Compaction of bacterial genomic DNA: clarifying the concepts

Journal of Physics. Condensed Matter : an Institute of Physics Journal
Marc Joyeux

Abstract

The unconstrained genomic DNA of bacteria forms a coil, whose volume exceeds 1000 times the volume of the cell. Since prokaryotes lack a membrane-bound nucleus, in sharp contrast with eukaryotes, the DNA may consequently be expected to occupy the whole available volume when constrained to fit in the cell. Still, it has been known for more than half a century that the DNA is localized in a well-defined region of the cell, called the nucleoid, which occupies only 15% to 25% of the total volume. Although this problem has focused the attention of many scientists in recent decades, there is still no certainty concerning the mechanism that enables such a dramatic compaction. The goal of this Topical Review is to take stock of our knowledge on this question by listing all possible compaction mechanisms with the proclaimed desire to clarify the physical principles they are based upon and discuss them in the light of experimental results and the results of simulations based on coarse-grained models. In particular, the fundamental differences between ψ-condensation and segregative phase separation and between the condensation by small and long polycations are highlighted. This review suggests that the importance of certain mechanisms, li...Continue Reading

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Citations

Jun 10, 2017·The Journal of Physical Chemistry. B·Marc Joyeux
Dec 21, 2017·Journal of Physics. Condensed Matter : an Institute of Physics Journal·Tejal AgarwalApratim Chatterji
Oct 2, 2019·Neurosurgical Focus·Pravesh S GadjradjTjeerd H R de Jong
Apr 15, 2019·The Journal of Chemical Physics·Tejal AgarwalApratim Chatterji
May 21, 2019·Nucleic Acids Research·Tiedong SunLars Nordenskiöld
May 12, 2016·Amino Acids·T J ThomasThresia Thomas
Aug 3, 2017·The Journal of Chemical Physics·M C F PereiraE Orlandini
Nov 16, 2018·Scientific Reports·Antoine MalabiradeVéronique Arluison
Jan 2, 2019·Proceedings of the National Academy of Sciences of the United States of America·Yanyu ZhuJames C Weisshaar
Dec 25, 2019·Physical Review. E·N Al-Naamani, I Ali
Jul 25, 2019·Microorganisms·Marc Joyeux
Oct 21, 2019·Biophysical Journal·Marc Joyeux
Aug 4, 2021·Annual Review of Microbiology·Virginia S LioyFrédéric Boccard

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