1. Modeling supercoiled DNA interacting with an anchored cluster of proteins: towards a quantitative estimation of chromosomal DNA supercoiling
- Author
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Walter, Jean-Charles, Lepage, Thibaut, Dorignac, Jérôme, Geniet, Frédéric, Parmeggiani, Andrea, Palmeri, John, Bouet, Jean-Yves, Junier, Ivan, Laboratoire Charles Coulomb (L2C), and Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)
- Subjects
Quantitative Biology - Biomolecules ,[SDV.BBM.BS]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Structural Biology [q-bio.BM] ,Biological Physics (physics.bio-ph) ,FOS: Biological sciences ,[PHYS.PHYS.PHYS-BIO-PH]Physics [physics]/Physics [physics]/Biological Physics [physics.bio-ph] ,FOS: Physical sciences ,Biomolecules (q-bio.BM) ,Physics - Biological Physics - Abstract
We investigate the measurement of DNA supercoiling density ($\sigma$) 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 $\sigma$ 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., Comment: 5 pages + Supplementary Info (including 3 figures)
- Published
- 2020