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Joyeux M. Bacterial Nucleoid: Interplay of DNA Demixing and Supercoiling. Biophys J 2020; 118:2141-2150. [PMID: 31629479 PMCID: PMC7202931 DOI: 10.1016/j.bpj.2019.09.026] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2019] [Revised: 09/03/2019] [Accepted: 09/23/2019] [Indexed: 01/17/2023] Open
Abstract
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 work, 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 in which 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.
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Affiliation(s)
- Marc Joyeux
- Laboratoire Interdisciplinaire de Physique, CNRS and Université Grenoble Alpes, Grenoble, France.
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Nakano SI, Sugimoto N. Model studies of the effects of intracellular crowding on nucleic acid interactions. MOLECULAR BIOSYSTEMS 2017; 13:32-41. [PMID: 27819369 DOI: 10.1039/c6mb00654j] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Molecular interactions and reactions in living cells occur with high concentrations of background molecules and ions. Many research studies have shown that intracellular molecules have characteristics different from those obtained using simple aqueous solutions. To better understand the behavior of biomolecules in intracellular environments, biophysical experiments were conducted under cell-mimicking conditions in a test tube. It has been shown that the molecular environments at the physiological level of macromolecular crowding, spatial confinement, water activity and dielectric constant, have significant effects on the interactions of DNA and RNA for hybridization, higher-order folding, and catalytic activity. The experimental approaches using in vitro model systems are useful to reveal the origin of the environmental effects and to bridge the gap between the behaviors of nucleic acids in vitro and in vivo. This paper highlights the model experiments used to evaluate the influences of intracellular environment on nucleic acid interactions.
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Affiliation(s)
- Shu-Ichi Nakano
- Department of Nanobiochemistry, Faculty of Frontiers of Innovative Research in Science and Technology (FIRST), Konan University, 7-1-20, Minatojima-minamimachi, Chuo-ku, Kobe, 650-0047, Japan.
| | - Naoki Sugimoto
- Frontier Institute for Biomolecular Engineering Research (FIBER), Konan University, 7-1-20, Minatojima-minamimachi, Chuo-ku, Kobe, 650-0047, Japan. and Graduate School of Frontiers of Innovative Research in Science and Technology (FIRST), Konan University, 7-1-20, Minatojima-minamimachi, Chuo-ku, Kobe, 650-0047, Japan
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Ramisetty SK, Langlete P, Lale R, Dias RS. In vitro studies of DNA condensation by bridging protein in a crowding environment. Int J Biol Macromol 2017; 103:845-853. [PMID: 28536019 DOI: 10.1016/j.ijbiomac.2017.05.079] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2016] [Revised: 05/02/2017] [Accepted: 05/15/2017] [Indexed: 11/15/2022]
Abstract
The macromolecules of the bacterial cell occupy 20-40% of the total cytosol volume, and crowded environments have long been known to compact and stabilize DNA. Nevertheless, investigations on DNA-protein binding are generally performed in the absence of crowding, which may yield an incomplete understanding of how nucleoid-assembling proteins work. A family of such proteins, abundant in Gram-negative bacteria, is the histone-like nucleoid structuring proteins (H-NS). Herein, the synergistic role of macromolecular crowding (mimicked using polyethylene glycol, PEG) and H-NS was investigated using fluorescence correlation spectroscopy (FCS) and enzyme protection assays. We show that crowding enhances the binding of H-NS to the AT-rich tracks of the DNA, where it preferentially binds to, protecting these tracks towards enzyme digestion, inducing some DNA condensation, and inhibiting the biological function of DNA. We further suggest that the looping of DNA chains, induced by H-NS, contributes to the synergistic effect of DNA-binding protein and crowding agents, on DNA condensation.
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Affiliation(s)
- Sravani K Ramisetty
- Biophysics and Medical Technology, Department of Physics, NTNU Norwegian University of Science and Technology, NO-7491 Trondheim, Norway
| | - Petter Langlete
- Biophysics and Medical Technology, Department of Physics, NTNU Norwegian University of Science and Technology, NO-7491 Trondheim, Norway
| | - Rahmi Lale
- Department of Biotechnology, PhotoSynLab, Faculty of Natural Sciences and Technology, NTNU Norwegian University of Science and Technology, NO-7491 Trondheim, Norway
| | - Rita S Dias
- Biophysics and Medical Technology, Department of Physics, NTNU Norwegian University of Science and Technology, NO-7491 Trondheim, Norway.
