Mechanism of 6 Mediated Transcription Activation in Bacillus subtilis: Interaction with a CTD of RNA Polymerase Stabilizes 6 and Successively Facilitates the Open Complex Formation

The a CTD (C-terminal domain of the a subunit) of RNA polymerase (RNAP) is a target for transcriptional regulators. In the transcription activation at Class I, Class II, and Class III promoters of bacteria, the transcriptional regulator, binds to DNA at different sites and interacts with the a CTD to stabilize the RNAP at the promoter or it binds to the a CTD to form a prerecruitment complex that searches for its cognate binding site. This 'simple recruitment mechanism' of the transcriptional machinery at the promoter is responsible for the activation of transcription. Strikingly, in B. subtilis the binding of RNAP at the promoter stabilizes the transcriptional regulator, d at the -41 site of the promoter DNA through an interaction with its a CTD and successively facilitates the open complex formation. Two residues R293 and K294 of a CTD (equivalent to K297 and K298 of E. coli) are involved in the interactions with d and essential for the activation of transcription. R293 is responsible for the stabilization of d, while K294 is responsible for facilitating the open complex formation. Based on our data we propose a new model of transcription activation by d of B. subtilis that is similar to (its binding location and interaction with a CTD), but distinct from (the recruitment of transcription factor by RNAP at the DNA, and enhancement of the open complex formation) the model Class II promoters in bacteria.