Information Analysis of Fis Binding Sites

Originally discovered in the bacteriophage Mu DNA inversion system gin, Fis (Factor for Inversion Stimulation) regulates many genetic systems. To determine the base frequency conservation required for Fis to locate its binding sites, we collected a set of 60 experimentally defined wild-type Fis DNA...

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Bibliographic Details
Published in:Nucleic acids research 1997-12, Vol.25 (24), p.4994-5002
Main Authors: Hengen, Paul N., Bartram, Stacy L., Stewart, Lisa E., Schneider, Thomas D.
Format: Article
Language:English
Subjects:
Bacterial Proteins - metabolism
Base Sequence
Binding Sites
Carrier Proteins - genetics
Carrier Proteins - metabolism
DNA - chemistry
DNA - metabolism
DNA-Binding Proteins - genetics
DNA-Binding Proteins - metabolism
Escherichia coli - genetics
Escherichia coli - metabolism
Escherichia coli Proteins
Factor For Inversion Stimulation Protein
Integration Host Factors
Molecular Sequence Data
Nucleic Acid Conformation
Promoter Regions, Genetic
Protein Binding
RNA - chemistry
RNA - metabolism
RNA-Binding Proteins - genetics
RNA-Binding Proteins - metabolism
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Summary:Originally discovered in the bacteriophage Mu DNA inversion system gin, Fis (Factor for Inversion Stimulation) regulates many genetic systems. To determine the base frequency conservation required for Fis to locate its binding sites, we collected a set of 60 experimentally defined wild-type Fis DNA binding sequences. The sequence logo for Fis binding sites showed the significance and likely kinds of base contacts, and these are consistent with available experimental data. Scanning with an information theory based weight matrix within fis, nrd, tgtl sec and gin revealed Fis sites not previously identified, but for which there are published footprinting and biochemical data. DNA mobility shift experiments showed that a site predicted to be 11 bases from the proximal Salmonella typhimurium hin site and a site predicted to be 7 bases from the proximal P1 cin site are bound by Fis in vitro. Two predicted sites separated by 11 bp found within the nrd promoter region, and one in the tgtl sec promoter, were also confirmed by gel shift analysis. A sequence in aldB previously reported to be a Fis site, for which information theory predicts no site, did not shift. These results demonstrate that information analysis is useful for predicting Fis DNA binding.
ISSN:0305-1048
1362-4962
1362-4962
DOI:10.1093/nar/25.24.4994