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Joyeux M. Compaction of bacterial genomic DNA: clarifying the concepts. JOURNAL OF PHYSICS. CONDENSED MATTER : AN INSTITUTE OF PHYSICS JOURNAL 2015; 27:383001. [PMID: 26345139 DOI: 10.1088/0953-8984/27/38/383001] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
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, like supercoiling and the architectural properties of DNA-bridging and DNA-bending nucleoid proteins, may have been overestimated, whereas other mechanisms, like segregative phase separation and the self-association of nucleoid proteins, as well as the possible role of the synergy of two or more mechanisms, may conversely deserve more attention.
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Affiliation(s)
- Marc Joyeux
- Laboratoire Interdisciplinaire de Physique (CNRS UMR5588), Université Joseph Fourier Grenoble 1, BP 87, 38402 St Martin d'Hères, France
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Benedetti F, Japaridze A, Dorier J, Racko D, Kwapich R, Burnier Y, Dietler G, Stasiak A. Effects of physiological self-crowding of DNA on shape and biological properties of DNA molecules with various levels of supercoiling. Nucleic Acids Res 2015; 43:2390-9. [PMID: 25653164 PMCID: PMC4344501 DOI: 10.1093/nar/gkv055] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023] Open
Abstract
DNA in bacterial chromosomes and bacterial plasmids is supercoiled. DNA supercoiling is essential for DNA replication and gene regulation. However, the density of supercoiling in vivo is circa twice smaller than in deproteinized DNA molecules isolated from bacteria. What are then the specific advantages of reduced supercoiling density that is maintained in vivo? Using Brownian dynamics simulations and atomic force microscopy we show here that thanks to physiological DNA–DNA crowding DNA molecules with reduced supercoiling density are still sufficiently supercoiled to stimulate interaction between cis-regulatory elements. On the other hand, weak supercoiling permits DNA molecules to modulate their overall shape in response to physiological changes in DNA crowding. This plasticity of DNA shapes may have regulatory role and be important for the postreplicative spontaneous segregation of bacterial chromosomes.
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Affiliation(s)
- Fabrizio Benedetti
- Center for Integrative Genomics, University of Lausanne, 1015-Lausanne, Switzerland SIB Swiss Institute of Bioinformatics, 1015-Lausanne, Switzerland
| | - Aleksandre Japaridze
- Institute of Physics of Biological Systems, École Polytechnique Fédérale de Lausanne (EPFL), 1015-Lausanne, Switzerland
| | - Julien Dorier
- Center for Integrative Genomics, University of Lausanne, 1015-Lausanne, Switzerland Vital-IT, SIB Swiss Institute of Bioinformatics, 1015-Lausanne, Switzerland
| | - Dusan Racko
- Center for Integrative Genomics, University of Lausanne, 1015-Lausanne, Switzerland SIB Swiss Institute of Bioinformatics, 1015-Lausanne, Switzerland Polymer Institute of the Slovak Academy of Sciences, 845 41 Bratislava, Slovakia
| | - Robert Kwapich
- Institute of Physics of Biological Systems, École Polytechnique Fédérale de Lausanne (EPFL), 1015-Lausanne, Switzerland Department of Medical Physics, University of Silesia in Katowice, 40-007 Katowice, Poland
| | - Yannis Burnier
- Center for Integrative Genomics, University of Lausanne, 1015-Lausanne, Switzerland Institute of Theoretical Physics, École Polytechnique Fédérale de Lausanne (EPFL), 1015-Lausanne, Switzerland
| | - Giovanni Dietler
- Institute of Physics of Biological Systems, École Polytechnique Fédérale de Lausanne (EPFL), 1015-Lausanne, Switzerland
| | - Andrzej Stasiak
- Center for Integrative Genomics, University of Lausanne, 1015-Lausanne, Switzerland SIB Swiss Institute of Bioinformatics, 1015-Lausanne, Switzerland
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Nakano SI, Miyoshi D, Sugimoto N. Effects of molecular crowding on the structures, interactions, and functions of nucleic acids. Chem Rev 2013; 114:2733-58. [PMID: 24364729 DOI: 10.1021/cr400113m] [Citation(s) in RCA: 369] [Impact Index Per Article: 33.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Shu-ichi Nakano
- Department of Nanobiochemistry, Faculty of Frontiers of Innovative Research in Science and Technology (FIRST) and Frontier Institute for Biomolecular Engineering Research (FIBER), Konan University , 7-1-20 Minatojima-minamimachi, Chuo-ku, Kobe 650-0047, Japan
