Journal
NUCLEIC ACIDS RESEARCH
Volume 46, Issue 11, Pages 5525-5546Publisher
OXFORD UNIV PRESS
DOI: 10.1093/nar/gky265
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Funding
- NIH [GM38660]
- Netherlands Organisation for Scientific Research (VICI) [016.160.613]
- China Scholarship Council [201506880001]
- National Science Foundation Graduate Research Fellowship [DGE-1256259]
- Department of Biochemistry, University of Wisconsin, Madison, William H. Peterson Fellowship
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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 degrees C. StpA: H-NS or StpA-only filaments also stimulate pausing at 37 degrees 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.
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