Key: Click on "details" for more information on a particular experiment or article. "Result" is a short description of the experiment result. "Methods" use a ontology to describe the methods of the experiment.
  Results:Regulatory site mappingMethods:Footprinting
The base removal experiment was applied to assess the role of individual base residues in the specific interaction between the ppsA promoter region and FruR. The DNA fragment containing the ppsA promoter was partially depurinated and depyrimidinated in experimental conditions such that an average of one base per DNA fragment was modified. Gapped DNA was incubated with FruR, then free and complexed molecules were separated by gel-shift electrophoresis. Comparision of the band intensities between free and bound DNA fractions allowed detection of certain bases whose removal interferes with RNAP binding (see site description). The intensities of the bands representing fragments cleaved at base positions -40 to -55 on the non-template strand (top-strand) and at positions -41 to -49 on the template strand (bottom strand), is generally increased in the free fraction and decreased in the bound fraction. These interference footprints thus define precisely the FruR operator as a site centered at position -45.5 on the opposite face of the DNA helix with respect to the downstream ppsA promoter. This site exhibits the imperfect palindromic consensus sequence already published.
Experiment Elements
site: FruR protected fragment at ppsA gene Escherichia coli
gene: ppsA Escherichia coli
regulator: FruR Escherichia coli
N+ègre D,Oudot C,Prost JF,Murakami K,Ishihama A,Cozzone AJ,Cortay JC
FruR-mediated transcriptional activation at the ppsA promoter of Escherichia coli.J Mol Biol 1998 Feb;276(2):355-65. (details)
PubMed: 9512708