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PMID: 11238372 Published · ppublish English Journal Article Research Support, Non-U.S. Gov't Research Support, U.S. Gov't, P.H.S.

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

Genes & development ·Vol. 15 ·No. 5 ·2001-03-01 ·Pages 491-506

Ross W, Ernst A, Gourse RL

Abstract

The alpha 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 sigma 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 alpha 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 alpha binding. On the basis of these and previous results, we propose a model in which alpha 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 sigma(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.

MeSH Terms
Amino Acid Motifs Base Sequence Binding Sites DNA Footprinting DNA, Bacterial/metabolism DNA-Directed RNA Polymerases/metabolism Distamycins/pharmacology Escherichia coli/genetics,metabolism Models, Molecular Molecular Sequence Data Nucleic Acid Conformation Promoter Regions, Genetic Protein Binding Protein Subunits
Chemicals
DNA, Bacterial Distamycins Protein Subunits stallimycin DNA-Directed RNA Polymerases
Authors & Affiliations
3 authors, click to expand affiliations / ORCID
Ross W
Department of Bacteriology, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA.
Ernst A
Gourse R L
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Article Info
Journal
Genes & development
Abbr.
Genes Dev
ISSN
0890-9369
DOI
10.1101/gad.870001
Published
2001-03-01
Pages
491-506
Language
English
Region
United States
NLM ID
8711660
PMCID
PMC312649
Subset
IM
Grants
NIGMS NIH HHS · R01 GM037048 · United States
NIGMS NIH HHS · R37 GM037048 · United States
NIGMS NIH HHS · GM37048 · United States
External Links
PubMed source DOI: 10.1101/gad.870001 PMC Full Text View journal details
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