The two α subunits of Escherichia coli RNA polymerase are asymmetrically arranged and contact different halves of the DNA upstream element

Murakami, Katsuhiko; Kimura, Makoto; Owens, Jeffrey T.; Meares, Claude F.; Ishihama, Akira

The two α subunits of Escherichia coli RNA polymerase are asymmetrically arranged and contact different halves of the DNA upstream element

Authors

Publisher

National Academy of Sciences

Description

RNA polymerase core enzyme of Escherichia coli is composed of two α subunits and one each of the β and β′ subunits. The C-terminal domain of the RNA polymerase α subunit plays a key role in molecular communications with class I transcription factors and upstream (UP) elements of promoter DNA, using the same protein surface. To identify possible differences in the functional roles of the two α subunits, we have developed a reconstitution method for hybrid RNA polymerases containing two distinct α subunit derivatives in a defined orientation (“oriented α-heterodimer”). The binding sites of two α C-terminal domains on the UP element DNA were determined by hydroxyl radical-based DNA cleavage mediated by (p-bromoacetamidobenzyl)-EDTA·Fe, which was bound at Cys-269 on the UP recognition surface of one or both α subunits. The results clearly indicated that the two α subunits bind in tandem to two helix turns of the rrnBP1 UP element, and that the β′-associated α subunit is bound to the promoter–distal region.