title: Recognition of overlapping nucleotides by AraC and the sigma subunit of RNA polymerase.
abstract: The Escherichia coli promoter p(BAD), under the control of the AraC protein, drives the expression of mRNA encoding the AraB, AraA, and AraD gene products of the arabinose operon. The binding site of AraC at p(BAD) overlaps the RNA polymerase -35 recognition region by 4 bases, leaving 2 bases of the region not contacted by AraC. This overlap raises the question of whether AraC substitutes for the sigma subunit of RNA polymerase in recognition of the -35 region or whether both AraC and sigma make important contacts with the DNA in the -35 region. If sigma does not contact DNA near the -35 region, p(BAD) activity should be independent of the identity of the bases in the hexamer region that are not contacted by AraC. We have examined this issue in the p(BAD) promoter and in a second promoter where the AraC binding site overlaps the -35 region by only 2 bases. In both cases promoter activity is sensitive to changes in bases not contacted by AraC, showing that despite the overlap, sigma does read DNA in the -35 region. Since sigma and AraC are thus closely positioned at p(BAD), it is possible that AraC and sigma contact one another during transcription initiation. DNA migration retardation assays, however, showed that there exists only a slight degree of DNA binding cooperativity between AraC and sigma, thus suggesting either that the normal interactions between AraC and sigma are weak or that the presence of the entire RNA polymerase is necessary for significant interaction.
authors.affiliation: Department of Biology, The Johns Hopkins University, Baltimore, Maryland 21218, USA.
authors.forename: A
authors.initials: A
authors.lastname: Dhiman
authors.forename: R
authors.initials: R
authors.lastname: Schleif
mesh_terms: D051777:AraC Transcription Factor; D001426:Bacterial Proteins; D001483:Base Sequence; D001665:Binding Sites; D016384:Consensus Sequence; D004269:DNA, Bacterial / Q000737:chemistry / Q000378:metabolism; D012321:DNA-Directed RNA Polymerases / Q000378:metabolism; D004926:Escherichia coli / Q000235:genetics*; D029968:Escherichia coli Proteins; D014644:Genetic Variation; D008958:Models, Molecular; D008969:Molecular Sequence Data; D016297:Mutagenesis, Site-Directed; D009690:Nucleic Acid Conformation; D010957:Plasmids; D011401:Promoter Regions, Genetic; D012097:Repressor Proteins / Q000378:metabolism*; D012808:Sigma Factor / Q000378:metabolism*; D013698:Templates, Genetic; D014157:Transcription Factors
chemical_list: D051777:AraC Transcription Factor; C497371:AraC protein, E coli; D001426:Bacterial Proteins; D004269:DNA, Bacterial; D029968:Escherichia coli Proteins; D012097:Repressor Proteins; D012808:Sigma Factor; D014157:Transcription Factors; D012321:DNA-Directed RNA Polymerases