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Kobayashi K, Tateishi-Karimata H, Tsutsui K, Wada Y, Sugimoto N. DNA Morphologic Changes Induced by Spermine on a Gold Surface under DNA Crowding Conditions. CHEM LETT 2011. [DOI: 10.1246/cl.2011.855] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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Do TT, Tang VJ, Aguilera JA, Perry CC, Milligan JR. Characterization of a Lipophilic Plasmid DNA Condensate Formed with a Cationic Peptide Fatty Acid Conjugate. Biomacromolecules 2011; 12:1731-7. [DOI: 10.1021/bm200127u] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Trinh T. Do
- Department of Radiology, University of California at San Diego, 9500 Gilman Drive, La Jolla, California 92093-0610, United States
| | - Vicky J. Tang
- Department of Radiology, University of California at San Diego, 9500 Gilman Drive, La Jolla, California 92093-0610, United States
| | - Joe A. Aguilera
- Department of Radiology, University of California at San Diego, 9500 Gilman Drive, La Jolla, California 92093-0610, United States
| | - Christopher C. Perry
- Department of Biochemistry, Loma Linda University, 11085 Campus Street, Loma Linda, California 92350, United States
| | - Jamie R. Milligan
- Department of Radiology, University of California at San Diego, 9500 Gilman Drive, La Jolla, California 92093-0610, United States
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Zhu X, Ng SY, Gupta AN, Feng YP, Ho B, Lapp A, Egelhaaf SU, Forsyth VT, Haertlein M, Moulin M, Schweins R, van der Maarel JRC. Effect of crowding on the conformation of interwound DNA strands from neutron scattering measurements and Monte Carlo simulations. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2010; 81:061905. [PMID: 20866438 DOI: 10.1103/physreve.81.061905] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/28/2009] [Revised: 03/18/2010] [Indexed: 05/29/2023]
Abstract
With a view to determining the distance between the two opposing duplexes in supercoiled DNA, we have measured small angle neutron scattering from pHSG298 plasmid (2675 base pairs) dispersed in saline solutions. Experiments were carried out under full and zero average DNA neutron scattering contrast using hydrogenated plasmid and a 1:1 mixture of hydrogenated and perdeuterated plasmid, respectively. In the condition of zero average contrast, the scattering intensity is directly proportional to the single DNA molecule scattering function (form factor), irrespective of the DNA concentration and without complications from intermolecular interference. The form factors are interpreted with Monte Carlo computer simulation. For this purpose, the many body problem of a dense DNA solution was reduced to the one of a single DNA molecule in a congested state by confinement in a cylindrical potential. It was observed that the interduplex distance decreases with increasing concentration of salt as well as plasmid. Therefore, besides ionic strength, DNA crowding is shown to be important in controlling the interwound structure and site juxtaposition of distal segments of supercoiled DNA. This first study exploiting zero average DNA contrast has been made possible by the availability of perdeuterated plasmid.
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Affiliation(s)
- Xiaoying Zhu
- Department of Physics, National University of Singapore, Singapore
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Tsoi M, Do TT, Tang V, Aguilera JA, Perry CC, Milligan JR. Characterization of condensed plasmid DNA models for studying the direct effect of ionizing radiation. Biophys Chem 2010; 147:104-10. [PMID: 20096988 DOI: 10.1016/j.bpc.2009.12.006] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2009] [Revised: 12/19/2009] [Accepted: 12/19/2009] [Indexed: 10/20/2022]
Abstract
We have examined the changes in physical properties of aqueous solutions of the plasmid pUC18 that take place on the addition of the cationic oligopeptide penta-arginine. An increase in sedimentation rate and static light scattering, and changes in the nucleic acid CD spectrum all suggest that this ligand acts to condense the plasmid. Dynamic light scattering suggests the hydrodynamic radii of the condensate particles are a few micrometers, ca. 50-fold larger than that of the monomeric plasmid. Condensation of the plasmid also produces a ca. 100-fold decrease in the strand break yield produced by gamma irradiation. This extensive protection against reactive intermediates in the bulk of the solution implies that condensed plasmid DNA may offer a model system with which to study the direct effect of ionizing radiation (ionization of the DNA itself). The use of peptide ligands as condensing agents in this application is attractive because the derivatives of several amino acids (particularly tryptophan and tyrosine) have been shown to modify the radiation chemistry of DNA extensively.
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Affiliation(s)
- Mandi Tsoi
- Department of Radiology, University of California at San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0610, USA
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