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PMID: 9707549 Published · ppublish English Journal Article Research Support, U.S. Gov't, Non-P.H.S. Research Support, U.S. Gov't, P.H.S.

Identification of an UP element consensus sequence for bacterial promoters.

Proceedings of the National Academy of Sciences of the United States of America ·Vol. 95 ·No. 17 ·1998-08-18 ·Pages 9761-6

Estrem ST, Gaal T, Ross W, Gourse RL

Abstract

The UP element, a component of bacterial promoters located upstream of the -35 hexamer, increases transcription by interacting with the RNA polymerase alpha-subunit. By using a modification of the SELEX procedure for identification of protein-binding sites, we selected in vitro and subsequently screened in vivo for sequences that greatly increased promoter activity when situated upstream of the Escherichia coli rrnB P1 core promoter. A set of 31 of these upstream sequences increased transcription from 136- to 326-fold in vivo, considerably more than the natural rrnB P1 UP element, and was used to derive a consensus sequence: -59 nnAAA(A/T)(A/T)T(A/T)TTTTnnAAAAnnn -38. The most active selected sequence contained the derived consensus, displayed all of the properties of an UP element, and the interaction of this sequence with the alpha C-terminal domain was similar to that of previously characterized UP elements. The identification of the UP element consensus should facilitate a detailed understanding of the alpha-DNA interaction. Based on the evolutionary conservation of the residues in alpha responsible for interaction with UP elements, we suggest that the UP element consensus sequence should be applicable throughout eubacteria, should generally facilitate promoter prediction, and may be of use for biotechnological applications.

MeSH Terms
Base Sequence Binding Sites/genetics Consensus Sequence DNA, Bacterial/chemistry,genetics,metabolism DNA-Directed RNA Polymerases/metabolism Escherichia coli/genetics,metabolism Evolution, Molecular Lac Operon Nucleic Acid Conformation Promoter Regions, Genetic Protein Binding
Chemicals
DNA, Bacterial DNA-Directed RNA Polymerases RNA polymerase alpha subunit
Authors & Affiliations
4 authors, click to expand affiliations / ORCID
Estrem S T
Department of Bacteriology, University of Wisconsin, 1550 Linden Drive, Madison, WI 53706, USA.
Gaal T
Ross W
Gourse R L
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Article Info
Journal
Proceedings of the National Academy of Sciences of the United States of America
Abbr.
Proc Natl Acad Sci U S A
ISSN
0027-8424
DOI
10.1073/pnas.95.17.9761
Published
1998-08-18
Pages
9761-6
Language
English
Region
United States
NLM ID
7505876
PMCID
PMC21410
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: 10.1073/pnas.95.17.9761 PMC Full Text View journal details
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