StpA and Hha stimulate pausing by RNA polymerase by promoting DNA-DNA bridging of H-NS filaments

Beth A. Boudreau, Daniel R. Hron, Liang Qin, Ramon A. Van Der Valk, Matthew V. Kotlajich, Remus T. Dame, Robert Landick*

*Corresponding author for this work

Research output: Contribution to JournalArticleAcademicpeer-review


In enterobacteria, AT-rich horizontally acquired genes, including virulence genes, are silenced through the actions of at least three nucleoid-associated proteins (NAPs): H-NS, StpA and Hha. These proteins form gene-silencing nucleoprotein filaments through direct DNA binding by H-NS and StpA homodimers or heterodimers. Both linear and bridged filaments, in which NAPs bind one or two DNA segments, respectively, have been observed. Hha can interact with H-NS or StpA filaments, but itself lacks a DNA-binding domain. Filaments composed of H-NS alone can inhibit transcription initiation and, in the bridged conformation, slow elongating RNA polymerase (RNAP) by promoting backtracking at pause sites. How the other NAPs modulate these effects of H-NS is unknown, despite evidence that they help regulate subsets of silenced genes in vivo (e.g. in pathogenicity islands). Here we report that Hha and StpA greatly enhance H-NS-stimulated pausing by RNAP at 20 C. StpA:H-NS or StpA-only filaments also stimulate pausing at 37 C, a temperature at which Hha:H-NS or H-NS-only filaments have much less effect. In addition, we report that both Hha and StpA greatly stimulate DNA-DNA bridging by H-NS filaments. Together, these observations indicate that Hha and StpA can affect H-NS-mediated gene regulation by stimulating bridging of H-NS/DNA filaments.

Original languageEnglish
Pages (from-to)5525-5546
Number of pages22
JournalNucleic acids research
Issue number11
Publication statusPublished - 1 Jan 2018
Externally publishedYes


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