DNA-BINDING DETERMINANTS OF THE ALPHA-SUBUNIT OF RNA-POLYMERASE - NOVEL DNA-BINDING DOMAIN ARCHITECTURE

The Escherichia coli RNA polymerase alpha-subunit binds through its ca rboxy-terminal domain (alpha CTD) to a recognition element, the upstre am (UP) element, in certain promoters. We used genetic and biochemical techniques to identify the residues in alpha CTD important for UP-ele ment-dependent transcription and DNA binding. These residues occur in two regions of alpha CTD, close to but distinct from, residues importa nt for interactions with certain transcription activators. We used NMR spectroscopy to determine the secondary structure of alpha CTD. alpha CTD contains a nonstandard helix followed by four alpha-helices. The two regions of alpha CTD important for DNA binding correspond to the f irst alpha-helix and the loop between the third and fourth alpha-helic es. The alpha CTD DNA-binding domain architecture is unlike any DNA-bi nding architecture identified to date, and we propose that alpha CTD h as a novel mode of interaction with DNA. Our results suggest models fo r alpha CTD-DNA and alpha CTD-DNA-activator interactions during transc ription initiation.