title: Proteins mediating DNA loops effectively block transcription.
abstract: Loops are ubiquitous topological elements formed when proteins simultaneously bind to two noncontiguous DNA sites. While a loop-mediating protein may regulate initiation at a promoter, the presence of the protein at the other site may be an obstacle for RNA polymerases (RNAP) transcribing a different gene. To test whether a DNA loop alters the extent to which a protein blocks transcription, the lac repressor (LacI) was used. The outcome of in vitro transcription along templates containing two LacI operators separated by 400 bp in the presence of LacI concentrations that produced both looped and unlooped molecules was visualized with scanning force microscopy (SFM). An analysis of transcription elongation complexes, moving for 60 s at an average of 10 nt/s on unlooped DNA templates, revealed that they more often surpassed LacI bound to the lower affinity O2 operator than to the highest affinity Os operator. However, this difference was abrogated in looped DNA molecules where LacI became a strong roadblock independently of the affinity of the operator. Recordings of transcription elongation complexes, using magnetic tweezers, confirmed that they halted for several minutes upon encountering a LacI bound to a single operator. The average pause lifetime is compatible with RNAP waiting for LacI dissociation, however, the LacI open conformation visualized in the SFM images also suggests that LacI could straddle RNAP to let it pass. Independently of the mechanism by which RNAP bypasses the LacI roadblock, the data indicate that an obstacle with looped topology more effectively interferes with transcription.
authors.affiliation: Department of Physics, Emory University, Atlanta, Georgia, 30322.
authors.forename: Zsuzsanna
authors.initials: Z
authors.lastname: Vörös
authors.affiliation: Department of Physics, Emory University, Atlanta, Georgia, 30322.
authors.forename: Yan
authors.initials: Y
authors.lastname: Yan
authors.affiliation: Department of Physics, Emory University, Atlanta, Georgia, 30322.
authors.forename: Daniel T
authors.initials: DT
authors.lastname: Kovari
authors.affiliation: Department of Physics, Emory University, Atlanta, Georgia, 30322.
authors.forename: Laura
authors.identifier: http://orcid.org/0000-0003-1173-5339
authors.initials: L
authors.lastname: Finzi
authors.affiliation: Department of Physics, Emory University, Atlanta, Georgia, 30322.
authors.forename: David
authors.initials: D
authors.lastname: Dunlap
mesh_terms: D004269:DNA, Bacterial / Q000737:chemistry* / Q000378:metabolism; D012321:DNA-Directed RNA Polymerases / Q000737:chemistry* / Q000378:metabolism; D004926:Escherichia coli / Q000737:chemistry* / Q000378:metabolism; D029968:Escherichia coli Proteins / Q000737:chemistry* / Q000378:metabolism; D007763:Lac Operon; D056968:Lac Repressors / Q000737:chemistry* / Q000378:metabolism; D009690:Nucleic Acid Conformation; D014158:Transcription, Genetic
chemical_list: D004269:DNA, Bacterial; D029968:Escherichia coli Proteins; D056968:Lac Repressors; C539064:LacI protein, E coli; D012321:DNA-Directed RNA Polymerases
keywords: DNA looping; RNAP; lac repressor protein; magnetic tweezers; scanning force microscopy; transcription elongation