Bacterial Nucleoid: Interplay of DNA Demixing and Supercoiling
| Autor: | Marc Joyeux |
|---|---|
| Přispěvatelé: | Laboratoire Interdisciplinaire de Physique [Saint Martin d’Hères] (LIPhy ), Centre National de la Recherche Scientifique (CNRS)-Université Grenoble Alpes (UGA) |
| Jazyk: | angličtina |
| Rok vydání: | 2020 |
| Předmět: |
DNA
Bacterial Work (thermodynamics) Macromolecular Substances [PHYS.PHYS.PHYS-BIO-PH]Physics [physics]/Physics [physics]/Biological Physics [physics.bio-ph] Biophysics FOS: Physical sciences Molecular Dynamics Simulation Condensed Matter - Soft Condensed Matter 03 medical and health sciences chemistry.chemical_compound 0302 clinical medicine [SDV.BBM.GTP]Life Sciences [q-bio]/Biochemistry Molecular Biology/Genomics [q-bio.GN] Nucleoid Physics - Biological Physics 030304 developmental biology 0303 health sciences biology DNA Superhelical Chemistry Topoisomerase DNA Articles Bacterial nucleoid Biological Physics (physics.bio-ph) biology.protein Brownian dynamics Nucleic Acid Conformation DNA supercoil Soft Condensed Matter (cond-mat.soft) 030217 neurology & neurosurgery Macromolecule |
| Zdroj: | Biophysical Journal Biophysical Journal, Biophysical Society, 2020, 118, pp.2141-2150. ⟨10.1016/j.bpj.2019.09.026⟩ Biophys J |
| ISSN: | 0006-3495 1542-0086 |
| DOI: | 10.1016/j.bpj.2019.09.026⟩ |
| Popis: | This work addresses the question of the interplay of DNA demixing and supercoiling in bacterial cells. Demixing of DNA from other globular macromolecules results from the overall repulsion between all components of the system and leads to the formation of the nucleoid, which is the region of the cell that contains the genomic DNA in a rather compact form. Supercoiling describes the coiling of the axis of the DNA double helix to accommodate the torsional stress injected in the molecule by topoisomerases. Supercoiling is able to induce some compaction of the bacterial DNA, although to a lesser extent than demixing. In this paper, we investigate the interplay of these two mechanisms, with the goal of determining whether the total compaction ratio of the DNA is the mere sum or some more complex function of the compaction ratios due to each mechanism. To this end, we developed a coarse-grained bead-and-spring model and investigated its properties through Brownian dynamics simulations. This work reveals that there actually exist different regimes, depending on the crowder volume ratio and the DNA superhelical density. In particular, a regime where the effects of DNA demixing and supercoiling on the compaction of the DNA coil simply add up is shown to exist up to moderate values of the superhelical density. In contrast, the mean radius of the DNA coil no longer decreases above this threshold and may even increase again for sufficiently large crowder concentrations. Finally, the model predicts that the DNA coil may depart from the spherical geometry very close to the jamming threshold, as a trade-off between the need to minimize both the bending energy of the stiff plectonemes and the volume of the DNA coil to accommodate demixing. Biophysical Journal, in press (doi.org/10.1016/j.bpj.2019.09.026) |
| Databáze: | OpenAIRE |
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