Modeling supercoiled DNA interacting with an anchored cluster of proteins: towards a quantitative estimation of chromosomal DNA supercoiling

We investigate the measurement of DNA supercoiling density ($σ$) along chromosomes using interaction frequencies between DNA and DNA-anchored clusters of proteins. Specifically, we show how the physics of DNA supercoiling leads, in bacteria, to the quantitative modeling of binding properties of ParB...

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Bibliographic Details
Published in:PLoS computational biology Vol. 56; no. 6
Main Authors: Walter, Jean-Charles, Lepage, Thibaut, Dorignac, Jérôme, Geniet, Frédéric, Parmeggiani, Andrea, Palmeri, John, Bouet, Jean-Yves, Junier, Ivan
Format: Journal Article
Language:English
Published: PLOS 31.01.2020
Subjects:
Biological Physics
Physics
FOS: Biological sciences
FOS: Physical sciences
Biological Physics (physics.bio-ph)
Biomolecules (q-bio.BM)
ISSN:1553-734X, 1553-7358
Online Access:Get full text
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Summary:We investigate the measurement of DNA supercoiling density ($σ$) along chromosomes using interaction frequencies between DNA and DNA-anchored clusters of proteins. Specifically, we show how the physics of DNA supercoiling leads, in bacteria, to the quantitative modeling of binding properties of ParB proteins around their centromere-like site, {\it parS}. Using this framework, we provide an upper bound for $σ$ in the {\it Escherichia coli} chromosome, consistent with plasmid values, and offer a proof of concept for a high accuracy measurement. To reach these conclusions, we revisit the problem of the formation of ParB clusters. We predict, in particular, that they result from a non-equilibrium, stationary balance between an influx of produced proteins and an outflux of excess proteins, i.e., they behave like liquid-like protein condensates with unconventional ``leaky'' boundaries.
ISSN:1553-734X
1553-7358
DOI:10.48550/arXiv.2002.00111