Interaction of the C-terminal domain of the E. coli RNA polymerase α subunit with the UP element: recognizing the backbone structure in the minor groove surface

The C-terminal domain of the α-subunit of Escherichia coli RNA polymerase (αCTD) is responsible for transcriptional activation through interaction with both activator proteins and UP element DNA. Previously, we determined the solution structure of αCTD. Here, we investigated the interaction between αCTD and UP element DNA by NMR. DNA titration curves and intermolecular NOE measurements indicate that αCTD can bind to multiple sites on the UP element DNA. Unlike many transcription factors, αCTD does not have a strict base sequence requirement for binding. There is a good correlation between the strength of the interaction and the extent of intrinsic bending of the DNA oligomer estimated from the gel retardation assay. We propose that αCTD recognizes the backbone structure of DNA oligomers responsible for the intrinsic bending. Moreover, NMR studies and drug competition experiments indicated that αCTD interacts with the UP element on the minor groove side of the DNA. The C-terminal end of helix-1, the N-terminal end of helix-4, and the loop between helices 3 and 4 are used for the interaction. Based on these observations, we propose a model for the UP element-αCTD complex.