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Global DNA Compaction in Stationary-Phase Bacteria Does Not Affect Transcription. / Janissen, Richard; Arens, Mathia M.A.; Vtyurina, Natalia N.; Rivai, Zaïda; Sunday, Nicholas D.; Eslami-Mossallam, Behrouz; Gritsenko, Alexey A.; Laan, Liedewij; de Ridder, Dick; Artsimovitch, Irina; Dekker, Nynke H.; Abbondanzieri, Elio A.; Meyer, Anne S.

In: Cell, Vol. 174, No. 5, 2018, p. 1188-1199.e14.

Research output: Contribution to journalArticleScientificpeer-review

Harvard

Janissen, R, Arens, MMA, Vtyurina, NN, Rivai, Z, Sunday, ND, Eslami-Mossallam, B, Gritsenko, AA, Laan, L, de Ridder, D, Artsimovitch, I, Dekker, NH, Abbondanzieri, EA & Meyer, AS 2018, 'Global DNA Compaction in Stationary-Phase Bacteria Does Not Affect Transcription' Cell, vol. 174, no. 5, pp. 1188-1199.e14. https://doi.org/10.1016/j.cell.2018.06.049

APA

Janissen, R., Arens, M. M. A., Vtyurina, N. N., Rivai, Z., Sunday, N. D., Eslami-Mossallam, B., ... Meyer, A. S. (2018). Global DNA Compaction in Stationary-Phase Bacteria Does Not Affect Transcription. Cell, 174(5), 1188-1199.e14. https://doi.org/10.1016/j.cell.2018.06.049

Vancouver

Janissen R, Arens MMA, Vtyurina NN, Rivai Z, Sunday ND, Eslami-Mossallam B et al. Global DNA Compaction in Stationary-Phase Bacteria Does Not Affect Transcription. Cell. 2018;174(5):1188-1199.e14. https://doi.org/10.1016/j.cell.2018.06.049

Author

Janissen, Richard ; Arens, Mathia M.A. ; Vtyurina, Natalia N. ; Rivai, Zaïda ; Sunday, Nicholas D. ; Eslami-Mossallam, Behrouz ; Gritsenko, Alexey A. ; Laan, Liedewij ; de Ridder, Dick ; Artsimovitch, Irina ; Dekker, Nynke H. ; Abbondanzieri, Elio A. ; Meyer, Anne S. / Global DNA Compaction in Stationary-Phase Bacteria Does Not Affect Transcription. In: Cell. 2018 ; Vol. 174, No. 5. pp. 1188-1199.e14.

BibTeX

@article{029cc781452a45cab504d9bb8fb756a2,
title = "Global DNA Compaction in Stationary-Phase Bacteria Does Not Affect Transcription",
abstract = "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. Despite markedly condensing the bacterial chromosome, the nucleoid-structuring protein Dps selectively allows access by RNA polymerase and transcription factors at normal rates while excluding other factors such as restriction endonucleases.",
keywords = "DNA condensation, Dps, magnetic tweezers, nucleoid, RNA polymerase, single-molecule biophysics, stationary phase, stress response, transcription",
author = "Richard Janissen and Arens, {Mathia M.A.} and Vtyurina, {Natalia N.} and Za{\"i}da Rivai and Sunday, {Nicholas D.} and Behrouz Eslami-Mossallam and Gritsenko, {Alexey A.} and Liedewij Laan and {de Ridder}, Dick and Irina Artsimovitch and Dekker, {Nynke H.} and Abbondanzieri, {Elio A.} and Meyer, {Anne S.}",
year = "2018",
doi = "10.1016/j.cell.2018.06.049",
language = "English",
volume = "174",
pages = "1188--1199.e14",
journal = "Cell",
issn = "0092-8674",
publisher = "Cell Press",
number = "5",

}

RIS

TY - JOUR

T1 - Global DNA Compaction in Stationary-Phase Bacteria Does Not Affect Transcription

AU - Janissen, Richard

AU - Arens, Mathia M.A.

AU - Vtyurina, Natalia N.

AU - Rivai, Zaïda

AU - Sunday, Nicholas D.

AU - Eslami-Mossallam, Behrouz

AU - Gritsenko, Alexey A.

AU - Laan, Liedewij

AU - de Ridder, Dick

AU - Artsimovitch, Irina

AU - Dekker, Nynke H.

AU - Abbondanzieri, Elio A.

AU - Meyer, Anne S.

PY - 2018

Y1 - 2018

N2 - 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. Despite markedly condensing the bacterial chromosome, the nucleoid-structuring protein Dps selectively allows access by RNA polymerase and transcription factors at normal rates while excluding other factors such as restriction endonucleases.

AB - 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. Despite markedly condensing the bacterial chromosome, the nucleoid-structuring protein Dps selectively allows access by RNA polymerase and transcription factors at normal rates while excluding other factors such as restriction endonucleases.

KW - DNA condensation

KW - Dps

KW - magnetic tweezers

KW - nucleoid

KW - RNA polymerase

KW - single-molecule biophysics

KW - stationary phase

KW - stress response

KW - transcription

UR - http://www.scopus.com/inward/record.url?scp=85053907858&partnerID=8YFLogxK

U2 - 10.1016/j.cell.2018.06.049

DO - 10.1016/j.cell.2018.06.049

M3 - Article

VL - 174

SP - 1188-1199.e14

JO - Cell

T2 - Cell

JF - Cell

SN - 0092-8674

IS - 5

ER -

ID: 46951189