title: Bacterial repression loops require enhanced DNA flexibility.
abstract: The Escherichia coli lac operon provides a classic paradigm for understanding regulation of gene transcription. It is now appreciated that lac promoter repression involves cooperative binding of the bidentate lac repressor tetramer to pairs of lac operators via DNA looping. We have adapted components of this system to create an artificial assay of DNA flexibility in E.coli. This approach allows for systematic study of endogenous and exogenous proteins as architectural factors that enhance apparent DNA flexibility in vivo. We show that inducer binding does not completely remove repression loops but it does alter their geometries. Deletion of the E.coli HU protein drastically destabilizes small repression loops, an effect that can be partially overcome by expression of a heterologous mammalian HMG protein. These results emphasize that the inherent torsional inflexibility of DNA restrains looping and must be modulated in vivo.
authors.affiliation: Department of Biochemistry and Molecular Biology, Mayo Clinic College of Medicine, Rochester, MN 55905, USA.
authors.forename: Nicole A
authors.initials: NA
authors.lastname: Becker
authors.forename: Jason D
authors.initials: JD
authors.lastname: Kahn
authors.forename: L James
authors.initials: LJ
authors.lastname: Maher
mesh_terms: D000818:Animals; D001483:Base Sequence; D004269:DNA, Bacterial / Q000737:chemistry* / Q000235:genetics* / Q000378:metabolism; D004278:DNA, Superhelical / Q000737:chemistry / Q000235:genetics / Q000378:metabolism; D004268:DNA-Binding Proteins / Q000235:genetics / Q000378:metabolism; D004926:Escherichia coli / Q000235:genetics*; D029968:Escherichia coli Proteins / Q000235:genetics / Q000378:metabolism; D015964:Gene Expression Regulation, Bacterial; D020868:Gene Silencing; D024002:HMGB Proteins / Q000235:genetics / Q000378:metabolism; D007763:Lac Operon / Q000235:genetics; D008969:Molecular Sequence Data; D009690:Nucleic Acid Conformation; D018583:Pliability; D011401:Promoter Regions, Genetic / Q000235:genetics; D016415:Sequence Alignment
chemical_list: D004269:DNA, Bacterial; D004278:DNA, Superhelical; D004268:DNA-Binding Proteins; D029968:Escherichia coli Proteins; D024002:HMGB Proteins; C116822:hns protein, E coli