Cell
Volume 174, Issue 5, 23 August 2018, Pages 1188-1199.e14
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Article
Global DNA Compaction in Stationary-Phase Bacteria Does Not Affect Transcription

https://doi.org/10.1016/j.cell.2018.06.049Get rights and content
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Highlights

  • In E. coli, the condensation of DNA by Dps is decoupled from transcription

  • Dps provides selective access of proteins to the encased DNA

  • RNA polymerase readily initiates transcription on Dps-protected promoters

  • Dps maintains a dynamic condensed structure during RNA chain elongation

Summary

In stationary-phase Escherichia coli, Dps (DNA-binding protein from starved cells) is the most abundant protein component of the nucleoid. Dps compacts DNA into a dense complex and protects it from damage. Dps has also been proposed to act as a global regulator of transcription. Here, we directly examine the impact of Dps-induced compaction of DNA on the activity of RNA polymerase (RNAP). Strikingly, deleting the dps gene decompacted the nucleoid but did not significantly alter the transcriptome and only mildly altered the proteome during stationary phase. Complementary in vitro assays demonstrated that Dps blocks restriction endonucleases but not RNAP from binding DNA. Single-molecule assays demonstrated that Dps dynamically condenses DNA around elongating RNAP without impeding its progress. We conclude that Dps forms a dynamic structure that excludes some DNA-binding proteins yet allows RNAP free access to the buried genes, a behavior characteristic of phase-separated organelles.

Keywords

Dps
nucleoid
stationary phase
transcription
stress response
RNA polymerase
single-molecule biophysics
magnetic tweezers
DNA condensation

Cited by (0)

5

These authors contributed equally

6

Present address: Groningen Research Institute of Pharmacy, Groningen University, Groningen, Groningen 9713AV, the Netherlands

7

Present address: Department of Biology, University of Rochester, Rochester, NY 14627, USA

8

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