Versatility of the carboxy-terminal domain of the α subunit of RNA polymerase in transcriptional activation: use of the DNA contact site as a protein contact site for MarA

Summary The transcriptional activator, MarA, interacts with RNA polymerase (RNAP) to activate promoters of the mar regulon. Here, we identify the interacting surfaces of MarA and of the carboxy-terminal domain of the α subunit of RNAP (α-CTD) by NMR-based chemical shift mapping. Spectral changes were monitored for a MarA-DNA complex upon titration with α-CTD, and for α-CTD upon titration with MarA-DNA. The mapping results were confirmed by mutational studies and retention chromatography. A model of the ternary complex shows that α-CTD uses a ‘265-like determinant’ to contact MarA at a surface distant from the DNA. This is unlike the interaction of α-CTD with the CRP or Fis activators where the ‘265 determinant’ contacts DNA while another surface of the same α-CTD molecule contacts the activator. These results reveal a new versatility for α-CTD in transcriptional activation.