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Vol. 15, No. 5, pp. 491-506, March 1, 2001
subunit binding to the UP element minor groove
1 Department of Bacteriology, University of
Wisconsin-Madison, Madison, Wisconsin 53706, USA;
2 Department of Chemistry and Chemical Biology, Harvard
University, Cambridge, Massachusetts 02138, USA
The 
subunit of E. coli RNAP plays an important role in
the recognition of many promoters by binding to the A+T-rich UP
element, a DNA sequence located upstream of the recognition elements
for the 
subunit, the 
35 and 10 hexamers. We examined DNA-RNAP interactions using high resolution interference and protection footprinting methods and using the minor groove-binding drug
distamycin. Our results suggest that interacts with bases 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
contribution to binding. On the basis of these and previous
results, we propose a model in which contacts UP element DNA
through amino acid residues located in a pair of helix-hairpin-helix
motifs. Furthermore, our experiments extend existing information about
recognition of the core promoter by 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.
[Key Words: RNA polymerase; promoter; alpha subunit; UP element; minor groove; helix-hairpin-helix]
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