrp) and the integration host factor (IHF) inh ibit transcription initiation at the osmY promoter, The binding site for CR P 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 mob ility shift assay, permanganate reactivity and in vitro transcription exper iments, 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 comp lex formation more efficiently with E sigma(70) than with E sigma(S). This different ability of the two holoenzymes to interact productively with prom oters once assembled in complex nucleoprotein structures may be a crucial f actor in generating sigma(S) selectivity in vivo.