The kinetics of sigma subunit directed promoter recognition by E-coli RNA polymerase

Time-resolved laser UV irradiation and controlled proteolysis have been used to study the sequential recognition of the Inc UV5 promoter by Escherichia coli RNA polymerase. Local rearrangements in the DNA, the appearance of intimate protein-DNA contacts, and structural changes within the sigma subunit together provide specific signatures that define major species populated during this process. At 22 degrees C, a first closed complex is characterised by a transient conformational change in the sigma subunit and by a distortion in the -35 region. Subsequently, direct contacts at -34 and at positions -8, -5 and -3 on the non-template strand appear prior to DNA strand separation. The contact in the -35 consensus region involves only the sigma subunit. This intermediate possesses different structural parameters from that formed by quenching open complexes from 37 degrees C to 14 degrees C. Sigma thus appears as the principal partner acting during promoter recognition, a strongly coupled process involving two major intermediates only.