β Subunit Residues 186–433 and 436–445 are Commonly Used by Eσ54 and Eσ70 RNA Polymerase for Open Promoter Complex Formation

During transcription initiation by DNA-dependent RNA polymerase (RNAP) promoter DNA has to be melted locally to allow the synthesis of RNA transcript. Localized melting of promoter DNA is a target for genetic regulation and is poorly understood at the molecular level. The Escherichia coli RNAP holoenzyme is a six-subunit (α2ββ′ωσ; Eσ) protein complex. The σ subunit is directly responsible for promoter recognition and contributes to localized DNA melting. Mutations in the β subunit have profound effects on promoter melting by Eσ70. The σ54 subunit is a representative of an unrelated class of the σ subunits. Here, we determined whether mutations in the β subunit that affect late stages of promoter complex formation by Eσ70 also influence promoter complex formation by the enhancer-dependent Eσ54. Analyses of in vitro defects in promoter complex formation and transcription initiation exhibited by mutant Eσ54 suggest that during promoter complex formation by Eσ54 and Eσ70 a common set of β subunit sequences is used. Late stages of promoter complex formation and localized melting of promoter DNA by Eσ70 and Eσ54 thus proceed through a common pathway.