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Bong S, Park CB, Cho SG, Bae J, Hapsari N, Jin X, Heo S, Lee JE, Hashiya K, Bando T, Sugiyama H, Jung KH, Sung B, Jo K. AT-specific DNA visualization revisits the directionality of bacteriophage λ DNA ejection. Nucleic Acids Res 2023; 51:5634-5646. [PMID: 37158237 PMCID: PMC10287942 DOI: 10.1093/nar/gkad340] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2022] [Revised: 03/14/2023] [Accepted: 04/21/2023] [Indexed: 05/10/2023] Open
Abstract
In this study, we specifically visualized DNA molecules at their AT base pairs after in vitro phage ejection. Our AT-specific visualization revealed that either end of the DNA molecule could be ejected first with a nearly 50% probability. This observation challenges the generally accepted theory of Last In First Out (LIFO), which states that the end of the phage λ DNA that enters the capsid last during phage packaging is the first to be ejected, and that both ends of the DNA are unable to move within the extremely condensed phage capsid. To support our observations, we conducted computer simulations that revealed that both ends of the DNA molecule are randomized, resulting in the observed near 50% probability. Additionally, we found that the length of the ejected DNA by LIFO was consistently longer than that by First In First Out (FIFO) during in vitro phage ejection. Our simulations attributed this difference in length to the stiffness difference of the remaining DNA within the phage capsid. In conclusion, this study demonstrates that a DNA molecule within an extremely dense phage capsid exhibits a degree of mobility, allowing it to switch ends during ejection.
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Affiliation(s)
- Serang Bong
- Department of Chemistry, Sogang University, Seoul 04107, Korea
| | - Chung Bin Park
- Department of Chemistry, Sogang University, Seoul 04107, Korea
| | - Shin-Gyu Cho
- Department of Life Science, Sogang University, Seoul 04107, Korea
| | - Jaeyoung Bae
- Department of Chemistry, Sogang University, Seoul 04107, Korea
| | - Natalia Diyah Hapsari
- Department of Chemistry, Sogang University, Seoul 04107, Korea
- Chemistry Education Program, Department of Mathematics and Science Education, Sanata Dharma University, Yogyakarta 55282, Indonesia
| | - Xuelin Jin
- Department of Chemistry, Sogang University, Seoul 04107, Korea
- College of Agriculture, Yanbian University, Yanji133000, China
| | - Sujung Heo
- Department of Chemistry, Sogang University, Seoul 04107, Korea
| | - Ji-eun Lee
- Department of Life Science, Sogang University, Seoul 04107, Korea
| | - Kaori Hashiya
- Department of Chemistry, Graduate School of Science, Kyoto University, Sakyo-Ku, Kyoto606-8502, Japan
| | - Toshikazu Bando
- Department of Chemistry, Graduate School of Science, Kyoto University, Sakyo-Ku, Kyoto606-8502, Japan
| | - Hiroshi Sugiyama
- Department of Chemistry, Graduate School of Science, Kyoto University, Sakyo-Ku, Kyoto606-8502, Japan
| | - Kwang-Hwan Jung
- Department of Life Science, Sogang University, Seoul 04107, Korea
| | - Bong June Sung
- Department of Chemistry, Sogang University, Seoul 04107, Korea
| | - Kyubong Jo
- Department of Chemistry, Sogang University, Seoul 04107, Korea
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Liu P, Arsuaga J, Calderer MC, Golovaty D, Vazquez M, Walker S. Ion-dependent DNA configuration in bacteriophage capsids. Biophys J 2021; 120:3292-3302. [PMID: 34265262 DOI: 10.1016/j.bpj.2021.07.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2020] [Revised: 05/01/2021] [Accepted: 07/07/2021] [Indexed: 11/24/2022] Open
Abstract
Bacteriophages densely pack their long double-stranded DNA genome inside a protein capsid. The conformation of the viral genome inside the capsid is consistent with a hexagonal liquid crystalline structure. Experiments have confirmed that the details of the hexagonal packing depend on the electrochemistry of the capsid and its environment. In this work, we propose a biophysical model that quantifies the relationship between DNA configurations inside bacteriophage capsids and the types and concentrations of ions present in a biological system. We introduce an expression for the free energy that combines the electrostatic energy with contributions from bending of individual segments of DNA and Lennard-Jones-type interactions between these segments. The equilibrium points of this energy solve a partial differential equation that defines the distributions of DNA and the ions inside the capsid. We develop a computational approach that allows us to simulate much larger systems than what is possible using the existing molecular-level methods. In particular, we are able to estimate bending and repulsion between the DNA segments as well as the full electrochemistry of the solution, both inside and outside of the capsid. The numerical results show good agreement with existing experiments and with molecular dynamics simulations for small capsids.
