DNA-binding determinants of the α subunit of RNA polymerase: Novel DNA-binding domain architecture

Abstract

The Escherichia coli RNA polymerase α-subunit binds through its carboxy-terminal domain (αCTD) to a recognition element, the upstream (UP) element, in certain promoters. We used genetic and biochemical techniques to identify the residues in αCTD important for UP-element-dependent transcription and DNA binding. These residues occur in two regions of αCTD, close to but distinct from, residues important for interactions with certain transcription activators. We used NMR spectroscopy to determine the secondary structure of αCTD. αCTD contains a nonstandard helix followed by four α-helices. The two regions of αCTD important for DNA binding correspond to the first α-helix and the loop between the third and fourth α-helices. The αCTD DNA-binding domain architecture is unlike any DNA-binding architecture identified to date, and we propose that αCTD has a novel mode of interaction with DNA. Our results suggest models for αCTD-DNA and αCTD-DNA-activator interactions during transcription initiation.