title: Upstream binding of idling RNA polymerase modulates transcription initiation from a nearby promoter.
abstract: The bacterial gene regulatory regions often demonstrate distinctly organized arrays of RNA polymerase binding sites of ill-defined function. Previously we observed a module of closely spaced polymerase binding sites upstream of the canonical promoter of the Escherichia coli fis operon. FIS is an abundant nucleoid-associated protein involved in adjusting the chromosomal DNA topology to changing cellular physiology. Here we show that simultaneous binding of the polymerase at the canonical fis promoter and an upstream transcriptionally inactive site stabilizes a RNAP oligomeric complex in vitro. We further show that modulation of the upstream binding of RNA polymerase affects the fis promoter activity both in vivo and in vitro. The effect of the upstream RNA polymerase binding on the fis promoter activity depends on the spatial arrangement of polymerase binding sites and DNA supercoiling. Our data suggest that a specific DNA geometry of the nucleoprotein complex stabilized on concomitant binding of RNA polymerase molecules at the fis promoter and the upstream region acts as a topological device regulating the fis transcription. We propose that transcriptionally inactive RNA polymerase molecules can act as accessory factors regulating the transcription initiation from a nearby promoter.
authors: From the School of Engineering and Science, Jacobs University Bremen, Campus Ring 1, D-28759 Bremen, Germany.
authors: Veneta
authors: V
authors: Gerganova
authors: From the School of Engineering and Science, Jacobs University Bremen, Campus Ring 1, D-28759 Bremen, Germany.
authors: Sebastian
authors: S
authors: Maurer
authors: From the School of Engineering and Science, Jacobs University Bremen, Campus Ring 1, D-28759 Bremen, Germany.
authors: Liubov
authors: L
authors: Stoliar
authors: the Laboratory of the Physics of Living Matter, EPFL, CH-1015 Lausanne, Switzerland.
authors: Aleksandre
authors: A
authors: Japaridze
authors: the Laboratory of the Physics of Living Matter, EPFL, CH-1015 Lausanne, Switzerland.
authors: Giovanni
authors: G
authors: Dietler
authors: the UMR5240 CNRS/INSA/UCB, Université de Lyon, F-69003, INSA-Lyon, Villeurbanne, F-69621, France.
authors: William
authors: W
authors: Nasser
authors: the Ivane Beritashvili Centre of Experimental Biomedicine, Gotua str.14, Tbilisi, Georgia, and.
authors: Tamara
authors: T
authors: Kutateladze
authors: the MRC Laboratory of Molecular Biology, Hills Road, Cambridge CB2 QH, United Kingdom.
authors: Andrew
authors: A
authors: Travers
authors: From the School of Engineering and Science, Jacobs University Bremen, Campus Ring 1, D-28759 Bremen, Germany, g.muskhelishvili@jacobs-university.de.
authors: Georgi
authors: G
authors: Muskhelishvili
mesh_terms: D004269:DNA, Bacterial / Q000235:genetics; D004278:DNA, Superhelical / Q000235:genetics; D012321:DNA-Directed RNA Polymerases / Q000502:physiology*; D004926:Escherichia coli / Q000201:enzymology; D029968:Escherichia coli Proteins / Q000235:genetics*; D035021:Factor For Inversion Stimulation Protein / Q000235:genetics*; D015964:Gene Expression Regulation, Bacterial; D018625:Microscopy, Atomic Force; D011401:Promoter Regions, Genetic; D011485:Protein Binding; D061785:Transcription Initiation, Genetic
chemical_list: D004269:DNA, Bacterial; D004278:DNA, Superhelical; D029968:Escherichia coli Proteins; D035021:Factor For Inversion Stimulation Protein; C501034:Fis protein, E coli; D012321:DNA-Directed RNA Polymerases
keywords: Atomic Force Microscopy (AFM); Bacterial Transcription; DNA Topology; Escherichia coli (E. coli); RNA Polymerase; Transcription Promoter; fis
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