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Affiliation(s)
- Pei Liu
- School of Mathematics, University of Minnesota, Twin Cities, Minneapolis, Minnesota
| | - Javier Arsuaga
- Department of Mathematics, University of California Davis, Davis, California; Department of Molecular and Cellular Biology, University of California Davis, Davis, California.
| | - M Carme Calderer
- School of Mathematics, University of Minnesota, Twin Cities, Minneapolis, Minnesota
| | - Dmitry Golovaty
- Department of Mathematics, The University of Akron, Akron, Ohio.
| | - Mariel Vazquez
- Department of Mathematics, University of California Davis, Davis, California; Department of Microbiology and Molecular Genetics, University of California Davis, Davis, California
| | - Shawn Walker
- Department of Mathematics, Louisiana State University, Baton Rouge, Louisiana
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Hiltner L, Carme Calderer M, Arsuaga J, Vázquez M. Chromonic liquid crystals and packing configurations of bacteriophage viruses. PHILOSOPHICAL TRANSACTIONS. SERIES A, MATHEMATICAL, PHYSICAL, AND ENGINEERING SCIENCES 2021; 379:20200111. [PMID: 34024128 DOI: 10.1098/rsta.2020.0111] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 12/01/2020] [Indexed: 06/12/2023]
Abstract
We study equilibrium configurations of hexagonal columnar liquid crystals in the context of characterizing packing structures of bacteriophage viruses in a protein capsid. These are viruses that infect bacteria and are currently the focus of intense research efforts, with the goal of finding new therapies for bacteria-resistant antibiotics. The energy that we propose consists of the Oseen-Frank free energy of nematic liquid crystals that penalizes bending of the columnar directions, in addition to the cross-sectional elastic energy accounting for distortions of the transverse hexagonal structure; we also consider the isotropic contribution of the core and the energy of the unknown interface between the outer ordered region of the capsid and the inner disordered core. The problem becomes of free boundary type, with constraints. We show that the concentric, azimuthal, spool-like configuration is the absolute minimizer. Moreover, we present examples of toroidal structures formed by DNA in free solution and compare them with the analogous ones occurring in experiments with other types of lyotropic liquid crystals, such as food dyes and additives. This article is part of the theme issue 'Topics in mathematical design of complex materials'.
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Affiliation(s)
- Lindsey Hiltner
- School of Mathematics, University of Minnesota, Minneapolis, MN 55442, USA
| | - M Carme Calderer
- School of Mathematics, University of Minnesota, Minneapolis, MN 55442, USA
| | - Javier Arsuaga
- Department of Cellular and Molecular Biology, Briggs Hall, Davis, CA 09
- Department of Mathematics, MSB, 2115, University of California Davis, One Shields Avenue, Davis, CA 95616, USA
| | - Mariel Vázquez
- Department of Mathematics, MSB, 2150, University of California Davis, One Shields Avenue, Davis, CA 95616, USA
- Department of Microbiology and Molecular Genetics, Briggs Hall, Davis, CA 09
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Cruz B, Zhu Z, Calderer C, Arsuaga J, Vazquez M. Quantitative Study of the Chiral Organization of the Phage Genome Induced by the Packaging Motor. Biophys J 2020; 118:2103-2116. [PMID: 32353255 PMCID: PMC7203069 DOI: 10.1016/j.bpj.2020.03.030] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2019] [Revised: 11/04/2019] [Accepted: 03/16/2020] [Indexed: 12/11/2022] Open
Abstract
Molecular motors that translocate DNA are ubiquitous in nature. During morphogenesis of double-stranded DNA bacteriophages, a molecular motor drives the viral genome inside a protein capsid. Several models have been proposed for the three-dimensional geometry of the packaged genome, but very little is known of the signature of the molecular packaging motor. For instance, biophysical experiments show that in some systems, DNA rotates during the packaging reaction, but most current biophysical models fail to incorporate this property. Furthermore, studies including rotation mechanisms have reached contradictory conclusions. In this study, we compare the geometrical signatures imposed by different possible mechanisms for the packaging motors: rotation, revolution, and rotation with revolution. We used a previously proposed kinetic Monte Carlo model of the motor, combined with Brownian dynamics simulations of DNA to simulate deterministic and stochastic motor models. We find that rotation is necessary for the accumulation of DNA writhe and for the chiral organization of the genome. We observe that although in the initial steps of the packaging reaction, the torsional strain of the genome is released by rotation of the molecule, in the later stages, it is released by the accumulation of writhe. We suggest that the molecular motor plays a key role in determining the final structure of the encapsidated genome in bacteriophages.
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Affiliation(s)
- Brian Cruz
- Department of Mathematics, University of California, Berkeley, California
| | - Zihao Zhu
- Department of Microbiology and Molecular Genetics, University of California at Davis, Davis, California
| | - Carme Calderer
- School of Mathematics, University of Minnesota, Minneapolis, Minnesota
| | - Javier Arsuaga
- Department of Mathematics, University of California at Davis, Davis, California; Department of Molecular and Cellular Biology, University of California at Davis, Davis, California.
| | - Mariel Vazquez
- Department of Microbiology and Molecular Genetics, University of California at Davis, Davis, California; Department of Mathematics, University of California at Davis, Davis, California.
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