Fine structure of E-coli RNA polymerase-promoter interactions: alpha subunit binding to the UP element minor groove

The alpha subunit of E. coli RNAP plays an important role in the recognitio n of many promoters by binding to the A+T-rich UP element, a DNA sequence l ocated upstream of the recognition elements for the sigma subunit, the -35 and -10 hexamers. We examined DNA-RNAP interactions using high resolution i nterference and protection footprinting methods and using the minor groove- binding drug distamycin. Our results suggest that alpha interacts with base s in the DNA minor groove and with the DNA backbone along the minor groove, but that UP element major groove surfaces do not make a significant contri bution to alpha binding. On the basis of these and previous results, we pro pose a model in which a contacts UP element DNA through amino acid residues located in a pair of helix-hairpin-helix motifs. Furthermore, our experime nts extend existing information about recognition of the core promoter by s igma (70) by identifying functional groups in the major grooves of the -35 and -10 hexamers in which modifications interfere with RNAP binding. These studies greatly improve the resolution of our picture of the promoter-RNAP interaction.