Sequences within the DNA cross-linking patch of sigma(54) involved in promoter recognition, sigma isomerization, and open complex formation

The bacterial RNA polymerase holoenzyme containing the sigma(54) subunit fu nctions in enhancer-dependent transcription. Mutagenesis has been used to p robe the function of a sequence in the sigma(54) DNA binding domain that in cludes residues that cross-link to promoter DNA. Several activities of the sigma and holoenzyme are shown to depend on the cross linking patch. The pa tch contributes to promoter binding by sigma(54), and holoenzyme and is inv olved in activator-dependent sigma isomerization, As part of the sigma(54)- holoenzyme, some residues in the patch limit basal transcription. Other cro ss-linking patch sequences appear to limit activator-dependent open complex formation. Deletion of 19 residues adjacent to the cross-linking patch res ulted in a holoenzyme unable to respond to activator but capable of activat or-independent (bypass) transcription in vitro. Overall results are consist ent with the cross-linking patch directing interactions to the -12 promoter region to set basal and activated levels of transcription.