Conservation of sigma-core RNA polymerase proximity relationships between the enhancer-independent and enhancer-dependent sigma classes

Two distinct classes of RNA polymerase sigma factors (sigma) exist in bacte ria and are largely unrelated in primary amino acid sequence and their mode s of transcription activation. Using tethered iron chelate (Fe-BABE) deriva tives of the enhancer-dependent sigma 54, we mapped several sites of proxmi ty to the beta and beta' subunits of the core RNA polymerase. Remarkably, m ost sites localized to those previously identified as close to the enhancer -independent sigma(70) and sigma(38). This indicates a common use of sets o f sequences in core for interacting with the two sigma classes. Some sites chosen in sigma(54) for modification with Fe-BABE were positions, which whe n mutated, deregulate the sigma(54)- holoenzyme and allow activator-indepen dent initiation and holoenzyme isomerization. We infer that these sites in sigma(54) may be involved in interactions with the core that contribute to maintenance of alternative states of the holoenzyme needed for either the s table closed promoter complex conformation or the isomerized holoenzyme con formation associated with the open promoter complex. One site of sigma(54) proximity to the core is apparently not evident with sigma(70), and may rep resent a specialized interaction.