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

The C-terminal domain of the alpha -subunit of Escherichia coli RNA polymer ase (alpha CTD) is responsible for transcriptional activation through inter action with both activator proteins and UP element DNA. Previously, we dete rmined the solution structure of alpha CTD. Here, we investigated the inter action between alpha CTD and UP element DNA by NMR. DNA titration curves an d intermolecular NOE measurements indicate that alpha CTD can bind to multi ple sites on the UP element DNA. Unlike many transcription factors, alpha C TD 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 a ssay. We propose that alpha CTD recognizes the backbone structure of DNA ol igomers responsible for the intrinsic bending. Moreover, NMR studies and dr ug competition experiments indicated that alpha CTD interacts with the UP e lement 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 use d for the interaction. Based on these observations, we propose a model for the UP element-alpha CTD complex. (C) 2001 Academic Press.