title: Bridged filaments of histone-like nucleoid structuring protein pause RNA polymerase and aid termination in bacteria.
abstract: Bacterial H-NS forms nucleoprotein filaments that spread on DNA and bridge distant DNA sites. H-NS filaments co-localize with sites of Rho-dependent termination in Escherichia coli, but their direct effects on transcriptional pausing and termination are untested. In this study, we report that bridged H-NS filaments strongly increase pausing by E. coli RNA polymerase at a subset of pause sites with high potential for backtracking. Bridged but not linear H-NS filaments promoted Rho-dependent termination by increasing pause dwell times and the kinetic window for Rho action. By observing single H-NS filaments and elongating RNA polymerase molecules using atomic force microscopy, we established that bridged filaments surround paused complexes. Our results favor a model in which H-NS-constrained changes in DNA supercoiling driven by transcription promote pausing at backtracking-susceptible sites. Our findings provide a mechanistic rationale for H-NS stimulation of Rho-dependent termination in horizontally transferred genes and during pervasive antisense and noncoding transcription in bacteria.
authors.affiliation: Department of Biochemistry, University of Wisconsin-Madison, Madison, United States.
authors.forename: Matthew V
authors.initials: MV
authors.lastname: Kotlajich
authors.affiliation: Department of Biochemistry, University of Wisconsin-Madison, Madison, United States.
authors.forename: Daniel R
authors.initials: DR
authors.lastname: Hron
authors.affiliation: Department of Biochemistry, University of Wisconsin-Madison, Madison, United States.
authors.forename: Beth A
authors.initials: BA
authors.lastname: Boudreau
authors.affiliation: Department of Pharmaceutical Sciences, University of Nebraska Medical Center, Omaha, United States.
authors.forename: Zhiqiang
authors.initials: Z
authors.lastname: Sun
authors.affiliation: Department of Pharmaceutical Sciences, University of Nebraska Medical Center, Omaha, United States.
authors.forename: Yuri L
authors.initials: YL
authors.lastname: Lyubchenko
authors.affiliation: Department of Biochemistry, University of Wisconsin-Madison, Madison, United States.
authors.forename: Robert
authors.initials: R
authors.lastname: Landick
mesh_terms: D001419:Bacteria / Q000235:genetics* / Q000378:metabolism; D001426:Bacterial Proteins / Q000235:genetics / Q000378:metabolism*; D001483:Base Sequence; D004268:DNA-Binding Proteins / Q000235:genetics / Q000378:metabolism*; D012321:DNA-Directed RNA Polymerases / Q000378:metabolism*; D012329:RNA, Bacterial; D061806:Transcription Termination, Genetic
chemical_list: D001426:Bacterial Proteins; D004268:DNA-Binding Proteins; C031908:H-NS protein, bacteria; D012329:RNA, Bacterial; D012321:DNA-Directed RNA Polymerases
keywords: E. coli; GreB; H-NS; NusG; RNAP; biochemistry; chromosomes; genes; rho; transcription termination