title: The promoter-search mechanism of Escherichia coli RNA polymerase is dominated by three-dimensional diffusion.
abstract: Gene expression, DNA replication and genome maintenance are all initiated by proteins that must recognize specific targets from among a vast excess of nonspecific DNA. For example, to initiate transcription, Escherichia coli RNA polymerase (RNAP) must locate promoter sequences, which compose <2% of the bacterial genome. This search problem remains one of the least understood aspects of gene expression, largely owing to the transient nature of search intermediates. Here we visualize RNAP in real time as it searches for promoters, and we develop a theoretical framework for analyzing target searches at the submicroscopic scale on the basis of single-molecule target-association rates. We demonstrate that, contrary to long-held assumptions, the promoter search is dominated by three-dimensional diffusion at both the microscopic and submicroscopic scales in vitro, which has direct implications for understanding how promoters are located within physiological settings.
authors.affiliation: Department of Biochemistry and Molecular Biophysics, Columbia University, New York, New York, USA.
authors.forename: Feng
authors.initials: F
authors.lastname: Wang
authors.forename: Sy
authors.initials: S
authors.lastname: Redding
authors.forename: Ilya J
authors.initials: IJ
authors.lastname: Finkelstein
authors.forename: Jason
authors.initials: J
authors.lastname: Gorman
authors.forename: David R
authors.initials: DR
authors.lastname: Reichman
authors.forename: Eric C
authors.initials: EC
authors.lastname: Greene
mesh_terms: D001426:Bacterial Proteins / Q000378:metabolism*; D012321:DNA-Directed RNA Polymerases / Q000235:genetics*; D004058:Diffusion; D004926:Escherichia coli / Q000201:enzymology*; D007700:Kinetics; D011401:Promoter Regions, Genetic / Q000235:genetics*; D024363:Transcription Initiation Site; D014158:Transcription, Genetic / Q000235:genetics*
chemical_list: D001426:Bacterial Proteins; D012321:DNA-Directed RNA Polymerases