Bridged filaments of histone-like nucleoid structuring protein pause RNA polymerase and aid termination in bacteria

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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. Here 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.

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Matthew V Kotlajich

Biochemistry, University of Wisconsin-Madison, Department of Madison, United States

Competing interests
The authors declare that no competing interests exist.
Daniel R Hron

Department of Biochemistry, University of Wisconsin-Madison, Madison, United States

Competing interests
The authors declare that no competing interests exist.
Beth A Boudreau

Department of Biochemistry, University of Wisconsin-Madison, Madison, United States

Competing interests
The authors declare that no competing interests exist.
Zhiqiang Sun

Department of Pharmaceutical Sciences, University of Nebraska Medical Center, Omaha, United States

Competing interests
The authors declare that no competing interests exist.
Yuri Lyubchenko

Department of Pharmaceutical Sciences, University of Nebraska Medical Center, Omaha, United States

Competing interests
The authors declare that no competing interests exist.
Robert Landick

Department of Biochemistry, University of Wisconsin-Madison, Madison, United States

For correspondence
landick@biochem.wisc.edu

Competing interests
The authors declare that no competing interests exist.

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