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

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Abstract
Two distinct classes of RNA polymerase sigma factors (σ) exist in bacteria and are largely unrelated in primary amino acid sequence and their modes of transcription activation. Using tethered iron chelate (Fe‐BABE) derivatives of the enhancer‐dependent σ54, we mapped several sites of proximity to the β and β′ subunits of the core RNA polymerase. Remarkably, most sites localized to those previously identified as close to the enhancer‐independent σ70 and σ38. This indicates a common use of sets of sequences in core for interacting with the two σ classes. Some sites chosen in σ54 for modification with Fe‐BABE were positions, which when mutated, deregulate the σ54–holoenzyme and allow activator‐independent initiation and holoenzyme isomerization. We infer that these sites in σ54 may be involved in interactions with the core that contribute to maintenance of alternative states of the holoenzyme needed for either the stable closed promoter complex conformation or the isomerized holoenzyme conformation associated with the open promoter complex. One site of σ54 proximity to the core is apparently not evident with σ70, and may represent a specialized interaction.