A perspective on the enhancer dependent bacterial RNA polymerase

Abstract

Here we review recent findings and offer a perspective on how the major variant RNA polymerase of bacteria, which contains the sigma54 factor, functions for regulated gene expression. We consider what gaps exist in our understanding of its genetic, biochemical and biophysical functioning and how they might be addressed.

Keywords: AAA+ ATPase; RNA polymerase; Sigma54; transcription.

Figure 1

Domain organisation of Escherichia coli σ⁵⁴. The DNA binding function is mainly associated with σ⁵⁴ Region III, including the DNA crosslinking motif (Xlink), a putative helix-turn-helix motif (HTH) for −12 recognition via E378 and the RpoN box for −24 binding. Structures of two σ⁵⁴ Region III fragments have been obtained (PDB entries: 2K9L and 2O8K).

Figure 2

Domain architecture and the proposed mechanism of activation. (A) Cryo-EM reconstitution of the Eσ⁵⁴-PspF-ADP-AlF_x with the promoter DNA modelled in [21]; (B) Domain movements of σ⁵⁴ Regions I and III during the transcription activation cycle (modified from [24]). The white stars depict fluorophores used in the smFRET experiments.