title: Variation of half-site organization and DNA looping by AraC protein.
abstract: The dimeric AraC protein of Escherichia coli binds specifically to DNA sequences upstream of promoters whose transcription is regulated by arabinose. Here we show with affinity measurements, DNase footprinting, dimethyl sulfate premethylation interference and dimethyl sulfate footprinting studies that AraC protein can recognize paired half-sites in direct repeat orientation or inverted repeat orientation. A similar high degree of flexibility was also seen in the ability of the protein in the absence of arabinose to bind tightly and specifically when the separation of its half-sites was increased by 10 or 21 bp. In the presence of arabinose the protein could specifically contact both half-sites of a +10 bp spacing construct but could not contact both in a +21 bp construct. Reduced extensibility of AraC protein in the presence of arabinose provides a simple mechanism for the protein's shift from a non-inducing, DNA looping state to an inducing, non-looping state that contacts two adjacent half-sites at the arapBAD promoter.
authors.affiliation: Biology Department, Johns Hopkins University, Baltimore, MD 21218.
authors.forename: J H
authors.initials: JH
authors.lastname: Carra
authors.forename: R F
authors.initials: RF
authors.lastname: Schleif
mesh_terms: D051777:AraC Transcription Factor; D001089:Arabinose / Q000378:metabolism / Q000494:pharmacology; D001426:Bacterial Proteins; D001483:Base Sequence; D001665:Binding Sites; D004269:DNA, Bacterial / Q000235:genetics / Q000378:metabolism*; D003851:Deoxyribonucleases; D004926:Escherichia coli / Q000235:genetics / Q000378:metabolism*; D029968:Escherichia coli Proteins; D006834:Hydrazines / Q000494:pharmacology; D007700:Kinetics; D046911:Macromolecular Substances; D008969:Molecular Sequence Data; D009838:Oligodeoxyribonucleotides; D009876:Operon; D011401:Promoter Regions, Genetic; D012091:Repetitive Sequences, Nucleic Acid; D012097:Repressor Proteins / Q000378:metabolism*; D014157:Transcription Factors; D014158:Transcription, Genetic / Q000187:drug effects
chemical_list: D051777:AraC Transcription Factor; C497371:AraC protein, E coli; D001426:Bacterial Proteins; D004269:DNA, Bacterial; D029968:Escherichia coli Proteins; D006834:Hydrazines; D046911:Macromolecular Substances; D009838:Oligodeoxyribonucleotides; D012097:Repressor Proteins; D014157:Transcription Factors; C029424:hydrazine; D001089:Arabinose; D003851:Deoxyribonucleases