In vivo interaction of the Escherichia coli integration host factor with its specific binding sites.
The histone-like protein integration host factor (IHF) of Escherichia coli binds to specific binding sites on the chromosome or on mobile genetic elements, and is involved in many cellular processes. We have analyzed the interaction of IHF with five different binding sites in vitro and in vivo using UV laser footprinting, a technique that probes the immediate environment and conformation of a segment of DNA. Using this generally applicable technique we can directly compare the binding modes and interaction strengths of a DNA binding protein in its physiological environment within the cell to measurements performed in vitro. We conclude that the interactions between IHF and its specific binding sites are identical in vitro and in vivo. The footprinting signal is consistent with the model of IHF-binding to DNA proposed by Yang and Nash (1989). The occupancy of binding sites varies with the concentration of IHF in the cell and allows to estimate the concentration of free IHF protein in the cell.
Engelhorn
M
M
Department of Molecular Biology, University of Geneva, Switzerland.
Boccard
F
F
Murtin
C
C
Prentki
P
P
Geiselmann
J
J
D000251:Adenosine Triphosphatases / Q000235:genetics; D001287:Attachment Sites, Microbiological / Q000235:genetics; D001426:Bacterial Proteins / Q000235:genetics / Q000378:metabolism*; D001483:Base Sequence; D001665:Binding Sites; D002352:Carrier Proteins; D027081:DNA Gyrase; D004265:DNA Helicases; D004250:DNA Topoisomerases, Type II / Q000235:genetics; D004269:DNA, Bacterial / Q000737:chemistry / Q000235:genetics / Q000378:metabolism*; D004268:DNA-Binding Proteins / Q000235:genetics / Q000378:metabolism*; D004926:Escherichia coli / Q000378:metabolism*; D029968:Escherichia coli Proteins; D005798:Genes, Bacterial; D034982:Integration Host Factors; D008969:Molecular Sequence Data; D009690:Nucleic Acid Conformation; D033902:Periplasmic Binding Proteins; D012091:Repetitive Sequences, Nucleic Acid; D014466:Ultraviolet Rays
D001426:Bacterial Proteins; D002352:Carrier Proteins; D004269:DNA, Bacterial; D004268:DNA-Binding Proteins; D029968:Escherichia coli Proteins; D034982:Integration Host Factors; D033902:Periplasmic Binding Proteins; C066768:dppA protein, E coli; D000251:Adenosine Triphosphatases; D004265:DNA Helicases; D027081:DNA Gyrase; D004250:DNA Topoisomerases, Type II