Characterization of a transitionally occupied state and thermal unfolding of domain 1.1 of σ A factor of RNA polymerase from Bacillus subtilis

Abstract

$\sigma$ factors are essential parts of bacterial RNA polymerase (RNAP) as they allow to recognize promotor sequences and initiate transcription. Domain 1.1 of vegetative $\sigma$ factors occupies the primary channel of RNAP and also prevents binding of the $\sigma$ factor to promoter DNA alone. Here, we show that domain 1.1 of Bacillus subtilis ${\sigma }^A$ exists in more structurally distinct variants in dynamic equilibrium. The major conformation at room temperature is represented by a previously reported well-folded structure solved by nuclear magnetic resonance (NMR), but 4% of the protein molecules are present in a less thermodynamically favorable state. We show that this population increases with temperature and we predict its significant elevation at higher but still biologically relevant temperatures. We characterized the minor state of the domain 1.1 using specialized methods of NMR. We found that, in contrast to the major state, the detected minor state is partially unfolded. Its propensity to form secondary structure elements is especially decreased for the first and third $\alpha$ helices, while the second $\alpha$ helix and $\beta$ strand close to the C-terminus are more stable. We also analyzed thermal unfolding of the domain 1.1 and performed functional experiments with full length ${\sigma }^A$ and its shortened version lacking domain 1.1 ( ${\sigma }^{A\_\Delta 1.1}$ ). The results revealed that while full length ${\sigma }^A$ increases transcription activity of RNAP with increasing temperature, transcription with ${\sigma }^{A\_\Delta 1.1}$ remains constant. In summary, this study reveals conformational dynamics of domain 1.1 and provides a basis for studies of its interaction with RNAP and effects on transcription regulation.

Keywords: σ A factor; Bacillus subtilis; NMR; RNA polymerase; conformational exchange.