The structure and the characteristic DNA binding property of the C-terminal domain of the RNA polymerase alpha subunit from Thermus thermophilus

The C-terminal domain of the alpha subunit of the RNA polymerase (alpha CTD ) from Escherichia coli (Ec) regulates transcription by interacting with ma ny kinds of proteins and promoter upstream (UP) elements consisting of AT-r ich sequences. However, it is unclear how this system is common in all euba cteria. We investigate the structure and properties of alpha CTD from an ex tremely thermophilic eubacterium, Thermus thermophilus (Tt). The solution s tructure of Tt alpha CTD (85 amino acids) was determined by NMR, and the in teraction between Tt alpha CTD and DNA with different sequences was investi gated by means of chemical shift perturbation experiments. The tertiary str ucture of Tt alpha CTD is almost identical with that of Ec alpha CTD despit e 32% sequence homology. However, Tt alpha CTD interacts with the upstream region sequence of the promoter in the Tt 16 S ribosomal protein operon rat her than the Ec UP element DNA. The upstream region sequence of Tt is compo sed of 25 base pairs with 40% AT, unlike the Ec UP element with 80% AT. The DNA binding site in Tt alpha CTD is located on the surface composed of hel ix 4 and the loop preceding helix 4. The electric charges on this surface a re not remarkably localized like those of Ec alpha CTD.