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PMID: 9765569 Published · ppublish English Comparative Study Journal Article Research Support, U.S. Gov't, P.H.S.

Escherichia coli promoters with UP elements of different strengths: modular structure of bacterial promoters.

Journal of bacteriology ·Vol. 180 ·No. 20 ·1998-10-00 ·Pages 5375-83

Ross W, Aiyar SE, Salomon J, Gourse RL

Abstract

The alpha subunit of Escherichia coli RNA polymerase (RNAP) participates in promoter recognition through specific interactions with UP element DNA, a region upstream of the recognition hexamers for the sigma subunit (the -10 and -35 hexamers). UP elements have been described in only a small number of promoters, including the rRNA promoter rrnB P1, where the sequence has a very large (30- to 70-fold) effect on promoter activity. Here, we analyzed the effects of upstream sequences from several additional E. coli promoters (rrnD P1, rrnB P2, lambda pR, lac, merT, and RNA II). The relative effects of different upstream sequences were compared in the context of their own core promoters or as hybrids to the lac core promoter. Different upstream sequences had different effects, increasing transcription from 1.5- to approximately 90-fold, and several had the properties of UP elements: they increased transcription in vitro in the absence of accessory protein factors, and transcription stimulation required the C-terminal domain of the RNAP alpha subunit. The effects of the upstream sequences correlated generally with their degree of similarity to an UP element consensus sequence derived previously. Protection of upstream sequences by RNAP in footprinting experiments occurred in all cases and was thus not a reliable indicator of UP element strength. These data support a modular view of bacterial promoters in which activity reflects the composite effects of RNAP interactions with appropriately spaced recognition elements (-10, -35, and UP elements), each of which contributes to activity depending on its similarity to the consensus.

MeSH Terms
Bacterial Proteins Bacteriophage lambda/genetics Base Sequence Carrier Proteins/genetics Cation Transport Proteins Consensus Sequence DNA Footprinting DNA-Directed RNA Polymerases/metabolism Escherichia coli/genetics Genes, Bacterial Genes, rRNA/genetics Lac Operon/genetics Membrane Proteins/genetics Molecular Sequence Data Promoter Regions, Genetic Protein Binding RNA/genetics Transcription, Genetic
Chemicals
Bacterial Proteins Carrier Proteins Cation Transport Proteins Membrane Proteins RNA primers mercury transport protein, bacterial RNA DNA-Directed RNA Polymerases
Authors & Affiliations
4 authors, click to expand affiliations / ORCID
Ross W
Department of Bacteriology, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA.
Aiyar S E
Salomon J
Gourse R L
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Article Info
Journal
Journal of bacteriology
Abbr.
J Bacteriol
ISSN
0021-9193
DOI
10.1128/JB.180.20.5375-5383.1998
Published
1998-10-00
Pages
5375-83
Language
English
Region
United States
NLM ID
2985120R
PMCID
PMC107586
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: 10.1128/JB.180.20.5375-5383.1998 PMC Full Text View journal details
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