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Cited by 20Bacterial Genetics and BiotechnologyGenomics and Chromatin DynamicsDiffusion and Search Dynamics

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Bacterial H-NS contacts DNA at the same irregularly spaced sites in both bridged and hemi-sequestered linear filaments

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Shen, Beth A., Hustmyer, Christine M., Roston, Daniel, Wolfe, Michael B., Landick, Robert·2022·iScience
DOI 10.1016/j.isci.2022.104429PMC PMC9162952

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Abstract

Gene silencing in bacteria is mediated by chromatin proteins, of which Escherichia coli H-NS is a paradigmatic example. H-NS forms nucleoprotein filaments with either one or two DNA duplexes. However, the structures, arrangements of DNA-binding domains (DBDs), and positions of DBD–DNA contacts in linear and bridged filaments are uncertain. To characterize the H-NS DBD contacts that silence transcription by RNA polymerase, we combined ·OH footprinting, molecular dynamics, statistical modeling, and DBD mapping using a chemical nuclease (Fe 2+ -EDTA) tethered to the DBDs (TEN-map). We find that H-NS DBDs contact DNA at indistinguishable locations in bridged or linear filaments and that the DBDs vary in orientation and position with ∼10-bp average spacing. Our results support a hemi-sequestration model of linear-to-bridged H-NS switching. Linear filaments able to inhibit only transcription initiation switch to bridged filaments able to inhibit both initiation and elongation using the same irregularly spaced DNA contacts.

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Metadata

Authors
Shen, B. A., Hustmyer, C. M., Roston, D., Wolfe, M. B., & Landick, R.
Affiliations
University of Wisconsin–Madison (US)
Corresponding author
Landick, Robert
ORCID
Venue
iScience
Publisher
Elsevier BV
Published
2022-06
Volume
25
Issue
6
Pages
104429
ISSN
2589-0042 (ISSN-L)
DOI
10.1016/j.isci.2022.104429
PMC
PMC9162952
OpenAlex
W4280508027
Cited by
20
References
2
Citations by year
2026: 5 · 2025: 2 · 2024: 7 · 2023: 3 · 2022: 1
FWCI
1.96
Type
journal article
Language
en
Open access
Licence
Locations
  • iScience (publishedVersion, cc-by-nc-nd)
  • bioRxiv (Cold Spring Harbor Laboratory) (acceptedVersion, cc-by-nc-nd)
  • PubMed Central (publishedVersion, cc-by-nc-nd)
  • PubMed (publishedVersion)
  • DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion)
Funders
  • National Institutes of Health
  • National Science Foundation (ACI-1548562, DGE-1747503, DGE-1256259)
  • NIGMS (GM38660)
Topics
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Bacterial Genetics and Biotechnology
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Chromatin Dynamics
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Diffusion and Search Dynamics
Keywords
H-NS, gene silencing, chromatin proteins, DNA-binding domain, nucleoprotein filament, DNA footprinting, transcription initiation, RNA polymerase, Escherichia coli

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